NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2538967423|ref|WP_295243356|]
View 

MULTISPECIES: peptidoglycan-binding protein [Veillonella]

Protein Classification

3D domain-containing protein; LysM peptidoglycan-binding and 3D domain-containing protein( domain architecture ID 11465571)

3D (Asp-Asp-Asp) domain-containing protein similar to the stationary phase survival protein YuiC from Bacillus subtilis; LysM peptidoglycan-binding and 3D (Asp-Asp-Asp) domain-containing protein, similar to Bacillus subtilis cell wall-binding protein YocH

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
COG3584 COG3584
3D (Asp-Asp-Asp) domain, usually in lytic transglycosylases [Function unknown]; 3D ...
 171-258 3.54e-39

3D (Asp-Asp-Asp) domain, usually in lytic transglycosylases [Function unknown]; 3D (Asp-Asp-Asp) domain, usually in lytic transglycosylases is part of the Pathway/BioSystem: 3D


:

Pssm-ID: 442803 [Multi-domain]  Cd Length: 92  Bit Score: 131.38  E-value: 3.54e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2538967423 171 TMNATAYSA--YDPG-NSSYTARGNLLKRGY-VSVDPDVIPLGTAVYVEGYGYAVADDTGGGIIGNRIDLAMDSHGEAID 246
Cdd:COG3584     1 TVTATAYTAgpECTGkGGGITASGTRLRPGGvIAVDPDVIPLGTKVYIEGYGYAVAEDTGGAIKGNRIDIYMPSVSEALN 80

                          90
                  ....*....|..
gi 2538967423 247 FGRQTVKVYILE 258
Cdd:COG3584    81 WGRRTVTVYILE 92
PGRP COG3409
Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope ...
 96-156 1.96e-21

Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope biogenesis];


:

Pssm-ID: 442635 [Multi-domain]  Cd Length: 69  Bit Score: 84.96  E-value: 1.96e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2538967423  96 RFGDRGRSVSDLQARLAHSGFSPGSIDGIFGNGTANALKRFQKANGLTVTGEVDSKTMELL 156
Cdd:COG3409     7 RLGDSGEDVRELQQRLNALGYYPGPVDGIFGPATEAAVRAFQRANGLPVDGIVGPATWAAL 67
PGRP COG3409
Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope ...
 13-74 3.06e-19

Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope biogenesis];


:

Pssm-ID: 442635 [Multi-domain]  Cd Length: 69  Bit Score: 79.18  E-value: 3.06e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2538967423  13 RGDRGSEVQFVQRLMITQGYLVDTADGVFGNNTEYAVRMFQKQNGLSATGKVDSDTLAAMKE 74
Cdd:COG3409     8 LGDSGEDVRELQQRLNALGYYPGPVDGIFGPATEAAVRAFQRANGLPVDGIVGPATWAALRA 69
 
Name Accession Description Interval E-value
COG3584 COG3584
3D (Asp-Asp-Asp) domain, usually in lytic transglycosylases [Function unknown]; 3D ...
 171-258 3.54e-39

3D (Asp-Asp-Asp) domain, usually in lytic transglycosylases [Function unknown]; 3D (Asp-Asp-Asp) domain, usually in lytic transglycosylases is part of the Pathway/BioSystem: 3D


Pssm-ID: 442803 [Multi-domain]  Cd Length: 92  Bit Score: 131.38  E-value: 3.54e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2538967423 171 TMNATAYSA--YDPG-NSSYTARGNLLKRGY-VSVDPDVIPLGTAVYVEGYGYAVADDTGGGIIGNRIDLAMDSHGEAID 246
Cdd:COG3584     1 TVTATAYTAgpECTGkGGGITASGTRLRPGGvIAVDPDVIPLGTKVYIEGYGYAVAEDTGGAIKGNRIDIYMPSVSEALN 80

                          90
                  ....*....|..
gi 2538967423 247 FGRQTVKVYILE 258
Cdd:COG3584    81 WGRRTVTVYILE 92
DPBB_YuiC-like cd22786
double-psi beta-barrel fold of YuiC subfamily proteins; The YuiC subfamily includes a group of ...
 168-258 4.74e-38

double-psi beta-barrel fold of YuiC subfamily proteins; The YuiC subfamily includes a group of conserved double-psi beta-barrel (DPBB) fold proteins, such as Bacillus subtilis protein YuiC, cell wall shaping protein YabE, cell wall-binding protein YocH, as well as Clostridium tetani phosphatase-associated protein PapQ. YuiC is a Firmicute stationary phase survival (Sps) protein that closely resembles the Barwin-like endoglucanase beta barrel of MltA. It is a double-psi beta-barrel (DPBB) fold that consists of two interlocked "psi-structure" motifs related by a pseudo-2-fold axis and may be involved in substrate binding and catalysis.


Pssm-ID: 439263 [Multi-domain]  Cd Length: 96  Bit Score: 128.49  E-value: 4.74e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2538967423 168 KTMTMNATAYSAYD---PGNSSYTARGNLLKR-GYVSVDPDVIPLGTAVYVEGYGYAVADDTGGGIIGNRIDLAMDSHGE 243
Cdd:cd22786     2 KKITVEATAYSPCSssgGGCYGITASGTPLKRkGTIAVDPSVIPLGTKVYIPGYGYAVVADTGGAIKGNRIDLYFPTHEE 81

                          90
                  ....*....|....*
gi 2538967423 244 AIDFGRQTVKVYILE 258
Cdd:cd22786    82 AINWGRKTVEVYVLK 96
wall_bind_EntB NF040676
cell wall-binding protein EntB; This HMM describes the cell wall-binding protein EntB, as ...
 167-257 5.33e-26

cell wall-binding protein EntB; This HMM describes the cell wall-binding protein EntB, as found in Bacillus cereus. EntB is related to EntA, EntC, and EndD. All Ent family proteins have a signal peptide, an N-terminal SH3 domain and a C-terminal 3D (Asp-Asp-Asp) domain. EntB and EndC have a central region with a highly variable number of repeats resembling KAXEXX. The gene symbol derives from the notion that at least some members of the family function as enterotoxins, but more recent descriptions focus on roles in stress response and cell wall integrity.


Pssm-ID: 468642 [Multi-domain]  Cd Length: 476  Bit Score: 105.63  E-value: 5.33e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2538967423 167 KKTMTMNATAYSAyDPG-NSSY-----TARGNLLKRG----YVSVDPDVIPLGTAVYVEGYGYAVADDTGGGIIGNRIDL 236
Cdd:NF040676  377 KRELTVVATAYTA-DPSeNGTYggrvlTAMGHDLTANpnmrIIAVDPKVIPLGSKVWVEGYGEAIAGDTGSAIKGNRIDV 455

                          90       100
                  ....*....|....*....|.
gi 2538967423 237 AMDSHGEAIDFGRQTVKVYIL 257
Cdd:NF040676  456 LMGSKSKAMNWGRQTVKVKIL 476
PGRP COG3409
Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope ...
 96-156 1.96e-21

Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442635 [Multi-domain]  Cd Length: 69  Bit Score: 84.96  E-value: 1.96e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2538967423  96 RFGDRGRSVSDLQARLAHSGFSPGSIDGIFGNGTANALKRFQKANGLTVTGEVDSKTMELL 156
Cdd:COG3409     7 RLGDSGEDVRELQQRLNALGYYPGPVDGIFGPATEAAVRAFQRANGLPVDGIVGPATWAAL 67
PGRP COG3409
Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope ...
 13-74 3.06e-19

Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442635 [Multi-domain]  Cd Length: 69  Bit Score: 79.18  E-value: 3.06e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2538967423  13 RGDRGSEVQFVQRLMITQGYLVDTADGVFGNNTEYAVRMFQKQNGLSATGKVDSDTLAAMKE 74
Cdd:COG3409     8 LGDSGEDVRELQQRLNALGYYPGPVDGIFGPATEAAVRAFQRANGLPVDGIVGPATWAALRA 69
PG_binding_1 pfam01471
Putative peptidoglycan binding domain; This domain is composed of three alpha helices. This ...
 100-156 3.45e-18

Putative peptidoglycan binding domain; This domain is composed of three alpha helices. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. This family is found N-terminal to the catalytic domain of matrixins. The domain is found to bind peptidoglycan experimentally.


Pssm-ID: 460223 [Multi-domain]  Cd Length: 57  Bit Score: 76.01  E-value: 3.45e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2538967423 100 RGRSVSDLQARLAHSGFSPGSIDGIFGNGTANALKRFQKANGLTVTGEVDSKTMELL 156
Cdd:pfam01471   1 SGEDVKELQRYLNRLGYYPGPVDGYFGPSTEAAVKAFQRAFGLPVDGIVDPETLAAL 57
PG_binding_1 pfam01471
Putative peptidoglycan binding domain; This domain is composed of three alpha helices. This ...
 16-72 1.01e-16

Putative peptidoglycan binding domain; This domain is composed of three alpha helices. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. This family is found N-terminal to the catalytic domain of matrixins. The domain is found to bind peptidoglycan experimentally.


Pssm-ID: 460223 [Multi-domain]  Cd Length: 57  Bit Score: 72.16  E-value: 1.01e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2538967423  16 RGSEVQFVQRLMITQGYLVDTADGVFGNNTEYAVRMFQKQNGLSATGKVDSDTLAAM 72
Cdd:pfam01471   1 SGEDVKELQRYLNRLGYYPGPVDGYFGPSTEAAVKAFQRAFGLPVDGIVDPETLAAL 57
3D pfam06725
3D domain; This short presumed domain contains three conserved aspartate residues, hence the ...
 199-258 1.38e-16

3D domain; This short presumed domain contains three conserved aspartate residues, hence the name 3D. It has been shown to be part of the catalytic double psi beta barrel domain of MltA.


Pssm-ID: 399598 [Multi-domain]  Cd Length: 72  Bit Score: 72.24  E-value: 1.38e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2538967423 199 VSVDPDVIPLGTAVYVEG-------YGYAVADDTGGGIIGNRIDLAMDSHGEAID---FGRQTVKVYILE 258
Cdd:pfam06725   3 IAVDPSVIPLGTPVYVEGplggkpvYRLAIAQDTGGAIKGNRIDLYFGTGDEAGNlagLYRKTGRVYILL 72
 
Name Accession Description Interval E-value
COG3584 COG3584
3D (Asp-Asp-Asp) domain, usually in lytic transglycosylases [Function unknown]; 3D ...
 171-258 3.54e-39

3D (Asp-Asp-Asp) domain, usually in lytic transglycosylases [Function unknown]; 3D (Asp-Asp-Asp) domain, usually in lytic transglycosylases is part of the Pathway/BioSystem: 3D


Pssm-ID: 442803 [Multi-domain]  Cd Length: 92  Bit Score: 131.38  E-value: 3.54e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2538967423 171 TMNATAYSA--YDPG-NSSYTARGNLLKRGY-VSVDPDVIPLGTAVYVEGYGYAVADDTGGGIIGNRIDLAMDSHGEAID 246
Cdd:COG3584     1 TVTATAYTAgpECTGkGGGITASGTRLRPGGvIAVDPDVIPLGTKVYIEGYGYAVAEDTGGAIKGNRIDIYMPSVSEALN 80

                          90
                  ....*....|..
gi 2538967423 247 FGRQTVKVYILE 258
Cdd:COG3584    81 WGRRTVTVYILE 92
DPBB_YuiC-like cd22786
double-psi beta-barrel fold of YuiC subfamily proteins; The YuiC subfamily includes a group of ...
 168-258 4.74e-38

double-psi beta-barrel fold of YuiC subfamily proteins; The YuiC subfamily includes a group of conserved double-psi beta-barrel (DPBB) fold proteins, such as Bacillus subtilis protein YuiC, cell wall shaping protein YabE, cell wall-binding protein YocH, as well as Clostridium tetani phosphatase-associated protein PapQ. YuiC is a Firmicute stationary phase survival (Sps) protein that closely resembles the Barwin-like endoglucanase beta barrel of MltA. It is a double-psi beta-barrel (DPBB) fold that consists of two interlocked "psi-structure" motifs related by a pseudo-2-fold axis and may be involved in substrate binding and catalysis.


Pssm-ID: 439263 [Multi-domain]  Cd Length: 96  Bit Score: 128.49  E-value: 4.74e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2538967423 168 KTMTMNATAYSAYD---PGNSSYTARGNLLKR-GYVSVDPDVIPLGTAVYVEGYGYAVADDTGGGIIGNRIDLAMDSHGE 243
Cdd:cd22786     2 KKITVEATAYSPCSssgGGCYGITASGTPLKRkGTIAVDPSVIPLGTKVYIPGYGYAVVADTGGAIKGNRIDLYFPTHEE 81

                          90
                  ....*....|....*
gi 2538967423 244 AIDFGRQTVKVYILE 258
Cdd:cd22786    82 AINWGRKTVEVYVLK 96
3D_containing_proteins cd14667
Non-mltA associated 3D domain containing proteins, named for 3 conserved aspartate residues; ...
 172-257 9.50e-35

Non-mltA associated 3D domain containing proteins, named for 3 conserved aspartate residues; This family contains the 3D domain, named for its 3 conserved aspartates, including similar uncharacterized proteins. These proteins contain the critical active site aspartate of mltA-like lytic transglycosylases where the 3D domain forms a larger domain with the N-terminal region. This domain is also found in conjunction with numerous other domains such as the Escherichia coli MltA, a membrane-bound lytic transglycosylase comprised of 2 domains separated by a large groove, where the peptidoglycan strand binds. Domain A is made up of an N-terminal and a C-terminal portion, corresponding to the 3D domain and Domain B is inserted within the linear sequence of domain A. MltA is distinct from other bacterial LTs, which are similar to each other. Escherichia coli peptidoglycan lytic transglycosylase (LT) initiates cell wall recycling in response to damage, during bacterial fission, and cleaves peptidoglycan (PG) to create functional spaces in its wall. PG chains (also known as murein), the major components of the bacterial cell wall, are comprised of alternating beta-1-4-linked N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc), and lytic transglycosylases cleave this beta-1-4 bond.


Pssm-ID: 270620 [Multi-domain]  Cd Length: 90  Bit Score: 119.94  E-value: 9.50e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2538967423 172 MNATAYSAYDPGNSSYTAR----GNLLKRGYVSVDPDVIPLGTAVYVEGYGYAVADDTGGGIIGNRIDLAMDSHGEAIDF 247
Cdd:cd14667     1 FTATAYTSCEGCCGGGPGGtasgGLPVGGGTIAVDPSVIPLGTKVYIEGYGVYVVEDTGGAIKGNRIDIYMDSHAEALAF 80

                          90
                  ....*....|
gi 2538967423 248 GRQTVKVYIL 257
Cdd:cd14667    81 GRRYVEVYIL 90
wall_bind_EntB NF040676
cell wall-binding protein EntB; This HMM describes the cell wall-binding protein EntB, as ...
 167-257 5.33e-26

cell wall-binding protein EntB; This HMM describes the cell wall-binding protein EntB, as found in Bacillus cereus. EntB is related to EntA, EntC, and EndD. All Ent family proteins have a signal peptide, an N-terminal SH3 domain and a C-terminal 3D (Asp-Asp-Asp) domain. EntB and EndC have a central region with a highly variable number of repeats resembling KAXEXX. The gene symbol derives from the notion that at least some members of the family function as enterotoxins, but more recent descriptions focus on roles in stress response and cell wall integrity.


Pssm-ID: 468642 [Multi-domain]  Cd Length: 476  Bit Score: 105.63  E-value: 5.33e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2538967423 167 KKTMTMNATAYSAyDPG-NSSY-----TARGNLLKRG----YVSVDPDVIPLGTAVYVEGYGYAVADDTGGGIIGNRIDL 236
Cdd:NF040676  377 KRELTVVATAYTA-DPSeNGTYggrvlTAMGHDLTANpnmrIIAVDPKVIPLGSKVWVEGYGEAIAGDTGSAIKGNRIDV 455

                          90       100
                  ....*....|....*....|.
gi 2538967423 237 AMDSHGEAIDFGRQTVKVYIL 257
Cdd:NF040676  456 LMGSKSKAMNWGRQTVKVKIL 476
DPBB_MltA_YuiC-like cd22784
double-psi beta-barrel fold of membrane-bound lytic murein transglycosylase A (MltA) and ...
 172-256 5.35e-23

double-psi beta-barrel fold of membrane-bound lytic murein transglycosylase A (MltA) and YuiC-like proteins; This family includes two subfamilies of conserved double-psi beta-barrel (DPBB) domain proteins, such as membrane-bound lytic murein transglycosylase A (MltA)-like proteins and YuiC-like proteins. MltA, also called murein hydrolase A, is a murein-degrading enzyme that may play a role in the recycling of muropeptides during cell elongation and/or cell division. It degrades murein glycan strands and insoluble, high-molecular weight murein sacculi. Bacterial lytic transglycosylases (LTs) are classified into 4 families: family 1 includes slt70 MltC-MltF, family 2 includes MltA, family 3 includes MltB, and family 4 includes proteins of bacteriophage origin. MltA is distinct from other bacterial LTs, which are similar in structure and sequence with a lysozyme-like fold. MltA is a kidney bean-shaped monomeric protein comprised of two domains separated by a large groove, where the peptidoglycan strand binds. Domain A is made up of an N-terminal and a C-terminal portion, which corresponds to a double-psi beta-barrel (DPBB) fold. Domain B also has a beta-barrel fold topology, but it is inserted within the linear sequence of domain A. YuiC is a Firmicute stationary phase survival (Sps) protein that closely resembles the Barwin-like endoglucanase beta barrel of MltA. It is a DPBB fold that consists of two interlocked "psi-structure" motifs related by a pseudo-2-fold axis and may be involved in substrate binding and catalysis.


Pssm-ID: 439261 [Multi-domain]  Cd Length: 92  Bit Score: 89.63  E-value: 5.35e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2538967423 172 MNATAYSA---YDPGNSSYTARG-NLLKRGYVSVDPDVIPLGTAVYVEG---YGYAVADDTGGGIIGNRIDLAMDSHGEA 244
Cdd:cd22784     1 VTVTAYTPdeeQTDGGPGITASGvTLRGYGTVAVDRDLIPLGTKVKIEGpgsGGEYVVLDRGGAIKGNRIDIYFPSEKEA 80

                          90
                  ....*....|..
gi 2538967423 245 IDFGRQTVKVYI 256
Cdd:cd22784    81 KKFGRQKVTVTV 92
PGRP COG3409
Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope ...
 96-156 1.96e-21

Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442635 [Multi-domain]  Cd Length: 69  Bit Score: 84.96  E-value: 1.96e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2538967423  96 RFGDRGRSVSDLQARLAHSGFSPGSIDGIFGNGTANALKRFQKANGLTVTGEVDSKTMELL 156
Cdd:COG3409     7 RLGDSGEDVRELQQRLNALGYYPGPVDGIFGPATEAAVRAFQRANGLPVDGIVGPATWAAL 67
PGRP COG3409
Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope ...
 13-74 3.06e-19

Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442635 [Multi-domain]  Cd Length: 69  Bit Score: 79.18  E-value: 3.06e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2538967423  13 RGDRGSEVQFVQRLMITQGYLVDTADGVFGNNTEYAVRMFQKQNGLSATGKVDSDTLAAMKE 74
Cdd:COG3409     8 LGDSGEDVRELQQRLNALGYYPGPVDGIFGPATEAAVRAFQRANGLPVDGIVGPATWAALRA 69
PG_binding_1 pfam01471
Putative peptidoglycan binding domain; This domain is composed of three alpha helices. This ...
 100-156 3.45e-18

Putative peptidoglycan binding domain; This domain is composed of three alpha helices. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. This family is found N-terminal to the catalytic domain of matrixins. The domain is found to bind peptidoglycan experimentally.


Pssm-ID: 460223 [Multi-domain]  Cd Length: 57  Bit Score: 76.01  E-value: 3.45e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2538967423 100 RGRSVSDLQARLAHSGFSPGSIDGIFGNGTANALKRFQKANGLTVTGEVDSKTMELL 156
Cdd:pfam01471   1 SGEDVKELQRYLNRLGYYPGPVDGYFGPSTEAAVKAFQRAFGLPVDGIVDPETLAAL 57
PG_binding_1 pfam01471
Putative peptidoglycan binding domain; This domain is composed of three alpha helices. This ...
 16-72 1.01e-16

Putative peptidoglycan binding domain; This domain is composed of three alpha helices. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. This family is found N-terminal to the catalytic domain of matrixins. The domain is found to bind peptidoglycan experimentally.


Pssm-ID: 460223 [Multi-domain]  Cd Length: 57  Bit Score: 72.16  E-value: 1.01e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2538967423  16 RGSEVQFVQRLMITQGYLVDTADGVFGNNTEYAVRMFQKQNGLSATGKVDSDTLAAM 72
Cdd:pfam01471   1 SGEDVKELQRYLNRLGYYPGPVDGYFGPSTEAAVKAFQRAFGLPVDGIVDPETLAAL 57
3D pfam06725
3D domain; This short presumed domain contains three conserved aspartate residues, hence the ...
 199-258 1.38e-16

3D domain; This short presumed domain contains three conserved aspartate residues, hence the name 3D. It has been shown to be part of the catalytic double psi beta barrel domain of MltA.


Pssm-ID: 399598 [Multi-domain]  Cd Length: 72  Bit Score: 72.24  E-value: 1.38e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2538967423 199 VSVDPDVIPLGTAVYVEG-------YGYAVADDTGGGIIGNRIDLAMDSHGEAID---FGRQTVKVYILE 258
Cdd:pfam06725   3 IAVDPSVIPLGTPVYVEGplggkpvYRLAIAQDTGGAIKGNRIDLYFGTGDEAGNlagLYRKTGRVYILL 72
3D_domain cd14486
3D domain, named for 3 conserved aspartate residues, is found in mltA-like lytic ...
 163-257 8.11e-15

3D domain, named for 3 conserved aspartate residues, is found in mltA-like lytic transglycosylases and numerous other contexts; This family contains the 3D domain, named for its 3 conserved aspartates. It is found in conjunction with numerous other domains such as MltA (membrane-bound lytic murein transglycosylase A). These aspartates are critical active site residues of mltA-like lytic transglycosylases. Escherichia coli peptidoglycan lytic transglycosylase (LT) initiates cell wall recycling in response to damage, during bacterial fission, and cleaves peptidoglycan (PG) to create functional spaces in its wall. MltA has 2 domains, separated by a large groove, where the peptidoglycan strand binds. The C-terminus has a double-psi beta barrel fold within the 3D domain, which forms the larger A domain along with the N-terminal region of Mlts, but is also found in various other domain architectures. Peptigoglycan (also known as murein) chains, the primary structural component of bacterial cells walls, are comprised of alternating beta-1-4-linked N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc); lytic transglycosylases (LTs) cleave this beta-1-4 bond. Typically, LTs are exolytic, releasing Metabolite 1 (GlcNAc-anhMurNAc-L-Ala-D-Glu-m-Dap-D-Ala-D-Ala) from the ends of the PG strands. In contrast, membrane-bound lytic murein transglycosylase E (MltE) is endolytic , cleaving in the middle of PG strands, with further processing to Metabolite 1 accomplished by other LTs. In E. coli, there are six membrane- bound LTs: MltA-MltF and soluble Slt70. Slt35 is a soluble fragment cleaved from MltB. Bacterial LTs are classified in 4 families: Family 1 includes slt70 MltC-MltF, Family 2 includes MltA, Family 3 includes MltB, and family 4 of bacteriophage origin. While most LTs are related members of the lysozyme-like lytic transglycosylase family, MltA represents a distinct fold and sequence conservation.


Pssm-ID: 270619 [Multi-domain]  Cd Length: 104  Bit Score: 68.55  E-value: 8.11e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2538967423 163 PTEYKKTMTMNATAYSAYDPGNSSYTARGnllkRGYVSVDPDVIPLGTAVYVEGY------GYAVADDTGGGIIGNRIDL 236
Cdd:cd14486     8 EWDDGKRPSPPDEFSFSFRLTASGRPPVP----YRTIAVDPSVIPLGSVVYIPELrglpndGVFVAEDTGGAIKGNHIDV 83

                          90       100
                  ....*....|....*....|.
gi 2538967423 237 AMDSHGEAIDFGRQTVKVYIL 257
Cdd:cd14486    84 YTGDGPDARSNALKTVTVYVV 104
DPBB_MltA-like cd22785
double-psi beta-barrel fold of membrane-bound lytic murein transglycosylase A (MltA) and ...
 175-257 5.26e-12

double-psi beta-barrel fold of membrane-bound lytic murein transglycosylase A (MltA) and similar proteins; MltA, also called murein hydrolase A, is a murein-degrading enzyme that may play a role in the recycling of muropeptides during cell elongation and/or cell division. It degrades murein glycan strands and insoluble, high-molecular weight murein sacculi. Bacterial lytic transglycosylases (LTs) are classified into 4 families: family 1 includes slt70 MltC-MltF, family 2 includes MltA, family 3 includes MltB, and family 4 includes proteins of bacteriophage origin. MltA is distinct from other bacterial LTs, which are similar in structure and sequence with a lysozyme-like fold. MltA is a kidney bean-shaped monomeric protein comprised of two domains separated by a large groove, where the peptidoglycan strand binds. Domain A is made up of an N-terminal and a C-terminal portion, which corresponds to a double-psi beta-barrel (DPBB) fold. Domain B also has a beta-barrel fold topology, but it is inserted within the linear sequence of domain A. This model corresponds to the DPBB fold that consists of two interlocked "psi-structure" motifs related by a pseudo-2-fold axis. It is involved in substrate binding and catalysis.


Pssm-ID: 439262 [Multi-domain]  Cd Length: 97  Bit Score: 60.73  E-value: 5.26e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2538967423 175 TAYsaYDPGnssYTARGNLLKRGY-VSVDPDVIPLGTAVYVEGY------------GYAVADDTGGGIIGNRIDLAM--- 238
Cdd:cd22785     4 TGY--YTPP---RGALGVPLTPFRsVAVDPSVIPLGSVVYIPALdgvklpdgephdGLFIAQDTGGAIKGKHIDVFTgsg 78

                          90
                  ....*....|....*....
gi 2538967423 239 DSHGEAIDFGRQTVKVYIL 257
Cdd:cd22785    79 DEAGELAGKLNHTGRVYVL 97
YcbB COG2989
Murein L,D-transpeptidase YcbB/YkuD [Cell wall/membrane/envelope biogenesis];
14-72 9.53e-07

Murein L,D-transpeptidase YcbB/YkuD [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442228 [Multi-domain]  Cd Length: 529  Bit Score: 49.17  E-value: 9.53e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2538967423  14 GDRGSEV-QFVQRLMITqGYLVDTADG---VFGNNTEYAVRMFQKQNGLSATGKVDSDTLAAM 72
Cdd:COG2989   207 GDSDPRVpALRERLAAL-GDLPADAPSdsdVYDAELVEAVKRFQARHGLKADGVIGPATLAAL 268
mltA_like_LT_A cd14485
Domain A of MltA and related lytic transglycosylase; domain A is interrupted by domain B; ...
 199-236 2.76e-03

Domain A of MltA and related lytic transglycosylase; domain A is interrupted by domain B; Escherichia coli MltA is a membrane-bound lytic transglycosylase comprised of two domains separated by a large groove, where the peptidoglycan strand binds. Domain A is made up of an N-terminal and a C-terminal portion, which correspond to the 3D domain, named for 3 conserved aspartate residues. Domain B is inserted within the linear sequence of domain A. MltA is distinct from other bacterial lytic transglycosylases (LTs), which are similar to each other. Escherichia coli peptidoglycan lytic transglycosylase (LT) initiates cell wall recycling in response to damage, during bacterial fission, and cleaves peptidoglycan (PG) to create functional spaces in its wall. PG chains (also known as murein), the major components of the bacterial cell wall, are comprised of alternating beta-1-4-linked N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc), and lytic transglycosylases cleave this beta-1-4 bond. Typically, peptidoglycan lytic transglycosylases (LT) are exolytic, releasing Metabolite 1 (GlcNAc-anhMurNAc-L-Ala-D-Glu-m-Dap-D-Ala-D-Ala) from the ends of the PG strands. In contrast, MltE is endolytic , cleaving in the middle of PG strands, with further processing to Metabolite 1 accomplished by other LTs. In E. coli, there are six membrane-bound LTs: MltA-MltF and soluble Slt70. Slt35 is a soluble fragment cleaved from MltB. Bacterial LTs are classified in 4 families: Family 1 includes slt70 MltC-MltF, Family 2 includes MltA, Family 3 includes MltB, and Family 4 of bacteriophage origin. While most of the LT family members are similar in structure and sequence with a lysozyme-like fold, Family 2 (including mltA) is distinct.


Pssm-ID: 270618 [Multi-domain]  Cd Length: 159  Bit Score: 37.23  E-value: 2.76e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2538967423 199 VSVDPDVIPLGTAVYVEG------------YGYAVADDTGGGIIG-NRIDL 236
Cdd:cd14485    85 LAVDRSLIPLGAPVWLETplpdangggkplRRLVIAQDTGGAIKGpVRADL 135
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH