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Conserved domains on  [gi|2411116283|ref|WP_268571058|]
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N-acetylmuramoyl-L-alanine amidase, partial [Paenibacillus larvae]

Protein Classification

N-acetylmuramoyl-L-alanine amidase( domain architecture ID 11459553)

N-acetylmuramoyl-L-alanine amidase hydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides

CATH:  1.10.101.10|3.40.80.10
EC:  3.5.1.28
Gene Ontology:  GO:0008745|GO:0008270|GO:0071555|GO:0042834|GO:0046872
SCOP:  4000784|4001915

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
AmpD COG3023
N-acetyl-anhydromuramyl-L-alanine amidase AmpD [Cell wall/membrane/envelope biogenesis];
31-169 1.66e-18

N-acetyl-anhydromuramyl-L-alanine amidase AmpD [Cell wall/membrane/envelope biogenesis];


:

Pssm-ID: 442259  Cd Length: 167  Bit Score: 78.75  E-value: 1.66e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2411116283  31 NSKERTEDITHVMLHLVSNavqkpkdPYQENDIyNIFKD--YGLSSHYMINRKGDIYRLVNENRVAYHAGKESFprfpED 108
Cdd:COG3023    19 DERPAGAEIDLIVIHYTAG-------PPGGGAL-DWLTDpaLRVSAHYLIDRDGEIYQLVPEDDRAWHAGVSSW----RG 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2411116283 109 MDKINEYSIGIDILGIGTWDEmsstmsketydlvddsdvGWTDAQYRSLGLLLDDIYKRNP 169
Cdd:COG3023    87 RTNLNDFSIGIELENPGHGWA------------------PFTEAQYEALAALLRDLCARYG 129
 
Name Accession Description Interval E-value
AmpD COG3023
N-acetyl-anhydromuramyl-L-alanine amidase AmpD [Cell wall/membrane/envelope biogenesis];
31-169 1.66e-18

N-acetyl-anhydromuramyl-L-alanine amidase AmpD [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442259  Cd Length: 167  Bit Score: 78.75  E-value: 1.66e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2411116283  31 NSKERTEDITHVMLHLVSNavqkpkdPYQENDIyNIFKD--YGLSSHYMINRKGDIYRLVNENRVAYHAGKESFprfpED 108
Cdd:COG3023    19 DERPAGAEIDLIVIHYTAG-------PPGGGAL-DWLTDpaLRVSAHYLIDRDGEIYQLVPEDDRAWHAGVSSW----RG 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2411116283 109 MDKINEYSIGIDILGIGTWDEmsstmsketydlvddsdvGWTDAQYRSLGLLLDDIYKRNP 169
Cdd:COG3023    87 RTNLNDFSIGIELENPGHGWA------------------PFTEAQYEALAALLRDLCARYG 129
Amidase_2 pfam01510
N-acetylmuramoyl-L-alanine amidase; This family includes zinc amidases that have ...
 38-168 3.70e-16

N-acetylmuramoyl-L-alanine amidase; This family includes zinc amidases that have N-acetylmuramoyl-L-alanine amidase activity EC:3.5.1.28. This enzyme domain cleaves the amide bond between N-acetylmuramoyl and L-amino acids in bacterial cell walls (preferentially: D-lactyl-L-Ala). The structure is known for the bacteriophage T7 structure and shows that two of the conserved histidines are zinc binding.


Pssm-ID: 460236 [Multi-domain]  Cd Length: 122  Bit Score: 71.23  E-value: 3.70e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2411116283  38 DITHVMLHlvSNAVQKPKDPYQENDIYNIFKDYGLSSHYMINRKGDIYRLVNENRVAYHAGKESFprfpedmdkiNEYSI 117
Cdd:pfam01510   1 PIRYIVIH--HTAGPSFAGALLPYAACIARGWSDVSYHYLIDRDGTIYQLVPENGRAWHAGNGGG----------NDRSI 68

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2411116283 118 GIDILGIGTWDemsstmsketydlvddsdvGWTDAQYRSLGLLLDDIYKRN 168
Cdd:pfam01510  69 GIELEGNFGGD-------------------PPTDAQYEALARLLADLCKRY 100
PGRP cd06583
Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in ...
 64-169 3.49e-11

Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20 kDa) extracellular proteins; intermediate PGRPs (PGRP-I) that are 40-45 kDa and are predicted to be transmembrane proteins; and long PGRPs (PGRP-L), up to 90 kDa, which may be either intracellular or transmembrane. Several structures of PGRPs are known in insects and mammals, some bound with substrates like Muramyl Tripeptide (MTP) or Tracheal Cytotoxin (TCT). The substrate binding site is conserved in PGRP-LCx, PGRP-LE, and PGRP-Ialpha proteins. This family includes Zn-dependent N-Acetylmuramoyl-L-alanine Amidase, EC:3.5.1.28. This enzyme cleaves the amide bond between N-acetylmuramoyl and L-amino acids, preferentially D-lactyl-L-Ala, in bacterial cell walls. The structure for the bacteriophage T7 lysozyme shows that two of the conserved histidines and a cysteine are zinc binding residues. Site-directed mutagenesis of T7 lysozyme indicates that two conserved residues, a Tyr and a Lys, are important for amidase activity.


Pssm-ID: 133475 [Multi-domain]  Cd Length: 126  Bit Score: 58.45  E-value: 3.49e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2411116283  64 YNIFKDYGLSSHYMINRKGDIYRLVNENRVAYHAGkesfprfpedmDKINEYSIGIDILGigtwdemsstmsketydlvD 143
Cdd:cd06583    28 YHMRGWSDISYHFLVGGDGRIYQGRGWNYVGWHAG-----------GNYNSYSIGIELIG-------------------N 77

                          90       100
                  ....*....|....*....|....*.
gi 2411116283 144 DSDVGWTDAQYRSLGLLLDDIYKRNP 169
Cdd:cd06583    78 FDGGPPTAAQLEALAELLAYLVKRYG 103
PRK11789 PRK11789
1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD;
73-173 3.89e-10

1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD;


Pssm-ID: 236984  Cd Length: 185  Bit Score: 56.74  E-value: 3.89e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2411116283  73 SSHYMINRKGDIYRLVNENRVAYHAGKESFprfpEDMDKINEYSIGIDILGigtwdemsstmsketydlvDDsDVGWTDA 152
Cdd:PRK11789   75 SAHFLIRRDGEIVQFVSFDDRAWHAGVSSF----QGRERCNDFSIGIELEG-------------------TD-TLPFTDA 130

                          90       100
                  ....*....|....*....|.
gi 2411116283 153 QYRSLGLLLDDIYKRNPSILR 173
Cdd:PRK11789  131 QYQALAALTRALRAAYPIIAE 151
Ami_2 smart00644
Ami_2 domain;
73-173 9.22e-10

Ami_2 domain;


Pssm-ID: 214760 [Multi-domain]  Cd Length: 126  Bit Score: 54.29  E-value: 9.22e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2411116283   73 SSHYMINRKGDIYRLVNENRVAYHAGKESFPRFpedmdkiNEYSIGIDILGIGTWDEMSstmsketydlvddsdvgWTDA 152
Cdd:smart00644  34 GYHFLVGGDGRVYQGVGWNYVAWHAGGAHTPGY-------NDISIGIEFIGSFDSDDEP-----------------FAEA 89

                           90       100
                   ....*....|....*....|.
gi 2411116283  153 QYRSLGLLLDDIYKRNPSILR 173
Cdd:smart00644  90 LYAALDLLAKLLKGAGLPPDG 110
 
Name Accession Description Interval E-value
AmpD COG3023
N-acetyl-anhydromuramyl-L-alanine amidase AmpD [Cell wall/membrane/envelope biogenesis];
31-169 1.66e-18

N-acetyl-anhydromuramyl-L-alanine amidase AmpD [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442259  Cd Length: 167  Bit Score: 78.75  E-value: 1.66e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2411116283  31 NSKERTEDITHVMLHLVSNavqkpkdPYQENDIyNIFKD--YGLSSHYMINRKGDIYRLVNENRVAYHAGKESFprfpED 108
Cdd:COG3023    19 DERPAGAEIDLIVIHYTAG-------PPGGGAL-DWLTDpaLRVSAHYLIDRDGEIYQLVPEDDRAWHAGVSSW----RG 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2411116283 109 MDKINEYSIGIDILGIGTWDEmsstmsketydlvddsdvGWTDAQYRSLGLLLDDIYKRNP 169
Cdd:COG3023    87 RTNLNDFSIGIELENPGHGWA------------------PFTEAQYEALAALLRDLCARYG 129
Amidase_2 pfam01510
N-acetylmuramoyl-L-alanine amidase; This family includes zinc amidases that have ...
 38-168 3.70e-16

N-acetylmuramoyl-L-alanine amidase; This family includes zinc amidases that have N-acetylmuramoyl-L-alanine amidase activity EC:3.5.1.28. This enzyme domain cleaves the amide bond between N-acetylmuramoyl and L-amino acids in bacterial cell walls (preferentially: D-lactyl-L-Ala). The structure is known for the bacteriophage T7 structure and shows that two of the conserved histidines are zinc binding.


Pssm-ID: 460236 [Multi-domain]  Cd Length: 122  Bit Score: 71.23  E-value: 3.70e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2411116283  38 DITHVMLHlvSNAVQKPKDPYQENDIYNIFKDYGLSSHYMINRKGDIYRLVNENRVAYHAGKESFprfpedmdkiNEYSI 117
Cdd:pfam01510   1 PIRYIVIH--HTAGPSFAGALLPYAACIARGWSDVSYHYLIDRDGTIYQLVPENGRAWHAGNGGG----------NDRSI 68

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2411116283 118 GIDILGIGTWDemsstmsketydlvddsdvGWTDAQYRSLGLLLDDIYKRN 168
Cdd:pfam01510  69 GIELEGNFGGD-------------------PPTDAQYEALARLLADLCKRY 100
PGRP cd06583
Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in ...
 64-169 3.49e-11

Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20 kDa) extracellular proteins; intermediate PGRPs (PGRP-I) that are 40-45 kDa and are predicted to be transmembrane proteins; and long PGRPs (PGRP-L), up to 90 kDa, which may be either intracellular or transmembrane. Several structures of PGRPs are known in insects and mammals, some bound with substrates like Muramyl Tripeptide (MTP) or Tracheal Cytotoxin (TCT). The substrate binding site is conserved in PGRP-LCx, PGRP-LE, and PGRP-Ialpha proteins. This family includes Zn-dependent N-Acetylmuramoyl-L-alanine Amidase, EC:3.5.1.28. This enzyme cleaves the amide bond between N-acetylmuramoyl and L-amino acids, preferentially D-lactyl-L-Ala, in bacterial cell walls. The structure for the bacteriophage T7 lysozyme shows that two of the conserved histidines and a cysteine are zinc binding residues. Site-directed mutagenesis of T7 lysozyme indicates that two conserved residues, a Tyr and a Lys, are important for amidase activity.


Pssm-ID: 133475 [Multi-domain]  Cd Length: 126  Bit Score: 58.45  E-value: 3.49e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2411116283  64 YNIFKDYGLSSHYMINRKGDIYRLVNENRVAYHAGkesfprfpedmDKINEYSIGIDILGigtwdemsstmsketydlvD 143
Cdd:cd06583    28 YHMRGWSDISYHFLVGGDGRIYQGRGWNYVGWHAG-----------GNYNSYSIGIELIG-------------------N 77

                          90       100
                  ....*....|....*....|....*.
gi 2411116283 144 DSDVGWTDAQYRSLGLLLDDIYKRNP 169
Cdd:cd06583    78 FDGGPPTAAQLEALAELLAYLVKRYG 103
PRK11789 PRK11789
1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD;
73-173 3.89e-10

1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD;


Pssm-ID: 236984  Cd Length: 185  Bit Score: 56.74  E-value: 3.89e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2411116283  73 SSHYMINRKGDIYRLVNENRVAYHAGKESFprfpEDMDKINEYSIGIDILGigtwdemsstmsketydlvDDsDVGWTDA 152
Cdd:PRK11789   75 SAHFLIRRDGEIVQFVSFDDRAWHAGVSSF----QGRERCNDFSIGIELEG-------------------TD-TLPFTDA 130

                          90       100
                  ....*....|....*....|.
gi 2411116283 153 QYRSLGLLLDDIYKRNPSILR 173
Cdd:PRK11789  131 QYQALAALTRALRAAYPIIAE 151
Ami_2 smart00644
Ami_2 domain;
73-173 9.22e-10

Ami_2 domain;


Pssm-ID: 214760 [Multi-domain]  Cd Length: 126  Bit Score: 54.29  E-value: 9.22e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2411116283   73 SSHYMINRKGDIYRLVNENRVAYHAGKESFPRFpedmdkiNEYSIGIDILGIGTWDEMSstmsketydlvddsdvgWTDA 152
Cdd:smart00644  34 GYHFLVGGDGRVYQGVGWNYVAWHAGGAHTPGY-------NDISIGIEFIGSFDSDDEP-----------------FAEA 89

                           90       100
                   ....*....|....*....|.
gi 2411116283  153 QYRSLGLLLDDIYKRNPSILR 173
Cdd:smart00644  90 LYAALDLLAKLLKGAGLPPDG 110
 
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.
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