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Conserved domains on  [gi|323463172|pdb|3QJ1|B]
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Chain B, Peptidoglycan recognition protein 1

Protein Classification

peptidoglycan recognition protein( domain architecture ID 11274790)

peptidoglycan recognition protein (PGRP) is a pattern recognition receptor that binds and may also hydrolyze peptidoglycans (PGNs) of bacterial cell walls

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PGRP smart00701
Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme; The ...
 8-149 3.00e-72

Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme; The bacteriophage molecule, but not its moth homologue, has been shown to have N-acetylmuramoyl-L-alanine amidase activity. One member of this family, Tag7, is a cytokine.


:

Pssm-ID: 128941  Cd Length: 142  Bit Score: 214.08  E-value: 3.00e-72
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QJ1_B           8 SIVPRREWRALASECRERLTRPVRYVVVSHTAGSHCDTPASCAQQAQNVQSYHVRNLGWCDVGYNFLIGEDGLVYEGRGW 87
Cdd:smart00701   2 PIVPRSEWGAKPRGHTPRLTRPVRYVIIHHTATPNCYTDAQCAQILRNIQAYHMEELGWCDIGYNFLVGGDGKVYEGRGW 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
3QJ1_B          88 NIKGAHAGPtWNPISIGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDV 149
Cdd:smart00701  82 NVVGAHTGG-YNDISLGIAFIGNFTDKLPTDAALDAAQDLLACAVQRGHLSPDYKLVGHRQV 142
 
Name Accession Description Interval E-value
PGRP smart00701
Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme; The ...
 8-149 3.00e-72

Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme; The bacteriophage molecule, but not its moth homologue, has been shown to have N-acetylmuramoyl-L-alanine amidase activity. One member of this family, Tag7, is a cytokine.


Pssm-ID: 128941  Cd Length: 142  Bit Score: 214.08  E-value: 3.00e-72
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QJ1_B           8 SIVPRREWRALASECRERLTRPVRYVVVSHTAGSHCDTPASCAQQAQNVQSYHVRNLGWCDVGYNFLIGEDGLVYEGRGW 87
Cdd:smart00701   2 PIVPRSEWGAKPRGHTPRLTRPVRYVIIHHTATPNCYTDAQCAQILRNIQAYHMEELGWCDIGYNFLVGGDGKVYEGRGW 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
3QJ1_B          88 NIKGAHAGPtWNPISIGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDV 149
Cdd:smart00701  82 NVVGAHTGG-YNDISLGIAFIGNFTDKLPTDAALDAAQDLLACAVQRGHLSPDYKLVGHRQV 142
PGRP cd06583
Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in ...
 29-158 1.31e-48

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: 153.60  E-value: 1.31e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QJ1_B       29 PVRYVVVSHTAGSHCDTpasCAQQAQNVQSYHVRnlGWCDVGYNFLIGEDGLVYEGRGWNIKGAHAGPTWNPISIGISFM 108
Cdd:cd06583   1 PVKYVVIHHTANPNCYT---AAAAVRYLQNYHMR--GWSDISYHFLVGGDGRIYQGRGWNYVGWHAGGNYNSYSIGIELI 75

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
3QJ1_B      109 GNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDVQP-TLSPGDR 158
Cdd:cd06583  76 GNFDGGPPTAAQLEALAELLAYLVKRYGIPPDYRIVGHRDVSPgTECPGDA 126
Amidase_2 pfam01510
N-acetylmuramoyl-L-alanine amidase; This family includes zinc amidases that have ...
 29-157 2.57e-32

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: 112.06  E-value: 2.57e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QJ1_B         29 PVRYVVVSHTAGSHCDTPASCAQQAQNVqsyhvrnlGWCDVGYNFLIGEDGLVYE-----GRGWnikgaHAGPT-WNPIS 102
Cdd:pfam01510   1 PIRYIVIHHTAGPSFAGALLPYAACIAR--------GWSDVSYHYLIDRDGTIYQlvpenGRAW-----HAGNGgGNDRS 67

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
3QJ1_B        103 IGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDVQPTLSPGD 157
Cdd:pfam01510  68 IGIELEGNFGGDPPTDAQYEALARLLADLCKRYGIPPDRRIVGHRDVGRKTDPGP 122
PHA00447 PHA00447
lysozyme
 42-165 1.32e-13

lysozyme


Pssm-ID: 177282 [Multi-domain]  Cd Length: 142  Bit Score: 64.41  E-value: 1.32e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QJ1_B        42 HCD-TPASCAQQAQNVQSYHVRNlGWCDVGYNFLIGEDGLVYEGRGWNIKGAHAgPTWNPISIGISFMGNYMNRVPP--- 117
Cdd:PHA00447  16 HCSaTKPSMDVGVREIRQWHKEQ-GWLDVGYHFIIRRDGTVEEGRPEDVVGSHV-KGYNSNSVGVCLVGGIDDKGKFdan 93

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
3QJ1_B       118 --PRALRAAQNLLacgVALGALRSNYEVKGHRDVQPTLSPGDRLYEIIQT 165
Cdd:PHA00447  94 ftPAQMQSLKSLL---VTLKAKYPGAEIKAHHDVAPKACPSFDLQRWLKK 140
AmpD COG3023
N-acetyl-anhydromuramyl-L-alanine amidase AmpD [Cell wall/membrane/envelope biogenesis];
28-152 8.93e-03

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


Pssm-ID: 442259  Cd Length: 167  Bit Score: 35.23  E-value: 8.93e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QJ1_B       28 RPVRYVVVSHTAGshcDTPASCAQQAQNVQ---SYHvrnlgwcdvgynFLIGEDGLVY-----EGRGWnikgaHAGPTW- 98
Cdd:COG3023  25 AEIDLIVIHYTAG---PPGGGALDWLTDPAlrvSAH------------YLIDRDGEIYqlvpeDDRAW-----HAGVSSw 84

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
3QJ1_B       99 ------NPISIGISFMGNYMNRVPPPRA-LRAAQNLLAcgvalgALRSNY-----EVKGHRDVQPT 152
Cdd:COG3023  85 rgrtnlNDFSIGIELENPGHGWAPFTEAqYEALAALLR------DLCARYgippdHIVGHSDIAPG 144
 
Name Accession Description Interval E-value
PGRP smart00701
Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme; The ...
 8-149 3.00e-72

Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme; The bacteriophage molecule, but not its moth homologue, has been shown to have N-acetylmuramoyl-L-alanine amidase activity. One member of this family, Tag7, is a cytokine.


Pssm-ID: 128941  Cd Length: 142  Bit Score: 214.08  E-value: 3.00e-72
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QJ1_B           8 SIVPRREWRALASECRERLTRPVRYVVVSHTAGSHCDTPASCAQQAQNVQSYHVRNLGWCDVGYNFLIGEDGLVYEGRGW 87
Cdd:smart00701   2 PIVPRSEWGAKPRGHTPRLTRPVRYVIIHHTATPNCYTDAQCAQILRNIQAYHMEELGWCDIGYNFLVGGDGKVYEGRGW 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
3QJ1_B          88 NIKGAHAGPtWNPISIGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDV 149
Cdd:smart00701  82 NVVGAHTGG-YNDISLGIAFIGNFTDKLPTDAALDAAQDLLACAVQRGHLSPDYKLVGHRQV 142
PGRP cd06583
Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in ...
 29-158 1.31e-48

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: 153.60  E-value: 1.31e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QJ1_B       29 PVRYVVVSHTAGSHCDTpasCAQQAQNVQSYHVRnlGWCDVGYNFLIGEDGLVYEGRGWNIKGAHAGPTWNPISIGISFM 108
Cdd:cd06583   1 PVKYVVIHHTANPNCYT---AAAAVRYLQNYHMR--GWSDISYHFLVGGDGRIYQGRGWNYVGWHAGGNYNSYSIGIELI 75

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
3QJ1_B      109 GNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDVQP-TLSPGDR 158
Cdd:cd06583  76 GNFDGGPPTAAQLEALAELLAYLVKRYGIPPDYRIVGHRDVSPgTECPGDA 126
Ami_2 smart00644
Ami_2 domain;
28-155 3.09e-37

Ami_2 domain;


Pssm-ID: 214760 [Multi-domain]  Cd Length: 126  Bit Score: 124.39  E-value: 3.09e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QJ1_B          28 RPVRYVVVSHTAGShcdtPASCAQQAQNVQSYHVRnlgwcDVGYNFLIGEDGLVYEGRGWNIKGAHAG----PTWNPISI 103
Cdd:smart00644   1 PPPRGIVIHHTANS----NASCANEARYMQNNHMN-----DIGYHFLVGGDGRVYQGVGWNYVAWHAGgahtPGYNDISI 71

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
3QJ1_B         104 GISFMGNYMNR-VPPPRALRAAQNLLACGV--ALGALRSNYEVKGHRDVQPTLSP 155
Cdd:smart00644  72 GIEFIGSFDSDdEPFAEALYAALDLLAKLLkgAGLPPDGRYRIVGHRDVAPTEDP 126
Amidase_2 pfam01510
N-acetylmuramoyl-L-alanine amidase; This family includes zinc amidases that have ...
 29-157 2.57e-32

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: 112.06  E-value: 2.57e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QJ1_B         29 PVRYVVVSHTAGSHCDTPASCAQQAQNVqsyhvrnlGWCDVGYNFLIGEDGLVYE-----GRGWnikgaHAGPT-WNPIS 102
Cdd:pfam01510   1 PIRYIVIHHTAGPSFAGALLPYAACIAR--------GWSDVSYHYLIDRDGTIYQlvpenGRAW-----HAGNGgGNDRS 67

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
3QJ1_B        103 IGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDVQPTLSPGD 157
Cdd:pfam01510  68 IGIELEGNFGGDPPTDAQYEALARLLADLCKRYGIPPDRRIVGHRDVGRKTDPGP 122
PHA00447 PHA00447
lysozyme
 42-165 1.32e-13

lysozyme


Pssm-ID: 177282 [Multi-domain]  Cd Length: 142  Bit Score: 64.41  E-value: 1.32e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QJ1_B        42 HCD-TPASCAQQAQNVQSYHVRNlGWCDVGYNFLIGEDGLVYEGRGWNIKGAHAgPTWNPISIGISFMGNYMNRVPP--- 117
Cdd:PHA00447  16 HCSaTKPSMDVGVREIRQWHKEQ-GWLDVGYHFIIRRDGTVEEGRPEDVVGSHV-KGYNSNSVGVCLVGGIDDKGKFdan 93

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
3QJ1_B       118 --PRALRAAQNLLacgVALGALRSNYEVKGHRDVQPTLSPGDRLYEIIQT 165
Cdd:PHA00447  94 ftPAQMQSLKSLL---VTLKAKYPGAEIKAHHDVAPKACPSFDLQRWLKK 140
AmpD COG3023
N-acetyl-anhydromuramyl-L-alanine amidase AmpD [Cell wall/membrane/envelope biogenesis];
28-152 8.93e-03

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


Pssm-ID: 442259  Cd Length: 167  Bit Score: 35.23  E-value: 8.93e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QJ1_B       28 RPVRYVVVSHTAGshcDTPASCAQQAQNVQ---SYHvrnlgwcdvgynFLIGEDGLVY-----EGRGWnikgaHAGPTW- 98
Cdd:COG3023  25 AEIDLIVIHYTAG---PPGGGALDWLTDPAlrvSAH------------YLIDRDGEIYqlvpeDDRAW-----HAGVSSw 84

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
3QJ1_B       99 ------NPISIGISFMGNYMNRVPPPRA-LRAAQNLLAcgvalgALRSNY-----EVKGHRDVQPT 152
Cdd:COG3023  85 rgrtnlNDFSIGIELENPGHGWAPFTEAqYEALAALLR------DLCARYgippdHIVGHSDIAPG 144
 
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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