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Conserved domains on  [gi|1498198571|gb|RMG53573|]
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N-acetylmuramoyl-L-alanine amidase [Chloroflexi bacterium]

Protein Classification

peptidoglycan recognition family protein( domain architecture ID 10159278)

peptidoglycan recognition protein (PGRP) family protein is a pattern recognition receptor that binds, and in certain cases, hydrolyzes peptidoglycans (PGNs) of bacterial cell walls

CATH:  3.40.80.10
Gene Ontology:  GO:0042834|GO:0046872
PubMed:  16930467
SCOP:  4001915

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PGRP cd06583
Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in ...
 232-369 7.90e-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: 60.38  E-value: 7.90e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198571 232 PRGVVIHQLAVDIPPSATlSYLRAllIYQTSVLDWDDLIYHYIIDNEGNLFEGRlggPTSLVRQVAGSEAD---VHVALL 308
Cdd:cd06583     2 VKYVVIHHTANPNCYTAA-AAVRY--LQNYHMRGWSDISYHFLVGGDGRIYQGR---GWNYVGWHAGGNYNsysIGIELI 75

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1498198571 309 TPADQ-APSAAAQSRLVALLAWLTQTYAIAPtdlqptatdgilRPAIAGHFEVSATAVDPYP 369
Cdd:cd06583    76 GNFDGgPPTAAQLEALAELLAYLVKRYGIPP------------DYRIVGHRDVSPGTECPGD 125
 
Name Accession Description Interval E-value
PGRP cd06583
Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in ...
 232-369 7.90e-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: 60.38  E-value: 7.90e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198571 232 PRGVVIHQLAVDIPPSATlSYLRAllIYQTSVLDWDDLIYHYIIDNEGNLFEGRlggPTSLVRQVAGSEAD---VHVALL 308
Cdd:cd06583     2 VKYVVIHHTANPNCYTAA-AAVRY--LQNYHMRGWSDISYHFLVGGDGRIYQGR---GWNYVGWHAGGNYNsysIGIELI 75

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1498198571 309 TPADQ-APSAAAQSRLVALLAWLTQTYAIAPtdlqptatdgilRPAIAGHFEVSATAVDPYP 369
Cdd:cd06583    76 GNFDGgPPTAAQLEALAELLAYLVKRYGIPP------------DYRIVGHRDVSPGTECPGD 125
Amidase_2 pfam01510
N-acetylmuramoyl-L-alanine amidase; This family includes zinc amidases that have ...
 231-369 8.98e-08

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: 51.20  E-value: 8.98e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198571 231 DPRGVVIHQLAVDIPPSATLSYlralliYQTSVLDWDDLIYHYIIDNEGNLFEgrlGGPTSLVRQVAGSEAD----VHVA 306
Cdd:pfam01510   1 PIRYIVIHHTAGPSFAGALLPY------AACIARGWSDVSYHYLIDRDGTIYQ---LVPENGRAWHAGNGGGndrsIGIE 71

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1498198571 307 LLTPA-DQAPSAAAQSRLVALLAWLTQTYAIAPtdlqptatdgilRPAIAGHFEVSATAvDPYP 369
Cdd:pfam01510  72 LEGNFgGDPPTDAQYEALARLLADLCKRYGIPP------------DRRIVGHRDVGRKT-DPGP 122
PGRP smart00701
Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme; The ...
 214-343 3.08e-05

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: 44.59  E-value: 3.08e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198571  214 IARTDWAEPAAARPDR--RDPRGVVIHQLAV---DIPPSATLSyLRALLIYQTSVLDWDDLIYHYIIDNEGNLFEGRlGG 288
Cdd:smart00701   4 VPRSEWGAKPRGHTPRltRPVRYVIIHHTATpncYTDAQCAQI-LRNIQAYHMEELGWCDIGYNFLVGGDGKVYEGR-GW 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1498198571  289 PtslvrqVAGSEA------DVHVALL-TPADQAPSAAAQSRLVALLAWltqtyAIAPTDLQP 343
Cdd:smart00701  82 N------VVGAHTggyndiSLGIAFIgNFTDKLPTDAALDAAQDLLAC-----AVQRGHLSP 132
 
Name Accession Description Interval E-value
PGRP cd06583
Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in ...
 232-369 7.90e-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: 60.38  E-value: 7.90e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198571 232 PRGVVIHQLAVDIPPSATlSYLRAllIYQTSVLDWDDLIYHYIIDNEGNLFEGRlggPTSLVRQVAGSEAD---VHVALL 308
Cdd:cd06583     2 VKYVVIHHTANPNCYTAA-AAVRY--LQNYHMRGWSDISYHFLVGGDGRIYQGR---GWNYVGWHAGGNYNsysIGIELI 75

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1498198571 309 TPADQ-APSAAAQSRLVALLAWLTQTYAIAPtdlqptatdgilRPAIAGHFEVSATAVDPYP 369
Cdd:cd06583    76 GNFDGgPPTAAQLEALAELLAYLVKRYGIPP------------DYRIVGHRDVSPGTECPGD 125
Amidase_2 pfam01510
N-acetylmuramoyl-L-alanine amidase; This family includes zinc amidases that have ...
 231-369 8.98e-08

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: 51.20  E-value: 8.98e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198571 231 DPRGVVIHQLAVDIPPSATLSYlralliYQTSVLDWDDLIYHYIIDNEGNLFEgrlGGPTSLVRQVAGSEAD----VHVA 306
Cdd:pfam01510   1 PIRYIVIHHTAGPSFAGALLPY------AACIARGWSDVSYHYLIDRDGTIYQ---LVPENGRAWHAGNGGGndrsIGIE 71

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1498198571 307 LLTPA-DQAPSAAAQSRLVALLAWLTQTYAIAPtdlqptatdgilRPAIAGHFEVSATAvDPYP 369
Cdd:pfam01510  72 LEGNFgGDPPTDAQYEALARLLADLCKRYGIPP------------DRRIVGHRDVGRKT-DPGP 122
PGRP smart00701
Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme; The ...
 214-343 3.08e-05

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: 44.59  E-value: 3.08e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198571  214 IARTDWAEPAAARPDR--RDPRGVVIHQLAV---DIPPSATLSyLRALLIYQTSVLDWDDLIYHYIIDNEGNLFEGRlGG 288
Cdd:smart00701   4 VPRSEWGAKPRGHTPRltRPVRYVIIHHTATpncYTDAQCAQI-LRNIQAYHMEELGWCDIGYNFLVGGDGKVYEGR-GW 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1498198571  289 PtslvrqVAGSEA------DVHVALL-TPADQAPSAAAQSRLVALLAWltqtyAIAPTDLQP 343
Cdd:smart00701  82 N------VVGAHTggyndiSLGIAFIgNFTDKLPTDAALDAAQDLLAC-----AVQRGHLSP 132
Ami_2 smart00644
Ami_2 domain;
230-363 3.62e-03

Ami_2 domain;


Pssm-ID: 214760 [Multi-domain]  Cd Length: 126  Bit Score: 38.11  E-value: 3.62e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198571  230 RDPRGVVIHQLAVDipPSATLSYLRALliyQTSvlDWDDLIYHYIIDNEGNLFEGRlgGPTSLVRQVAGSEAD------V 303
Cdd:smart00644   1 PPPRGIVIHHTANS--NASCANEARYM---QNN--HMNDIGYHFLVGGDGRVYQGV--GWNYVAWHAGGAHTPgyndisI 71

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1498198571  304 HVALL--TPADQAPSAAAQSRLVALLAWLTQTYAIAPTDlqptatdgilRPAIAGHFEVSAT 363
Cdd:smart00644  72 GIEFIgsFDSDDEPFAEALYAALDLLAKLLKGAGLPPDG----------RYRIVGHRDVAPT 123
 
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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