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Conserved domains on  [gi|2084915352|ref|WP_221578607|]
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N-acetylmuramoyl-L-alanine amidase [Pseudomonas cichorii]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PGRP super family cl02712
Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in ...
 51-149 8.21e-14

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.


The actual alignment was detected with superfamily member smart00701:

Pssm-ID: 470657  Cd Length: 142  Bit Score: 66.55  E-value: 8.21e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084915352   51 RSAWGA--MEGKPNMEKDWDYTMIalHHAG-----RSYECSpggtQQMQDIQHFQM-NNKFDDIGYHYGISCDGTVLEGR 122
Cdd:smart00701   6 RSEWGAkpRGHTPRLTRPVRYVII--HHTAtpncyTDAQCA----QILRNIQAYHMeELGWCDIGYNFLVGGDGKVYEGR 79

                           90       100
                   ....*....|....*....|....*..
gi 2084915352  123 DIRLQASSVKLFNTGVIGIVLLENLTT 149
Cdd:smart00701  80 GWNVVGAHTGGYNDISLGIAFIGNFTD 106
 
Name Accession Description Interval E-value
PGRP smart00701
Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme; The ...
 51-149 8.21e-14

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: 66.55  E-value: 8.21e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084915352   51 RSAWGA--MEGKPNMEKDWDYTMIalHHAG-----RSYECSpggtQQMQDIQHFQM-NNKFDDIGYHYGISCDGTVLEGR 122
Cdd:smart00701   6 RSEWGAkpRGHTPRLTRPVRYVII--HHTAtpncyTDAQCA----QILRNIQAYHMeELGWCDIGYNFLVGGDGKVYEGR 79

                           90       100
                   ....*....|....*....|....*..
gi 2084915352  123 DIRLQASSVKLFNTGVIGIVLLENLTT 149
Cdd:smart00701  80 GWNVVGAHTGGYNDISLGIAFIGNFTD 106
PGRP cd06583
Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in ...
 70-218 4.87e-13

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: 63.85  E-value: 4.87e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084915352  70 TMIALHHAGRSYecSPGGTQQMQDIQHFQMNNkFDDIGYHYGISCDGTVLEGRDIRLQASSVK-LFNTGVIGIvllenlt 148
Cdd:cd06583     3 KYVVIHHTANPN--CYTAAAAVRYLQNYHMRG-WSDISYHFLVGGDGRIYQGRGWNYVGWHAGgNYNSYSIGI------- 72

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2084915352 149 taeeggdiiakgrealERLGYSTTNVIPAAQIDALMHLIEALKSVFFI---ERFGGHKEFPGQdregKICPGN 218
Cdd:cd06583    73 ----------------ELIGNFDGGPPTAAQLEALAELLAYLVKRYGIppdYRIVGHRDVSPG----TECPGD 125
PHA00447 PHA00447
lysozyme
 92-217 2.19e-09

lysozyme


Pssm-ID: 177282 [Multi-domain]  Cd Length: 142  Bit Score: 54.40  E-value: 2.19e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084915352  92 QDIQHFQMNNKFDDIGYHYGISCDGTVLEGRDIRLQASSVKLFNTGVIGIVLLenlttaeegGDIIAKGRealerlgyST 171
Cdd:PHA00447   29 REIRQWHKEQGWLDVGYHFIIRRDGTVEEGRPEDVVGSHVKGYNSNSVGVCLV---------GGIDDKGK--------FD 91

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2084915352 172 TNVIPaAQIDALMHLIEALKSVFFIERFGGHkefpgQDREGKICPG 217
Cdd:PHA00447   92 ANFTP-AQMQSLKSLLVTLKAKYPGAEIKAH-----HDVAPKACPS 131
Amidase_2 pfam01510
N-acetylmuramoyl-L-alanine amidase; This family includes zinc amidases that have ...
 70-218 1.01e-05

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: 43.50  E-value: 1.01e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084915352  70 TMIALHHAGRsyecspGGTQQMQDIQHFQMNNKFDDIGYHYGISCDGTVLEGRDIRLQA--SSVKLFNTGVIGIVLLENL 147
Cdd:pfam01510   3 RYIVIHHTAG------PSFAGALLPYAACIARGWSDVSYHYLIDRDGTIYQLVPENGRAwhAGNGGGNDRSIGIELEGNF 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2084915352 148 TTAEeggdiiakgrealerlgysttnvIPAAQIDALMHLIEALKSVFFIERFG---GHkefpgQDREGKICPGN 218
Cdd:pfam01510  77 GGDP-----------------------PTDAQYEALARLLADLCKRYGIPPDRrivGH-----RDVGRKTDPGP 122
 
Name Accession Description Interval E-value
PGRP smart00701
Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme; The ...
 51-149 8.21e-14

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: 66.55  E-value: 8.21e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084915352   51 RSAWGA--MEGKPNMEKDWDYTMIalHHAG-----RSYECSpggtQQMQDIQHFQM-NNKFDDIGYHYGISCDGTVLEGR 122
Cdd:smart00701   6 RSEWGAkpRGHTPRLTRPVRYVII--HHTAtpncyTDAQCA----QILRNIQAYHMeELGWCDIGYNFLVGGDGKVYEGR 79

                           90       100
                   ....*....|....*....|....*..
gi 2084915352  123 DIRLQASSVKLFNTGVIGIVLLENLTT 149
Cdd:smart00701  80 GWNVVGAHTGGYNDISLGIAFIGNFTD 106
PGRP cd06583
Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in ...
 70-218 4.87e-13

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: 63.85  E-value: 4.87e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084915352  70 TMIALHHAGRSYecSPGGTQQMQDIQHFQMNNkFDDIGYHYGISCDGTVLEGRDIRLQASSVK-LFNTGVIGIvllenlt 148
Cdd:cd06583     3 KYVVIHHTANPN--CYTAAAAVRYLQNYHMRG-WSDISYHFLVGGDGRIYQGRGWNYVGWHAGgNYNSYSIGI------- 72

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2084915352 149 taeeggdiiakgrealERLGYSTTNVIPAAQIDALMHLIEALKSVFFI---ERFGGHKEFPGQdregKICPGN 218
Cdd:cd06583    73 ----------------ELIGNFDGGPPTAAQLEALAELLAYLVKRYGIppdYRIVGHRDVSPG----TECPGD 125
PHA00447 PHA00447
lysozyme
 92-217 2.19e-09

lysozyme


Pssm-ID: 177282 [Multi-domain]  Cd Length: 142  Bit Score: 54.40  E-value: 2.19e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084915352  92 QDIQHFQMNNKFDDIGYHYGISCDGTVLEGRDIRLQASSVKLFNTGVIGIVLLenlttaeegGDIIAKGRealerlgyST 171
Cdd:PHA00447   29 REIRQWHKEQGWLDVGYHFIIRRDGTVEEGRPEDVVGSHVKGYNSNSVGVCLV---------GGIDDKGK--------FD 91

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2084915352 172 TNVIPaAQIDALMHLIEALKSVFFIERFGGHkefpgQDREGKICPG 217
Cdd:PHA00447   92 ANFTP-AQMQSLKSLLVTLKAKYPGAEIKAH-----HDVAPKACPS 131
Ami_2 smart00644
Ami_2 domain;
68-152 1.92e-07

Ami_2 domain;


Pssm-ID: 214760 [Multi-domain]  Cd Length: 126  Bit Score: 48.51  E-value: 1.92e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084915352   68 DYTMIALHHAGRSYEcspGGTQQMQDIQHFQMNnkfdDIGYHYGISCDGTVLEGRDIRLQA-----SSVKLFNTGVIGIV 142
Cdd:smart00644   2 PPRGIVIHHTANSNA---SCANEARYMQNNHMN----DIGYHFLVGGDGRVYQGVGWNYVAwhaggAHTPGYNDISIGIE 74

                           90
                   ....*....|
gi 2084915352  143 LLENLTTAEE 152
Cdd:smart00644  75 FIGSFDSDDE 84
Amidase_2 pfam01510
N-acetylmuramoyl-L-alanine amidase; This family includes zinc amidases that have ...
 70-218 1.01e-05

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: 43.50  E-value: 1.01e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2084915352  70 TMIALHHAGRsyecspGGTQQMQDIQHFQMNNKFDDIGYHYGISCDGTVLEGRDIRLQA--SSVKLFNTGVIGIVLLENL 147
Cdd:pfam01510   3 RYIVIHHTAG------PSFAGALLPYAACIARGWSDVSYHYLIDRDGTIYQLVPENGRAwhAGNGGGNDRSIGIELEGNF 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2084915352 148 TTAEeggdiiakgrealerlgysttnvIPAAQIDALMHLIEALKSVFFIERFG---GHkefpgQDREGKICPGN 218
Cdd:pfam01510  77 GGDP-----------------------PTDAQYEALARLLADLCKRYGIPPDRrivGH-----RDVGRKTDPGP 122
 
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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