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Conserved domains on  [gi|2027880674|ref|YP_010050561|]
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amidase [Arthrobacter phage Wawa]

Protein Classification

N-acetylmuramoyl-L-alanine amidase( domain architecture ID 10478845)

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Amidase_2 pfam01510
N-acetylmuramoyl-L-alanine amidase; This family includes zinc amidases that have ...
 30-139 1.07e-17

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: 77.01  E-value: 1.07e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2027880674  30 RVESITIHWWGNYGQEFWQVENFLCTNTKP--TSAHFVV-QEGLVSCIVNPDDAAWHAGNPYGNTTSIGIEC-----RPE 101
Cdd:pfam01510   1 PIRYIVIHHTAGPSFAGALLPYAACIARGWsdVSYHYLIdRDGTIYQLVPENGRAWHAGNGGGNDRSIGIELegnfgGDP 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2027880674 102 ATDGDYQTIAELVAFLRKIYGDVPLVH---HYEWQSTACPG 139
Cdd:pfam01510  81 PTDAQYEALARLLADLCKRYGIPPDRRivgHRDVGRKTDPG 121
 
Name Accession Description Interval E-value
Amidase_2 pfam01510
N-acetylmuramoyl-L-alanine amidase; This family includes zinc amidases that have ...
 30-139 1.07e-17

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: 77.01  E-value: 1.07e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2027880674  30 RVESITIHWWGNYGQEFWQVENFLCTNTKP--TSAHFVV-QEGLVSCIVNPDDAAWHAGNPYGNTTSIGIEC-----RPE 101
Cdd:pfam01510   1 PIRYIVIHHTAGPSFAGALLPYAACIARGWsdVSYHYLIdRDGTIYQLVPENGRAWHAGNGGGNDRSIGIELegnfgGDP 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2027880674 102 ATDGDYQTIAELVAFLRKIYGDVPLVH---HYEWQSTACPG 139
Cdd:pfam01510  81 PTDAQYEALARLLADLCKRYGIPPDRRivgHRDVGRKTDPG 121
CwlA COG5632
N-acetylmuramoyl-L-alanine amidase CwlA [Cell wall/membrane/envelope biogenesis];
9-141 1.37e-16

N-acetylmuramoyl-L-alanine amidase CwlA [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 444359  Cd Length: 177  Bit Score: 75.78  E-value: 1.37e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2027880674   9 HTSNNFTPGSqanavwgqgPRRVESITIHWWGNYGQEFWQVENFLCTNTKPTSAHFVVQEGLVSCIVNPDDAAWHAGN-- 86
Cdd:COG5632    11 PKNNSYRPGY---------KMKPKGIVIHNTANPGATAENHANYFNNNNRSASWHYFVDDKEIIQHIPLNENAWHAGDgt 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2027880674  87 PYGNTTSIGIE-CRPEatDGDY-QTI---AELVAFLRKIYG----DVplVHHYEWQSTACPGTY 141
Cdd:COG5632    82 GPGNRRSIGIEiCENK--DGDFaKAYenaAELIAYLMKKYGipidNV--VRHYDWSGKNCPHGL 141
PGRP cd06583
Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in ...
 30-141 1.86e-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: 65.77  E-value: 1.86e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2027880674  30 RVESITIHWWGNYG-----QEFWQVENFLCTNTKPTSAHFVV-QEGLVSCIVNPDDAAWHAGNPYgNTTSIGIEC----- 98
Cdd:cd06583     1 PVKYVVIHHTANPNcytaaAAVRYLQNYHMRGWSDISYHFLVgGDGRIYQGRGWNYVGWHAGGNY-NSYSIGIELignfd 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2027880674  99 RPEATDGDYQTIAELVAFLRKIYGDVPLVH---HYEW-QSTACPGTY 141
Cdd:cd06583    80 GGPPTAAQLEALAELLAYLVKRYGIPPDYRivgHRDVsPGTECPGDA 126
Ami_2 smart00644
Ami_2 domain;
29-138 8.79e-09

Ami_2 domain;


Pssm-ID: 214760 [Multi-domain]  Cd Length: 126  Bit Score: 52.75  E-value: 8.79e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2027880674   29 RRVESITIHWWGNYGQ--EFWqVENFLCTNTKPTSAHFVV-QEGLVSCIVNPDDAAWHAGN---PYGNTTSIGIE-CRPE 101
Cdd:smart00644   1 PPPRGIVIHHTANSNAscANE-ARYMQNNHMNDIGYHFLVgGDGRVYQGVGWNYVAWHAGGahtPGYNDISIGIEfIGSF 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2027880674  102 ATDG-----DYQTIAELVAFLRKIYGDVP-----LVHHYEWQSTACP 138
Cdd:smart00644  80 DSDDepfaeALYAALDLLAKLLKGAGLPPdgryrIVGHRDVAPTEDP 126
PRK11789 PRK11789
1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD;
61-121 5.65e-06

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


Pssm-ID: 236984  Cd Length: 185  Bit Score: 45.95  E-value: 5.65e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2027880674  61 SAHFVVQ-EGLVSCIVNPDDAAWHAG----------NPYgnttSIGIECrpEATDGD------YQTIAELVAFLRKIY 121
Cdd:PRK11789   75 SAHFLIRrDGEIVQFVSFDDRAWHAGvssfqgrercNDF----SIGIEL--EGTDTLpftdaqYQALAALTRALRAAY 146
 
Name Accession Description Interval E-value
Amidase_2 pfam01510
N-acetylmuramoyl-L-alanine amidase; This family includes zinc amidases that have ...
 30-139 1.07e-17

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: 77.01  E-value: 1.07e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2027880674  30 RVESITIHWWGNYGQEFWQVENFLCTNTKP--TSAHFVV-QEGLVSCIVNPDDAAWHAGNPYGNTTSIGIEC-----RPE 101
Cdd:pfam01510   1 PIRYIVIHHTAGPSFAGALLPYAACIARGWsdVSYHYLIdRDGTIYQLVPENGRAWHAGNGGGNDRSIGIELegnfgGDP 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2027880674 102 ATDGDYQTIAELVAFLRKIYGDVPLVH---HYEWQSTACPG 139
Cdd:pfam01510  81 PTDAQYEALARLLADLCKRYGIPPDRRivgHRDVGRKTDPG 121
CwlA COG5632
N-acetylmuramoyl-L-alanine amidase CwlA [Cell wall/membrane/envelope biogenesis];
9-141 1.37e-16

N-acetylmuramoyl-L-alanine amidase CwlA [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 444359  Cd Length: 177  Bit Score: 75.78  E-value: 1.37e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2027880674   9 HTSNNFTPGSqanavwgqgPRRVESITIHWWGNYGQEFWQVENFLCTNTKPTSAHFVVQEGLVSCIVNPDDAAWHAGN-- 86
Cdd:COG5632    11 PKNNSYRPGY---------KMKPKGIVIHNTANPGATAENHANYFNNNNRSASWHYFVDDKEIIQHIPLNENAWHAGDgt 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2027880674  87 PYGNTTSIGIE-CRPEatDGDY-QTI---AELVAFLRKIYG----DVplVHHYEWQSTACPGTY 141
Cdd:COG5632    82 GPGNRRSIGIEiCENK--DGDFaKAYenaAELIAYLMKKYGipidNV--VRHYDWSGKNCPHGL 141
PGRP cd06583
Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in ...
 30-141 1.86e-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: 65.77  E-value: 1.86e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2027880674  30 RVESITIHWWGNYG-----QEFWQVENFLCTNTKPTSAHFVV-QEGLVSCIVNPDDAAWHAGNPYgNTTSIGIEC----- 98
Cdd:cd06583     1 PVKYVVIHHTANPNcytaaAAVRYLQNYHMRGWSDISYHFLVgGDGRIYQGRGWNYVGWHAGGNY-NSYSIGIELignfd 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2027880674  99 RPEATDGDYQTIAELVAFLRKIYGDVPLVH---HYEW-QSTACPGTY 141
Cdd:cd06583    80 GGPPTAAQLEALAELLAYLVKRYGIPPDYRivgHRDVsPGTECPGDA 126
Ami_2 smart00644
Ami_2 domain;
29-138 8.79e-09

Ami_2 domain;


Pssm-ID: 214760 [Multi-domain]  Cd Length: 126  Bit Score: 52.75  E-value: 8.79e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2027880674   29 RRVESITIHWWGNYGQ--EFWqVENFLCTNTKPTSAHFVV-QEGLVSCIVNPDDAAWHAGN---PYGNTTSIGIE-CRPE 101
Cdd:smart00644   1 PPPRGIVIHHTANSNAscANE-ARYMQNNHMNDIGYHFLVgGDGRVYQGVGWNYVAWHAGGahtPGYNDISIGIEfIGSF 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2027880674  102 ATDG-----DYQTIAELVAFLRKIYGDVP-----LVHHYEWQSTACP 138
Cdd:smart00644  80 DSDDepfaeALYAALDLLAKLLKGAGLPPdgryrIVGHRDVAPTEDP 126
AmpD COG3023
N-acetyl-anhydromuramyl-L-alanine amidase AmpD [Cell wall/membrane/envelope biogenesis];
53-151 4.55e-08

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


Pssm-ID: 442259  Cd Length: 167  Bit Score: 51.79  E-value: 4.55e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2027880674  53 LCTNTKPTSAHFVVQE-GLVSCIVNPDDAAWHAGNPYG------NTTSIGIECrpEATDGD--------YQTIAELVAFL 117
Cdd:COG3023    47 LTDPALRVSAHYLIDRdGEIYQLVPEDDRAWHAGVSSWrgrtnlNDFSIGIEL--ENPGHGwapfteaqYEALAALLRDL 124

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2027880674 118 RKIYGdVPLVH---HYEWQSTA--CPGTY-DLARI-DRLSR 151
Cdd:COG3023   125 CARYG-IPPDHivgHSDIAPGRktDPGPAfPWARLaALLAR 164
PRK11789 PRK11789
1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD;
61-121 5.65e-06

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


Pssm-ID: 236984  Cd Length: 185  Bit Score: 45.95  E-value: 5.65e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2027880674  61 SAHFVVQ-EGLVSCIVNPDDAAWHAG----------NPYgnttSIGIECrpEATDGD------YQTIAELVAFLRKIY 121
Cdd:PRK11789   75 SAHFLIRrDGEIVQFVSFDDRAWHAGvssfqgrercNDF----SIGIEL--EGTDTLpftdaqYQALAALTRALRAAY 146
 
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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