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MULTISPECIES: 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD [Enterobacter]

Protein Classification

N-acetylmuramoyl-L-alanine amidase( domain architecture ID 10793612)

N-acetylmuramoyl-L-alanine amidase specifically cleaves the amide bond between the lactyl group of N-acetylmuramic acid and the alpha-amino group of the L-alanine in degradation products containing an anhydro N-acetylmuramyl moiety

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PRK11789 PRK11789
1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD;
1-183 8.81e-143

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


:

Pssm-ID: 236984  Cd Length: 185  Bit Score: 394.56  E-value: 8.81e-143
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489953014   1 MLLENGWLVDARHVPSPHHDCRPEDEKPTLLVVHNISLPPGEFGGPWIDALFTGTIDPDAHPFFAEIAHLRVSAHCLIRR 80
Cdd:PRK11789   3 MLDEDGWLVGARRVPSPNFDARPDGEDISLLVIHNISLPPGEFGGPYIDALFTNRLDPDAHPYFAEIAGLRVSAHFLIRR 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489953014  81 DGEVVQYVPFDKRAWHAGVSKYQGRERCNDFSIGIELEGTDTTPYTDAQYEKLVAVTQTLIGRYPAIADNITGHSDIAPE 160
Cdd:PRK11789  83 DGEIVQFVSFDDRAWHAGVSSFQGRERCNDFSIGIELEGTDTLPFTDAQYQALAALTRALRAAYPIIAERITGHSDIAPG 162
                        170       180
                 ....*....|....*....|...
gi 489953014 161 RKTDPGPAFDWSRFHAMLTTSSD 183
Cdd:PRK11789 163 RKTDPGPAFDWQRFRALLALPTR 185
 
Name Accession Description Interval E-value
PRK11789 PRK11789
1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD;
1-183 8.81e-143

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


Pssm-ID: 236984  Cd Length: 185  Bit Score: 394.56  E-value: 8.81e-143
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489953014   1 MLLENGWLVDARHVPSPHHDCRPEDEKPTLLVVHNISLPPGEFGGPWIDALFTGTIDPDAHPFFAEIAHLRVSAHCLIRR 80
Cdd:PRK11789   3 MLDEDGWLVGARRVPSPNFDARPDGEDISLLVIHNISLPPGEFGGPYIDALFTNRLDPDAHPYFAEIAGLRVSAHFLIRR 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489953014  81 DGEVVQYVPFDKRAWHAGVSKYQGRERCNDFSIGIELEGTDTTPYTDAQYEKLVAVTQTLIGRYPAIADNITGHSDIAPE 160
Cdd:PRK11789  83 DGEIVQFVSFDDRAWHAGVSSFQGRERCNDFSIGIELEGTDTLPFTDAQYQALAALTRALRAAYPIIAERITGHSDIAPG 162
                        170       180
                 ....*....|....*....|...
gi 489953014 161 RKTDPGPAFDWSRFHAMLTTSSD 183
Cdd:PRK11789 163 RKTDPGPAFDWQRFRALLALPTR 185
AmpD COG3023
N-acetyl-anhydromuramyl-L-alanine amidase AmpD [Cell wall/membrane/envelope biogenesis];
10-178 2.61e-81

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


Pssm-ID: 442259  Cd Length: 167  Bit Score: 238.23  E-value: 2.61e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489953014  10 DARHVPSPHHDCRPEDEKPTLLVVHNISLPPGEfggpwidalftGTIDpdahpffaEIAH--LRVSAHCLIRRDGEVVQY 87
Cdd:COG3023    9 GARFVPSPNFDERPAGAEIDLIVIHYTAGPPGG-----------GALD--------WLTDpaLRVSAHYLIDRDGEIYQL 69
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489953014  88 VPFDKRAWHAGVSKYQGRERCNDFSIGIELEGTD--TTPYTDAQYEKLVAVTQTLIGRYPAIADNITGHSDIAPERKTDP 165
Cdd:COG3023   70 VPEDDRAWHAGVSSWRGRTNLNDFSIGIELENPGhgWAPFTEAQYEALAALLRDLCARYGIPPDHIVGHSDIAPGRKTDP 149
                        170
                 ....*....|...
gi 489953014 166 GPAFDWSRFHAML 178
Cdd:COG3023  150 GPAFPWARLAALL 162
Amidase_2 pfam01510
N-acetylmuramoyl-L-alanine amidase; This family includes zinc amidases that have ...
27-167 3.09e-35

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: 119.77  E-value: 3.09e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489953014   27 KPTLLVVHNislppgefggpWIDALFTGTIdpdaHPFFAEIAH--LRVSAHCLIRRDGEVVQYVPFDKRAWHAGVskyqg 104
Cdd:pfam01510   1 PIRYIVIHH-----------TAGPSFAGAL----LPYAACIARgwSDVSYHYLIDRDGTIYQLVPENGRAWHAGN----- 60
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489953014  105 rERCNDFSIGIELEGTD-TTPYTDAQYEKLVAVTQTLIGRYP-AIADNITGHSDIApeRKTDPGP 167
Cdd:pfam01510  61 -GGGNDRSIGIELEGNFgGDPPTDAQYEALARLLADLCKRYGiPPDRRIVGHRDVG--RKTDPGP 122
Ami_2 smart00644
Ami_2 domain;
27-163 4.48e-30

Ami_2 domain;


Pssm-ID: 214760 [Multi-domain]  Cd Length: 126  Bit Score: 107.06  E-value: 4.48e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489953014    27 KPTLLVVHNISLPPgEFGGPWIDALFTGTIDPdahpffaeiahlrVSAHCLIRRDGEVVQYVPFDKRAWHAGVSKYQGre 106
Cdd:smart00644   2 PPRGIVIHHTANSN-ASCANEARYMQNNHMND-------------IGYHFLVGGDGRVYQGVGWNYVAWHAGGAHTPG-- 65
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489953014   107 rCNDFSIGIELEGT---DTTPYTDAQYEKLVAVTQTLIGRYPAIADN--ITGHSDIAPERKT 163
Cdd:smart00644  66 -YNDISIGIEFIGSfdsDDEPFAEALYAALDLLAKLLKGAGLPPDGRyrIVGHRDVAPTEDP 126
PGRP cd06583
Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in ...
27-168 3.64e-28

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: 101.98  E-value: 3.64e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489953014  27 KPTLLVVHNISLPPGEFGGPWIDALFTGTIDPDAhpffaeiahlRVSAHCLIRRDGEVVQYVPFDKRAWHAGVSkyqgre 106
Cdd:cd06583    1 PVKYVVIHHTANPNCYTAAAAVRYLQNYHMRGWS----------DISYHFLVGGDGRIYQGRGWNYVGWHAGGN------ 64
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489953014 107 rCNDFSIGIELEGT-DTTPYTDAQYEKLVAVTQTLIGRYP-AIADNITGHSDIAPErKTDPGPA 168
Cdd:cd06583   65 -YNSYSIGIELIGNfDGGPPTAAQLEALAELLAYLVKRYGiPPDYRIVGHRDVSPG-TECPGDA 126
 
Name Accession Description Interval E-value
PRK11789 PRK11789
1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD;
1-183 8.81e-143

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


Pssm-ID: 236984  Cd Length: 185  Bit Score: 394.56  E-value: 8.81e-143
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489953014   1 MLLENGWLVDARHVPSPHHDCRPEDEKPTLLVVHNISLPPGEFGGPWIDALFTGTIDPDAHPFFAEIAHLRVSAHCLIRR 80
Cdd:PRK11789   3 MLDEDGWLVGARRVPSPNFDARPDGEDISLLVIHNISLPPGEFGGPYIDALFTNRLDPDAHPYFAEIAGLRVSAHFLIRR 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489953014  81 DGEVVQYVPFDKRAWHAGVSKYQGRERCNDFSIGIELEGTDTTPYTDAQYEKLVAVTQTLIGRYPAIADNITGHSDIAPE 160
Cdd:PRK11789  83 DGEIVQFVSFDDRAWHAGVSSFQGRERCNDFSIGIELEGTDTLPFTDAQYQALAALTRALRAAYPIIAERITGHSDIAPG 162
                        170       180
                 ....*....|....*....|...
gi 489953014 161 RKTDPGPAFDWSRFHAMLTTSSD 183
Cdd:PRK11789 163 RKTDPGPAFDWQRFRALLALPTR 185
AmpD COG3023
N-acetyl-anhydromuramyl-L-alanine amidase AmpD [Cell wall/membrane/envelope biogenesis];
10-178 2.61e-81

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


Pssm-ID: 442259  Cd Length: 167  Bit Score: 238.23  E-value: 2.61e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489953014  10 DARHVPSPHHDCRPEDEKPTLLVVHNISLPPGEfggpwidalftGTIDpdahpffaEIAH--LRVSAHCLIRRDGEVVQY 87
Cdd:COG3023    9 GARFVPSPNFDERPAGAEIDLIVIHYTAGPPGG-----------GALD--------WLTDpaLRVSAHYLIDRDGEIYQL 69
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489953014  88 VPFDKRAWHAGVSKYQGRERCNDFSIGIELEGTD--TTPYTDAQYEKLVAVTQTLIGRYPAIADNITGHSDIAPERKTDP 165
Cdd:COG3023   70 VPEDDRAWHAGVSSWRGRTNLNDFSIGIELENPGhgWAPFTEAQYEALAALLRDLCARYGIPPDHIVGHSDIAPGRKTDP 149
                        170
                 ....*....|...
gi 489953014 166 GPAFDWSRFHAML 178
Cdd:COG3023  150 GPAFPWARLAALL 162
Amidase_2 pfam01510
N-acetylmuramoyl-L-alanine amidase; This family includes zinc amidases that have ...
27-167 3.09e-35

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: 119.77  E-value: 3.09e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489953014   27 KPTLLVVHNislppgefggpWIDALFTGTIdpdaHPFFAEIAH--LRVSAHCLIRRDGEVVQYVPFDKRAWHAGVskyqg 104
Cdd:pfam01510   1 PIRYIVIHH-----------TAGPSFAGAL----LPYAACIARgwSDVSYHYLIDRDGTIYQLVPENGRAWHAGN----- 60
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489953014  105 rERCNDFSIGIELEGTD-TTPYTDAQYEKLVAVTQTLIGRYP-AIADNITGHSDIApeRKTDPGP 167
Cdd:pfam01510  61 -GGGNDRSIGIELEGNFgGDPPTDAQYEALARLLADLCKRYGiPPDRRIVGHRDVG--RKTDPGP 122
Ami_2 smart00644
Ami_2 domain;
27-163 4.48e-30

Ami_2 domain;


Pssm-ID: 214760 [Multi-domain]  Cd Length: 126  Bit Score: 107.06  E-value: 4.48e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489953014    27 KPTLLVVHNISLPPgEFGGPWIDALFTGTIDPdahpffaeiahlrVSAHCLIRRDGEVVQYVPFDKRAWHAGVSKYQGre 106
Cdd:smart00644   2 PPRGIVIHHTANSN-ASCANEARYMQNNHMND-------------IGYHFLVGGDGRVYQGVGWNYVAWHAGGAHTPG-- 65
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489953014   107 rCNDFSIGIELEGT---DTTPYTDAQYEKLVAVTQTLIGRYPAIADN--ITGHSDIAPERKT 163
Cdd:smart00644  66 -YNDISIGIEFIGSfdsDDEPFAEALYAALDLLAKLLKGAGLPPDGRyrIVGHRDVAPTEDP 126
PGRP cd06583
Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in ...
27-168 3.64e-28

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: 101.98  E-value: 3.64e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489953014  27 KPTLLVVHNISLPPGEFGGPWIDALFTGTIDPDAhpffaeiahlRVSAHCLIRRDGEVVQYVPFDKRAWHAGVSkyqgre 106
Cdd:cd06583    1 PVKYVVIHHTANPNCYTAAAAVRYLQNYHMRGWS----------DISYHFLVGGDGRIYQGRGWNYVGWHAGGN------ 64
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489953014 107 rCNDFSIGIELEGT-DTTPYTDAQYEKLVAVTQTLIGRYP-AIADNITGHSDIAPErKTDPGPA 168
Cdd:cd06583   65 -YNSYSIGIELIGNfDGGPPTAAQLEALAELLAYLVKRYGiPPDYRIVGHRDVSPG-TECPGDA 126
CwlA COG5632
N-acetylmuramoyl-L-alanine amidase CwlA [Cell wall/membrane/envelope biogenesis];
27-184 3.23e-15

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


Pssm-ID: 444359  Cd Length: 177  Bit Score: 69.61  E-value: 3.23e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489953014  27 KPTLLVVHNislppgefggpwidalfTGTIDPDAHpffAEIAHL-----RVSAHCLIRrDGEVVQYVPFDKRAWHAGVSK 101
Cdd:COG5632   23 KPKGIVIHN-----------------TANPGATAE---NHANYFnnnnrSASWHYFVD-DKEIIQHIPLNENAWHAGDGT 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489953014 102 YQGrercNDFSIGIELEGTDTTPYTDAqYEKLVAVTQTLIGRYPAIADNITGHSDIApeRKTDPGPAFD-----WSRFHA 176
Cdd:COG5632   82 GPG----NRRSIGIEICENKDGDFAKA-YENAAELIAYLMKKYGIPIDNVVRHYDWS--GKNCPHGLLAnggyrWDQFKA 154

                 ....*...
gi 489953014 177 MLTTSSDK 184
Cdd:COG5632  155 DVKSALNG 162
PHA00447 PHA00447
lysozyme
70-173 1.04e-04

lysozyme


Pssm-ID: 177282 [Multi-domain]  Cd Length: 142  Bit Score: 40.53  E-value: 1.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489953014  70 LRVSAHCLIRRDGEVVQYVPFDKRAWHagVSKYqgrercNDFSIGIEL------EGTDTTPYTDAQYEKLVAVTQTLIGR 143
Cdd:PHA00447  41 LDVGYHFIIRRDGTVEEGRPEDVVGSH--VKGY------NSNSVGVCLvggiddKGKFDANFTPAQMQSLKSLLVTLKAK 112
                         90       100       110
                 ....*....|....*....|....*....|
gi 489953014 144 YPAIAdnITGHSDIAPErktdPGPAFDWSR 173
Cdd:PHA00447 113 YPGAE--IKAHHDVAPK----ACPSFDLQR 136
 
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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