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Conserved domains on  [gi|1444982461|ref|WP_115598373|]
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N-acetylmuramoyl-L-alanine amidase [Corynebacterium amycolatum]

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 ...
 230-366 9.88e-34

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: 124.33  E-value: 9.88e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1444982461  230 PNVISRAAWGAdESIRSGSSSYSTFKGTCIHHTAGSNNYSESQGPAIVRGIYAYHAKTLGWGDVGYNALVDKYGNIYEGR 309
Cdd:smart00701   1 PPIVPRSEWGA-KPRGHTPRLTRPVRYVIIHHTATPNCYTDAQCAQILRNIQAYHMEELGWCDIGYNFLVGGDGKVYEGR 79

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1444982461  310 yGGldkNIEGAHAGGFNNGTFGISVMGNHDQLEIPDAAVTALGEMVGWRMKVGGVDP 366
Cdd:smart00701  80 -GW---NVVGAHTGGYNDISLGIAFIGNFTDKLPTDAALDAAQDLLACAVQRGHLSP 132
 
Name Accession Description Interval E-value
PGRP smart00701
Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme; The ...
 230-366 9.88e-34

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: 124.33  E-value: 9.88e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1444982461  230 PNVISRAAWGAdESIRSGSSSYSTFKGTCIHHTAGSNNYSESQGPAIVRGIYAYHAKTLGWGDVGYNALVDKYGNIYEGR 309
Cdd:smart00701   1 PPIVPRSEWGA-KPRGHTPRLTRPVRYVIIHHTATPNCYTDAQCAQILRNIQAYHMEELGWCDIGYNFLVGGDGKVYEGR 79

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1444982461  310 yGGldkNIEGAHAGGFNNGTFGISVMGNHDQLEIPDAAVTALGEMVGWRMKVGGVDP 366
Cdd:smart00701  80 -GW---NVVGAHTGGYNDISLGIAFIGNFTDKLPTDAALDAAQDLLACAVQRGHLSP 132
PGRP cd06583
Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in ...
 259-406 3.25e-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: 108.53  E-value: 3.25e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1444982461 259 IHHTAGSNNYsesQGPAIVRGIYAYHAktLGWGDVGYNALVDKYGNIYEGRygglDKNIEGAHAGG-FNNGTFGISVMGN 337
Cdd:cd06583     7 IHHTANPNCY---TAAAAVRYLQNYHM--RGWSDISYHFLVGGDGRIYQGR----GWNYVGWHAGGnYNSYSIGIELIGN 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1444982461 338 HDQLEIPDAAVTALGEMVGWRMKVGGVDPMSTaaltsagyskaryssgqtvnlpaIFGHRD-TGYTSCPG 406
Cdd:cd06583    78 FDGGPPTAAQLEALAELLAYLVKRYGIPPDYR-----------------------IVGHRDvSPGTECPG 124
Amidase_2 pfam01510
N-acetylmuramoyl-L-alanine amidase; This family includes zinc amidases that have ...
 259-406 1.98e-15

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: 72.39  E-value: 1.98e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1444982461 259 IHHTAGSNNYSesqgpaivRGIYAYHAKTLGWGDVGYNALVDKYGNIYEgrYGGLDKNIEGAHAGGFNNGTFGISVMGNH 338
Cdd:pfam01510   7 IHHTAGPSFAG--------ALLPYAACIARGWSDVSYHYLIDRDGTIYQ--LVPENGRAWHAGNGGGNDRSIGIELEGNF 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1444982461 339 DQLEIPDAAVTALGEMVGWRMKVGGVDPmstaaltsagyskaryssgqtvnLPAIFGHRDTGYTSCPG 406
Cdd:pfam01510  77 GGDPPTDAQYEALARLLADLCKRYGIPP-----------------------DRRIVGHRDVGRKTDPG 121
PHA00447 PHA00447
lysozyme
 277-406 3.23e-08

lysozyme


Pssm-ID: 177282 [Multi-domain]  Cd Length: 142  Bit Score: 52.47  E-value: 3.23e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1444982461 277 VRGIYAYHaKTLGWGDVGYNALVDKYGNIYEGRygglDKNIEGAHAGGFNNGTFGISVMGNHDQLEIPDAAVTaLGEMVG 356
Cdd:PHA00447   28 VREIRQWH-KEQGWLDVGYHFIIRRDGTVEEGR----PEDVVGSHVKGYNSNSVGVCLVGGIDDKGKFDANFT-PAQMQS 101

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1444982461 357 WRMKVGGVdpmstaaltSAGYSKARyssgqtvnlpaIFGHRDTGYTSCPG 406
Cdd:PHA00447  102 LKSLLVTL---------KAKYPGAE-----------IKAHHDVAPKACPS 131
Psp3 COG5479
LGFP repeat-containing protein, may be involved in cell wall binding [Cell wall/membrane ...
 219-323 9.54e-06

LGFP repeat-containing protein, may be involved in cell wall binding [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 444230 [Multi-domain]  Cd Length: 246  Bit Score: 47.04  E-value: 9.54e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1444982461 219 PVAYESSISGAPNVI--SRAAWGA-------------DESIRSGSSSYSTFKGTCIHHTAGSNNYSESqgpAIVRGIYAY 283
Cdd:COG5479    71 GSIYWSPATGAHAVVgaIRAKWGAlgwesgplgypttDEVPTPGGGRYQTFQGGSVYWTAGTGAHAVH---GAIRGKYAY 147

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1444982461 284 HaktlGW--GDVGYNALVDKYGNIYEGRY-----GGLD-KNIEGAHAG 323
Cdd:COG5479   148 H----GWedGPLGYPTSDEKATPDGGGRYqifegGGIYwSPATGAHAV 191
 
Name Accession Description Interval E-value
PGRP smart00701
Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme; The ...
 230-366 9.88e-34

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: 124.33  E-value: 9.88e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1444982461  230 PNVISRAAWGAdESIRSGSSSYSTFKGTCIHHTAGSNNYSESQGPAIVRGIYAYHAKTLGWGDVGYNALVDKYGNIYEGR 309
Cdd:smart00701   1 PPIVPRSEWGA-KPRGHTPRLTRPVRYVIIHHTATPNCYTDAQCAQILRNIQAYHMEELGWCDIGYNFLVGGDGKVYEGR 79

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1444982461  310 yGGldkNIEGAHAGGFNNGTFGISVMGNHDQLEIPDAAVTALGEMVGWRMKVGGVDP 366
Cdd:smart00701  80 -GW---NVVGAHTGGYNDISLGIAFIGNFTDKLPTDAALDAAQDLLACAVQRGHLSP 132
PGRP cd06583
Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in ...
 259-406 3.25e-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: 108.53  E-value: 3.25e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1444982461 259 IHHTAGSNNYsesQGPAIVRGIYAYHAktLGWGDVGYNALVDKYGNIYEGRygglDKNIEGAHAGG-FNNGTFGISVMGN 337
Cdd:cd06583     7 IHHTANPNCY---TAAAAVRYLQNYHM--RGWSDISYHFLVGGDGRIYQGR----GWNYVGWHAGGnYNSYSIGIELIGN 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1444982461 338 HDQLEIPDAAVTALGEMVGWRMKVGGVDPMSTaaltsagyskaryssgqtvnlpaIFGHRD-TGYTSCPG 406
Cdd:cd06583    78 FDGGPPTAAQLEALAELLAYLVKRYGIPPDYR-----------------------IVGHRDvSPGTECPG 124
Amidase_2 pfam01510
N-acetylmuramoyl-L-alanine amidase; This family includes zinc amidases that have ...
 259-406 1.98e-15

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: 72.39  E-value: 1.98e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1444982461 259 IHHTAGSNNYSesqgpaivRGIYAYHAKTLGWGDVGYNALVDKYGNIYEgrYGGLDKNIEGAHAGGFNNGTFGISVMGNH 338
Cdd:pfam01510   7 IHHTAGPSFAG--------ALLPYAACIARGWSDVSYHYLIDRDGTIYQ--LVPENGRAWHAGNGGGNDRSIGIELEGNF 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1444982461 339 DQLEIPDAAVTALGEMVGWRMKVGGVDPmstaaltsagyskaryssgqtvnLPAIFGHRDTGYTSCPG 406
Cdd:pfam01510  77 GGDPPTDAQYEALARLLADLCKRYGIPP-----------------------DRRIVGHRDVGRKTDPG 121
Ami_2 smart00644
Ami_2 domain;
259-405 1.45e-13

Ami_2 domain;


Pssm-ID: 214760 [Multi-domain]  Cd Length: 126  Bit Score: 67.38  E-value: 1.45e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1444982461  259 IHHTAGSNnyseSQGPAIVRGIYAYHAKtlgwgDVGYNALVDKYGNIYEGRYGG-LDKNIEGAHAGGFNNGTFGISVMGN 337
Cdd:smart00644   8 IHHTANSN----ASCANEARYMQNNHMN-----DIGYHFLVGGDGRVYQGVGWNyVAWHAGGAHTPGYNDISIGIEFIGS 78

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1444982461  338 HDQLEIPDAavtalgemvgwrmkvggvDPMSTAALTSAGYSKARYSSGQTvnLPAIFGHRDTGYTSCP 405
Cdd:smart00644  79 FDSDDEPFA------------------EALYAALDLLAKLLKGAGLPPDG--RYRIVGHRDVAPTEDP 126
PHA00447 PHA00447
lysozyme
 277-406 3.23e-08

lysozyme


Pssm-ID: 177282 [Multi-domain]  Cd Length: 142  Bit Score: 52.47  E-value: 3.23e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1444982461 277 VRGIYAYHaKTLGWGDVGYNALVDKYGNIYEGRygglDKNIEGAHAGGFNNGTFGISVMGNHDQLEIPDAAVTaLGEMVG 356
Cdd:PHA00447   28 VREIRQWH-KEQGWLDVGYHFIIRRDGTVEEGR----PEDVVGSHVKGYNSNSVGVCLVGGIDDKGKFDANFT-PAQMQS 101

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1444982461 357 WRMKVGGVdpmstaaltSAGYSKARyssgqtvnlpaIFGHRDTGYTSCPG 406
Cdd:PHA00447  102 LKSLLVTL---------KAKYPGAE-----------IKAHHDVAPKACPS 131
Psp3 COG5479
LGFP repeat-containing protein, may be involved in cell wall binding [Cell wall/membrane ...
 219-323 9.54e-06

LGFP repeat-containing protein, may be involved in cell wall binding [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 444230 [Multi-domain]  Cd Length: 246  Bit Score: 47.04  E-value: 9.54e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1444982461 219 PVAYESSISGAPNVI--SRAAWGA-------------DESIRSGSSSYSTFKGTCIHHTAGSNNYSESqgpAIVRGIYAY 283
Cdd:COG5479    71 GSIYWSPATGAHAVVgaIRAKWGAlgwesgplgypttDEVPTPGGGRYQTFQGGSVYWTAGTGAHAVH---GAIRGKYAY 147

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1444982461 284 HaktlGW--GDVGYNALVDKYGNIYEGRY-----GGLD-KNIEGAHAG 323
Cdd:COG5479   148 H----GWedGPLGYPTSDEKATPDGGGRYqifegGGIYwSPATGAHAV 191
 
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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