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Conserved domains on  [gi|589892919|ref|YP_009004248|]
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tail length tape measure protein [Clavibacter phage CN1A]

Protein Classification

M15 family metallopeptidase( domain architecture ID 13000415)

M15 family metallopeptidase may function as a carboxypeptidase or dipeptidase involved in bacterial cell wall biosynthesis and metabolism

CATH:  3.40.630.10
EC:  3.4.-.-
Gene Ontology:  GO:0006508|GO:0004181|GO:0008270
MEROPS:  M15
PubMed:  7674922|10493853

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Peptidase_M15 cd14814
Metalloproteases including zinc D-Ala-D-Ala carboxypeptidase, L-Ala-D-Glu peptidase, L, ...
 41-130 1.09e-25

Metalloproteases including zinc D-Ala-D-Ala carboxypeptidase, L-Ala-D-Glu peptidase, L,D-carboxypeptidase, bacteriophage endolysins, and related proteins; This family summarizes zinc-binding metallopeptidases which are mostly carboxypeptidases and dipeptidases, and includes zinc-dependent D-Ala-D-Ala carboxypeptidases, VanX, L-Ala-D-Glu peptidase, L,D-carboxypeptidase and bacteriophage endolysins, amongst other family members. These peptidases belong to MEROPS family M15 which are involved in bacterial cell wall biosynthesis and metabolism.


:

Pssm-ID: 350615 [Multi-domain]  Cd Length: 111  Bit Score: 97.90  E-value: 1.09e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 589892919  41 RATGKPLVILEGYRDLTRQKYLRNLYLSGRGNI--AAVPGLSNHGWGLACDFAAPLNSSGSEEHRWMRQNAPLFGFD--- 115
Cdd:cd14814   15 GAEGRTLTINSGYRTYAQQLRLFAAKGKGSGGRrwAAPPGTSNHQWGLAIDLGDGGGWRETQGYRWLKANAPRYGFDnpg 94

                         90
                 ....*....|....*.
gi 589892919 116 -WARGKADNEPWHWEY 130
Cdd:cd14814   95 gARRGGAFQEPWHWEY 110
 
Name Accession Description Interval E-value
Peptidase_M15 cd14814
Metalloproteases including zinc D-Ala-D-Ala carboxypeptidase, L-Ala-D-Glu peptidase, L, ...
 41-130 1.09e-25

Metalloproteases including zinc D-Ala-D-Ala carboxypeptidase, L-Ala-D-Glu peptidase, L,D-carboxypeptidase, bacteriophage endolysins, and related proteins; This family summarizes zinc-binding metallopeptidases which are mostly carboxypeptidases and dipeptidases, and includes zinc-dependent D-Ala-D-Ala carboxypeptidases, VanX, L-Ala-D-Glu peptidase, L,D-carboxypeptidase and bacteriophage endolysins, amongst other family members. These peptidases belong to MEROPS family M15 which are involved in bacterial cell wall biosynthesis and metabolism.


Pssm-ID: 350615 [Multi-domain]  Cd Length: 111  Bit Score: 97.90  E-value: 1.09e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 589892919  41 RATGKPLVILEGYRDLTRQKYLRNLYLSGRGNI--AAVPGLSNHGWGLACDFAAPLNSSGSEEHRWMRQNAPLFGFD--- 115
Cdd:cd14814   15 GAEGRTLTINSGYRTYAQQLRLFAAKGKGSGGRrwAAPPGTSNHQWGLAIDLGDGGGWRETQGYRWLKANAPRYGFDnpg 94

                         90
                 ....*....|....*.
gi 589892919 116 -WARGKADNEPWHWEY 130
Cdd:cd14814   95 gARRGGAFQEPWHWEY 110
LdcB COG1876
LD-carboxypeptidase LdcB, LAS superfamily [Cell wall/membrane/envelope biogenesis];
41-136 5.69e-23

LD-carboxypeptidase LdcB, LAS superfamily [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 441480  Cd Length: 168  Bit Score: 92.64  E-value: 5.69e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 589892919  41 RATGKPLVILEGYRDLTRQKYLRNLYLSGRG-----NIAAVPGLSNHGWGLACDFAAP-----LNSS--GSEEHRWMRQN 108
Cdd:COG1876   39 KKDGIDLVIVSGYRSYERQEALYNRKVARYGieaalRYSAPPGTSEHHTGLAIDIGDPdpgtdLEEEfeETPAGKWLAAN 118

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 589892919 109 APLFGFD--WARGKADN-----EPWHWEYgnVPVS 136
Cdd:COG1876  119 AAKYGFIlrYPKGKEDItgyayEPWHWRY--VGVE 151
VanY pfam02557
D-alanyl-D-alanine carboxypeptidase;
41-130 1.38e-16

D-alanyl-D-alanine carboxypeptidase;


Pssm-ID: 426830 [Multi-domain]  Cd Length: 131  Bit Score: 74.58  E-value: 1.38e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 589892919   41 RATGKPLVILEGYRDLTRQKYLRNLYLSGRGNIA-----AVPGLSNHGWGLACDFAAP-------LNSSGSEEHRWMRQN 108
Cdd:pfam02557  20 KKEGINLRAISGFRSYEYQEALFKKYVKGEGKKAilrwsAPPGTSEHHTGLAIDIGDPdnpweleESFEDTAAFKWLQAN 99

                          90       100
                  ....*....|....*....|....*....
gi 589892919  109 APLFGFDW--ARGKADN-----EPWHWEY 130
Cdd:pfam02557 100 AHKYGFVLryPKGKEQItgvsyEPWHWRY 128
 
Name Accession Description Interval E-value
Peptidase_M15 cd14814
Metalloproteases including zinc D-Ala-D-Ala carboxypeptidase, L-Ala-D-Glu peptidase, L, ...
 41-130 1.09e-25

Metalloproteases including zinc D-Ala-D-Ala carboxypeptidase, L-Ala-D-Glu peptidase, L,D-carboxypeptidase, bacteriophage endolysins, and related proteins; This family summarizes zinc-binding metallopeptidases which are mostly carboxypeptidases and dipeptidases, and includes zinc-dependent D-Ala-D-Ala carboxypeptidases, VanX, L-Ala-D-Glu peptidase, L,D-carboxypeptidase and bacteriophage endolysins, amongst other family members. These peptidases belong to MEROPS family M15 which are involved in bacterial cell wall biosynthesis and metabolism.


Pssm-ID: 350615 [Multi-domain]  Cd Length: 111  Bit Score: 97.90  E-value: 1.09e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 589892919  41 RATGKPLVILEGYRDLTRQKYLRNLYLSGRGNI--AAVPGLSNHGWGLACDFAAPLNSSGSEEHRWMRQNAPLFGFD--- 115
Cdd:cd14814   15 GAEGRTLTINSGYRTYAQQLRLFAAKGKGSGGRrwAAPPGTSNHQWGLAIDLGDGGGWRETQGYRWLKANAPRYGFDnpg 94

                         90
                 ....*....|....*.
gi 589892919 116 -WARGKADNEPWHWEY 130
Cdd:cd14814   95 gARRGGAFQEPWHWEY 110
LdcB COG1876
LD-carboxypeptidase LdcB, LAS superfamily [Cell wall/membrane/envelope biogenesis];
41-136 5.69e-23

LD-carboxypeptidase LdcB, LAS superfamily [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 441480  Cd Length: 168  Bit Score: 92.64  E-value: 5.69e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 589892919  41 RATGKPLVILEGYRDLTRQKYLRNLYLSGRG-----NIAAVPGLSNHGWGLACDFAAP-----LNSS--GSEEHRWMRQN 108
Cdd:COG1876   39 KKDGIDLVIVSGYRSYERQEALYNRKVARYGieaalRYSAPPGTSEHHTGLAIDIGDPdpgtdLEEEfeETPAGKWLAAN 118

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 589892919 109 APLFGFD--WARGKADN-----EPWHWEYgnVPVS 136
Cdd:COG1876  119 AAKYGFIlrYPKGKEDItgyayEPWHWRY--VGVE 151
VanY pfam02557
D-alanyl-D-alanine carboxypeptidase;
41-130 1.38e-16

D-alanyl-D-alanine carboxypeptidase;


Pssm-ID: 426830 [Multi-domain]  Cd Length: 131  Bit Score: 74.58  E-value: 1.38e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 589892919   41 RATGKPLVILEGYRDLTRQKYLRNLYLSGRGNIA-----AVPGLSNHGWGLACDFAAP-------LNSSGSEEHRWMRQN 108
Cdd:pfam02557  20 KKEGINLRAISGFRSYEYQEALFKKYVKGEGKKAilrwsAPPGTSEHHTGLAIDIGDPdnpweleESFEDTAAFKWLQAN 99

                          90       100
                  ....*....|....*....|....*....
gi 589892919  109 APLFGFDW--ARGKADN-----EPWHWEY 130
Cdd:pfam02557 100 AHKYGFVLryPKGKEQItgvsyEPWHWRY 128
LD-carboxypeptidase cd14852
L,D-carboxypeptidase DacB and LdcB, and related proteins; This L,D-carboxypeptidase family ...
 41-130 2.86e-09

L,D-carboxypeptidase DacB and LdcB, and related proteins; This L,D-carboxypeptidase family includes LdcB LD-Carboxypeptidase from Streptococcus pneumoniae, Bacillus anthracis, and Bacillus subtilis, and L,D-carboxypeptidase DacB from Streptococcus pneumonia and Lactococcus lactis. These enzymes are active against cell-wall-derived tetrapeptides and synthetic tetrapeptides lacking the sugar moiety but are inactive against tetrapeptides terminating in L-alanine. L,D-carboxypeptidase DacB plays a key role in the remodeling of S. pneumoniae peptidoglycan during cell division. It adopts a zinc-dependent carboxypeptidase fold and acts as an L,D-carboxypeptidase towards the tetrapeptide L-Ala-D-iGln-L-Lys-D-Ala of the peptidoglycan stem. This family also includes vanY D-Ala-D-Ala carboxypeptidase which is vancomycin-inducible and penicillin-resistant. VanY hydrolyzes depsipeptide- and D-alanyl-D-alanine-containing peptidoglycan precursors; it is insensitive to beta-lactams. All these enzymes belong to the MEROPS family M15 subfamily B.


Pssm-ID: 350624  Cd Length: 162  Bit Score: 54.94  E-value: 2.86e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 589892919  41 RATGKPLVILEGYRDLTRQKYLRNLYLSGRG-----NIAAVPGLSNHGWGLACDFAAP------LNSSGSEEHRWMRQNA 109
Cdd:cd14852   46 KKDGIDLTIVSGYRSYEYQQELYNNYVARYGkeeadRYSARPGYSEHQTGLAVDIGSTdgpcleESFEDTPAGKWLAENA 125

                         90       100
                 ....*....|....*....|....*...
gi 589892919 110 PLFGFD--WARGKAD-----NEPWHWEY 130
Cdd:cd14852  126 HKYGFIlrYPKGKENitgysYEPWHFRY 153
L-Ala-D-Glu_peptidase_like cd14845
L-Ala-D-Glu peptidase, also known as L-alanyl-D-glutamate endopeptidase; This L-Ala-D-Glu ...
 40-91 3.56e-06

L-Ala-D-Glu peptidase, also known as L-alanyl-D-glutamate endopeptidase; This L-Ala-D-Glu peptidase family includes L-alanyl-D-glutamate peptidase (bacteriophage T5) (also known as L-alanoyl-D-glutamate endopeptidase), and Ply118 and Ply500 L-Ala-D-Glu peptidase. Bacteriophage endolysin degrades the peptidoglycan of the bacterial host from within, leading to cell lysis and release of progeny virions. The bacteriophage endolysin Ply118 cleaves between L-Ala and D-Glu residues of Listeria cell wall peptidoglycan. This family belongs to the MEROPS peptidase M15 subfamily C.


Pssm-ID: 350620 [Multi-domain]  Cd Length: 126  Bit Score: 45.43  E-value: 3.56e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 589892919  40 TRATGKPLVILEGYRDLTRQKYLRNLYLSGRGNIA--AVPGLSNHGWGLACDFA 91
Cdd:cd14845   23 AEEEGIDFRITEGYRSPARQAALYAQGRTKPGLIVtnARGGQSYHNYGLAVDIV 76
DD-carboxypeptidase_like cd14847
Uncharacterized proteins of the MEROPS peptidase family M15, subfamily B; This family of ...
 47-130 1.58e-05

Uncharacterized proteins of the MEROPS peptidase family M15, subfamily B; This family of uncharacterized proteins similar to D-Ala-D-Ala carboxypeptidase pdcA (Myxococcus-type) are zinc-binding enzymes that belong to the peptidase M15 subfamily B. The enzyme D-Ala-D-Ala carbozypeptidase catalyzes carboxypeptidation reactions involved in bacterial cell wall metabolism.


Pssm-ID: 350622  Cd Length: 162  Bit Score: 44.11  E-value: 1.58e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 589892919  47 LVILEGYRDLTRQ------KY--LRNLY-----------LSGRGNIAAV------PGLSNHGWGlaCDF----AAPLNSS 97
Cdd:cd14847   23 LQIASSFRSFERQlaiwnrKWsgERPVLddngqpldissLSPEEKIHAIlrwsalPGASRHHWG--TDIdvydANALPAG 100

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 589892919  98 ---------------GSEEHRWMRQNAPLFGF----DWARGKADNEPWHWEY 130
Cdd:cd14847  101 yqlqltpseyeeggpFAKLYQWLDENAAKFGFfrpyTQDRGGVAPEPWHLSY 152
DD-dipeptidase_VanXYc cd14849
D-Ala-D-Ala dipeptidase/D-Ala-D-Ala carboxypeptidase (VanXYc) and related proteins; VanXYc ...
 48-130 9.58e-04

D-Ala-D-Ala dipeptidase/D-Ala-D-Ala carboxypeptidase (VanXYc) and related proteins; VanXYc peptidase (also known as vanXY(C) peptidase, D-alanyl-D-alanine carboxypeptidase D,D-dipeptidase/D,D-carboxypeptidase, vancomycin resistance D,D-dipeptidase) is a Zn2+-dependent enzyme that mediates resistance to the antibiotic vancomycin in Enterococci. Some of the vancomycin resistance operons encode VanXY D,D-carboxypeptidase which hydrolyzes both, dipeptide (D-Ala-D-Ala) or pentapeptide (UDP-MurNac-L-Ala-D-Glu-L-Lys-D-Ala-D-Ala). It is a bifunctional enzyme that catalyzes D,D-peptidase and D,D-carboxypeptidase activities. VanXY has higher sequence similarity to VanY than with VanX and hydrolyzes D,D-dipeptides such as D-Ala-D-Ala, whereas VanY is inactive against this substrate; thus having a less restrictive active site to accommodate larger substrates such as UDP-MurNAc-pentapeptide[Ala]. This family belongs to the MEROPS family M15, subfamily B, and includes the D,D-dipeptidases VanXYg and VanXYe.


Pssm-ID: 350623 [Multi-domain]  Cd Length: 127  Bit Score: 38.40  E-value: 9.58e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 589892919  48 VILEGYRDLTRQKYLRNLYLSGRG-----NIAAVPGLSNHGWGLACDFAapLNSSG----------SEEHRWMRQNAPLF 112
Cdd:cd14849   23 VPVSGYRSKEEQTAIYDDSLNENGeefteKYVALPGHSEHQTGLAIDLG--LNKKDidficpsfpdSGICDLFREQAADY 100

                         90       100
                 ....*....|....*....|....*
gi 589892919 113 GF--DWARGKAD-----NEPWHWEY 130
Cdd:cd14849  101 GFieRYPKDKEEitgisYEPWHFRY 125
 
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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