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Conserved domains on  [gi|516291729|ref|WP_017695036|]
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MULTISPECIES: peptidoglycan L-alanyl-D-glutamate endopeptidase CwlK [Bacillus]

Protein Classification

M15 family metallopeptidase( domain architecture ID 13000805)

M15 family metallopeptidase of the zinc-binding metallopeptidase family, which contains mostly carboxypeptidases and dipeptidases, is involved in bacterial cell wall biosynthesis and metabolism

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
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 ...
 41-164 3.59e-50

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: 157.14  E-value: 3.59e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516291729  41 SDLHPIVKQNADALKAAAANKGITVVITEGFRSFKEQDELYKQGRTKKGNIVTYARGGESYHNYGLAIDFALQKKDGSII 120
Cdd:cd14845    6 AGLHPEVRAVVKELIELAEEEGIDFRITEGYRSPARQAALYAQGRTKPGLIVTNARGGQSYHNYGLAVDIVPLVNGKLST 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 516291729 121 WdmeyDGNQNGKSDWLEVVEIAKTLGFEWGGDWKRFKDYPHLEM 164
Cdd:cd14845   86 G----GADPWVSKAYQKLGEIAKSLGLEWGGDWKSFKDYPHFQL 125
 
Name Accession Description Interval E-value
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 ...
 41-164 3.59e-50

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: 157.14  E-value: 3.59e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516291729  41 SDLHPIVKQNADALKAAAANKGITVVITEGFRSFKEQDELYKQGRTKKGNIVTYARGGESYHNYGLAIDFALQKKDGSII 120
Cdd:cd14845    6 AGLHPEVRAVVKELIELAEEEGIDFRITEGYRSPARQAALYAQGRTKPGLIVTNARGGQSYHNYGLAVDIVPLVNGKLST 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 516291729 121 WdmeyDGNQNGKSDWLEVVEIAKTLGFEWGGDWKRFKDYPHLEM 164
Cdd:cd14845   86 G----GADPWVSKAYQKLGEIAKSLGLEWGGDWKSFKDYPHFQL 125
Peptidase_M15_4 pfam13539
D-alanyl-D-alanine carboxypeptidase; This family resembles VanY, pfam02557, which is part of ...
 95-164 5.32e-21

D-alanyl-D-alanine carboxypeptidase; This family resembles VanY, pfam02557, which is part of the peptidase M15 family.


Pssm-ID: 433291 [Multi-domain]  Cd Length: 67  Bit Score: 81.22  E-value: 5.32e-21
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516291729   95 ARGGESYHNYGLAIDFALQKKDGsiiWDMEYDGNQNGKSDwlEVVEIAKTLGFEWGGDWKRFKDYPHLEM 164
Cdd:pfam13539   3 SKTGLSNHSYGLAIDINPLVNPY---WGAVLPENGIPYAD--EVVEAFEKLGFEWGGDWKSFKDYMHFEY 67
LdcB COG1876
LD-carboxypeptidase LdcB, LAS superfamily [Cell wall/membrane/envelope biogenesis];
62-110 6.20e-06

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


Pssm-ID: 441480  Cd Length: 168  Bit Score: 44.10  E-value: 6.20e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 516291729  62 GITVVITEGFRSFKEQDELYKQGRTKKG--NIVTY-ARGGESYHNYGLAIDF 110
Cdd:COG1876   42 GIDLVIVSGYRSYERQEALYNRKVARYGieAALRYsAPPGTSEHHTGLAIDI 93
 
Name Accession Description Interval E-value
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 ...
 41-164 3.59e-50

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: 157.14  E-value: 3.59e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516291729  41 SDLHPIVKQNADALKAAAANKGITVVITEGFRSFKEQDELYKQGRTKKGNIVTYARGGESYHNYGLAIDFALQKKDGSII 120
Cdd:cd14845    6 AGLHPEVRAVVKELIELAEEEGIDFRITEGYRSPARQAALYAQGRTKPGLIVTNARGGQSYHNYGLAVDIVPLVNGKLST 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 516291729 121 WdmeyDGNQNGKSDWLEVVEIAKTLGFEWGGDWKRFKDYPHLEM 164
Cdd:cd14845   86 G----GADPWVSKAYQKLGEIAKSLGLEWGGDWKSFKDYPHFQL 125
Peptidase_M15_4 pfam13539
D-alanyl-D-alanine carboxypeptidase; This family resembles VanY, pfam02557, which is part of ...
 95-164 5.32e-21

D-alanyl-D-alanine carboxypeptidase; This family resembles VanY, pfam02557, which is part of the peptidase M15 family.


Pssm-ID: 433291 [Multi-domain]  Cd Length: 67  Bit Score: 81.22  E-value: 5.32e-21
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516291729   95 ARGGESYHNYGLAIDFALQKKDGsiiWDMEYDGNQNGKSDwlEVVEIAKTLGFEWGGDWKRFKDYPHLEM 164
Cdd:pfam13539   3 SKTGLSNHSYGLAIDINPLVNPY---WGAVLPENGIPYAD--EVVEAFEKLGFEWGGDWKSFKDYMHFEY 67
VanY pfam02557
D-alanyl-D-alanine carboxypeptidase;
62-162 3.75e-15

D-alanyl-D-alanine carboxypeptidase;


Pssm-ID: 426830 [Multi-domain]  Cd Length: 131  Bit Score: 68.03  E-value: 3.75e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516291729   62 GITVVITEGFRSFKEQDELYK---QGRTKKGNIVTYARGGESYHNYGLAIDFAlqkkDGSIIWDMEYDGNQNGKSDWLev 138
Cdd:pfam02557  23 GINLRAISGFRSYEYQEALFKkyvKGEGKKAILRWSAPPGTSEHHTGLAIDIG----DPDNPWELEESFEDTAAFKWL-- 96

                          90       100
                  ....*....|....*....|....*
gi 516291729  139 VEIAKTLGFEWggdwkRF-KDYPHL 162
Cdd:pfam02557  97 QANAHKYGFVL-----RYpKGKEQI 116
Peptidase_M15 cd14814
Metalloproteases including zinc D-Ala-D-Ala carboxypeptidase, L-Ala-D-Glu peptidase, L, ...
 62-117 1.57e-10

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: 55.14  E-value: 1.57e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 516291729  62 GITVVITEGFRSFKEQDELYKQGRTKKGNIVTYARGGESYHNYGLAIDFALQKKDG 117
Cdd:cd14814   18 GRTLTINSGYRTYAQQLRLFAAKGKGSGGRRWAAPPGTSNHQWGLAIDLGDGGGWR 73
LdcB COG1876
LD-carboxypeptidase LdcB, LAS superfamily [Cell wall/membrane/envelope biogenesis];
62-110 6.20e-06

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


Pssm-ID: 441480  Cd Length: 168  Bit Score: 44.10  E-value: 6.20e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 516291729  62 GITVVITEGFRSFKEQDELYKQGRTKKG--NIVTY-ARGGESYHNYGLAIDF 110
Cdd:COG1876   42 GIDLVIVSGYRSYERQEALYNRKVARYGieAALRYsAPPGTSEHHTGLAIDI 93
DD-dipeptidase_VanXYc cd14849
D-Ala-D-Ala dipeptidase/D-Ala-D-Ala carboxypeptidase (VanXYc) and related proteins; VanXYc ...
 64-116 1.08e-05

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: 42.64  E-value: 1.08e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 516291729  64 TVVITEGFRSFKEQDELYKQGRTKKGNIVTY---ARGGESYHNYGLAIDFALQKKD 116
Cdd:cd14849   21 EIVPVSGYRSKEEQTAIYDDSLNENGEEFTEkyvALPGHSEHQTGLAIDLGLNKKD 76
LD-carboxypeptidase cd14852
L,D-carboxypeptidase DacB and LdcB, and related proteins; This L,D-carboxypeptidase family ...
 62-111 2.46e-05

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: 42.23  E-value: 2.46e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 516291729  62 GITVVITEGFRSFKEQDELYKQGRTKKGNIVT---YARGGESYHNYGLAIDFA 111
Cdd:cd14852   49 GIDLTIVSGYRSYEYQQELYNNYVARYGKEEAdrySARPGYSEHQTGLAVDIG 101
 
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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