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Conserved domains on  [gi|995957923|gb|AMJ43222|]
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VanY [Enterococcus faecium]

Protein Classification

D-alanyl-D-alanine carboxypeptidase family protein( domain architecture ID 11449003)

D-alanyl-D-alanine carboxypeptidase family protein such as Streptococcus pneumoniae L,D-carboxypeptidase Dacb and Enterococcus faecium D-alanyl-D-alanine carboxypeptidase, which removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LdcB COG1876
LD-carboxypeptidase LdcB, LAS superfamily [Cell wall/membrane/envelope biogenesis];
93-264 3.17e-63

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


:

Pssm-ID: 441480  Cd Length: 168  Bit Score: 195.87  E-value: 3.17e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 995957923  93 LVNRQNPIPAQYDVELEQlsNGERIDIRISPYLQDLFDAARTDGVYPIVASGYRTTEKQQEIMDEKIAEYkakgytsaqA 172
Cdd:COG1876    1 LVNKDHPLPADDLVPLPG--GGHRLRKEAAAAFEAMQAAAKKDGIDLVIVSGYRSYERQEALYNRKVARY---------G 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 995957923 173 KAEAETWVAVPGTSEHQLGLAVDINADGIHSTGNE------VYRWLDENSYRFGFIRRYPPDKTEITGVSNEPWHYRYVG 246
Cdd:COG1876   70 IEAALRYSAPPGTSEHHTGLAIDIGDPDPGTDLEEefeetpAGKWLAANAAKYGFILRYPKGKEDITGYAYEPWHWRYVG 149

                        170
                 ....*....|....*...
gi 995957923 247 IEAATEMYNQGVCLEEYL 264
Cdd:COG1876  150 VEAAKEIFEKGLTLEEYL 167
 
Name Accession Description Interval E-value
LdcB COG1876
LD-carboxypeptidase LdcB, LAS superfamily [Cell wall/membrane/envelope biogenesis];
93-264 3.17e-63

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


Pssm-ID: 441480  Cd Length: 168  Bit Score: 195.87  E-value: 3.17e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 995957923  93 LVNRQNPIPAQYDVELEQlsNGERIDIRISPYLQDLFDAARTDGVYPIVASGYRTTEKQQEIMDEKIAEYkakgytsaqA 172
Cdd:COG1876    1 LVNKDHPLPADDLVPLPG--GGHRLRKEAAAAFEAMQAAAKKDGIDLVIVSGYRSYERQEALYNRKVARY---------G 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 995957923 173 KAEAETWVAVPGTSEHQLGLAVDINADGIHSTGNE------VYRWLDENSYRFGFIRRYPPDKTEITGVSNEPWHYRYVG 246
Cdd:COG1876   70 IEAALRYSAPPGTSEHHTGLAIDIGDPDPGTDLEEefeetpAGKWLAANAAKYGFILRYPKGKEDITGYAYEPWHWRYVG 149

                        170
                 ....*....|....*...
gi 995957923 247 IEAATEMYNQGVCLEEYL 264
Cdd:COG1876  150 VEAAKEIFEKGLTLEEYL 167
LD-carboxypeptidase cd14852
L,D-carboxypeptidase DacB and LdcB, and related proteins; This L,D-carboxypeptidase family ...
 92-253 2.31e-59

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: 185.91  E-value: 2.31e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 995957923  92 ILVNRQNPIPAQYDVELEQ----LSNGERIDIRISPYLQDLFDAARTDGVYPIVASGYRTTEKQQEIMDEKIAEYKakgy 167
Cdd:cd14852    1 VLVNKDHPLPEDYVPEDLVpyvlLDNGLYLRKEAAEALEEMFDAAKKDGIDLTIVSGYRSYEYQQELYNNYVARYG---- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 995957923 168 tsaqaKAEAETWVAVPGTSEHQLGLAVDINADGIHSTGNEV-----YRWLDENSYRFGFIRRYPPDKTEITGVSNEPWHY 242
Cdd:cd14852   77 -----KEEADRYSARPGYSEHQTGLAVDIGSTDGPCLEESFedtpaGKWLAENAHKYGFILRYPKGKENITGYSYEPWHF 151

                        170
                 ....*....|.
gi 995957923 243 RYVGIEAATEM 253
Cdd:cd14852  152 RYVGKEAAKKI 162
VanY pfam02557
D-alanyl-D-alanine carboxypeptidase;
114-247 1.42e-47

D-alanyl-D-alanine carboxypeptidase;


Pssm-ID: 426830 [Multi-domain]  Cd Length: 131  Bit Score: 154.70  E-value: 1.42e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 995957923  114 GERIDIRISPYLQDLFDAARTDGVYPIVASGYRTTEKQQEIMDEkiaeykakgYTSAQAKAEAETWVAVPGTSEHQLGLA 193
Cdd:pfam02557   1 GIYLRKEAAEALEELFAAAKKEGINLRAISGFRSYEYQEALFKK---------YVKGEGKKAILRWSAPPGTSEHHTGLA 71

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 995957923  194 VDINADG------IHSTGNEVYRWLDENSYRFGFIRRYPPDKTEITGVSNEPWHYRYVGI 247
Cdd:pfam02557  72 IDIGDPDnpweleESFEDTAAFKWLQANAHKYGFVLRYPKGKEQITGVSYEPWHWRYVGI 131
 
Name Accession Description Interval E-value
LdcB COG1876
LD-carboxypeptidase LdcB, LAS superfamily [Cell wall/membrane/envelope biogenesis];
93-264 3.17e-63

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


Pssm-ID: 441480  Cd Length: 168  Bit Score: 195.87  E-value: 3.17e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 995957923  93 LVNRQNPIPAQYDVELEQlsNGERIDIRISPYLQDLFDAARTDGVYPIVASGYRTTEKQQEIMDEKIAEYkakgytsaqA 172
Cdd:COG1876    1 LVNKDHPLPADDLVPLPG--GGHRLRKEAAAAFEAMQAAAKKDGIDLVIVSGYRSYERQEALYNRKVARY---------G 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 995957923 173 KAEAETWVAVPGTSEHQLGLAVDINADGIHSTGNE------VYRWLDENSYRFGFIRRYPPDKTEITGVSNEPWHYRYVG 246
Cdd:COG1876   70 IEAALRYSAPPGTSEHHTGLAIDIGDPDPGTDLEEefeetpAGKWLAANAAKYGFILRYPKGKEDITGYAYEPWHWRYVG 149

                        170
                 ....*....|....*...
gi 995957923 247 IEAATEMYNQGVCLEEYL 264
Cdd:COG1876  150 VEAAKEIFEKGLTLEEYL 167
LD-carboxypeptidase cd14852
L,D-carboxypeptidase DacB and LdcB, and related proteins; This L,D-carboxypeptidase family ...
 92-253 2.31e-59

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: 185.91  E-value: 2.31e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 995957923  92 ILVNRQNPIPAQYDVELEQ----LSNGERIDIRISPYLQDLFDAARTDGVYPIVASGYRTTEKQQEIMDEKIAEYKakgy 167
Cdd:cd14852    1 VLVNKDHPLPEDYVPEDLVpyvlLDNGLYLRKEAAEALEEMFDAAKKDGIDLTIVSGYRSYEYQQELYNNYVARYG---- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 995957923 168 tsaqaKAEAETWVAVPGTSEHQLGLAVDINADGIHSTGNEV-----YRWLDENSYRFGFIRRYPPDKTEITGVSNEPWHY 242
Cdd:cd14852   77 -----KEEADRYSARPGYSEHQTGLAVDIGSTDGPCLEESFedtpaGKWLAENAHKYGFILRYPKGKENITGYSYEPWHF 151

                        170
                 ....*....|.
gi 995957923 243 RYVGIEAATEM 253
Cdd:cd14852  152 RYVGKEAAKKI 162
VanY pfam02557
D-alanyl-D-alanine carboxypeptidase;
114-247 1.42e-47

D-alanyl-D-alanine carboxypeptidase;


Pssm-ID: 426830 [Multi-domain]  Cd Length: 131  Bit Score: 154.70  E-value: 1.42e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 995957923  114 GERIDIRISPYLQDLFDAARTDGVYPIVASGYRTTEKQQEIMDEkiaeykakgYTSAQAKAEAETWVAVPGTSEHQLGLA 193
Cdd:pfam02557   1 GIYLRKEAAEALEELFAAAKKEGINLRAISGFRSYEYQEALFKK---------YVKGEGKKAILRWSAPPGTSEHHTGLA 71

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 995957923  194 VDINADG------IHSTGNEVYRWLDENSYRFGFIRRYPPDKTEITGVSNEPWHYRYVGI 247
Cdd:pfam02557  72 IDIGDPDnpweleESFEDTAAFKWLQANAHKYGFVLRYPKGKEQITGVSYEPWHWRYVGI 131
DD-dipeptidase_VanXYc cd14849
D-Ala-D-Ala dipeptidase/D-Ala-D-Ala carboxypeptidase (VanXYc) and related proteins; VanXYc ...
 125-246 1.82e-29

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: 107.73  E-value: 1.82e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 995957923 125 LQDLFDAAR-TDGVYPIvaSGYRTTEKQQEIMDEKIAEyKAKGYTsaqakaeaETWVAVPGTSEHQLGLAVD--INADGI 201
Cdd:cd14849    9 LKKLLEAIGgEDEIVPV--SGYRSKEEQTAIYDDSLNE-NGEEFT--------EKYVALPGHSEHQTGLAIDlgLNKKDI 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 995957923 202 -----HSTGNEVYRWLDENSYRFGFIRRYPPDKTEITGVSNEPWHYRYVG 246
Cdd:cd14849   78 dficpSFPDSGICDLFREQAADYGFIERYPKDKEEITGISYEPWHFRYVG 127
Peptidase_M15 cd14814
Metalloproteases including zinc D-Ala-D-Ala carboxypeptidase, L-Ala-D-Glu peptidase, L, ...
 125-245 2.44e-28

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: 104.45  E-value: 2.44e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 995957923 125 LQDLFDAARTDGVYPIVASGYRTTEKQQEIMDEKiaeykAKGYTSAqakaeaeTWVAVPGTSEHQLGLAVDINaDGIHST 204
Cdd:cd14814    7 LARMIAAAGAEGRTLTINSGYRTYAQQLRLFAAK-----GKGSGGR-------RWAAPPGTSNHQWGLAIDLG-DGGGWR 73

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 995957923 205 GNEVYRWLDENSYRFGFIRRYPPDKteiTGVSNEPWHYRYV 245
Cdd:cd14814   74 ETQGYRWLKANAPRYGFDNPGGARR---GGAFQEPWHWEYV 111
Peptidase_M15_like cd14846
Uncharacterized family of the peptidase family M15, subfamily B; This family of ...
 125-244 1.12e-15

Uncharacterized family of the peptidase family M15, subfamily B; This family of uncharacterized proteins, similar to endolysin lys (Clavibacter phage CMP1) and VanYn peptidase, are zinc-binding enzymes that belong to the peptidase M15 subfamily B, involved in bacterial cell wall metabolism.


Pssm-ID: 350621  Cd Length: 104  Bit Score: 70.80  E-value: 1.12e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 995957923 125 LQDLFDAARTDGVYPIVASGYRTTEKQQEIMDEKIAEYKakgytsaqAKAEAETWVAVPGTSEHQLGLAVDIN-ADGihs 203
Cdd:cd14846    9 LTAAATAAAADGVTLRITSGWRSPAEQQRLLDDAVRTYG--------SEEEARRWVAPPEDSAHVTGEAVDIGpADA--- 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 995957923 204 tgnevYRWLDENSYRFGFIRRYppdkteitgvSNEPWHYRY 244
Cdd:cd14846   78 -----AQWLERHGARYGLCRIY----------ANEWWHFEL 103
DD-carboxypeptidase_like cd14847
Uncharacterized proteins of the MEROPS peptidase family M15, subfamily B; This family of ...
 125-244 6.25e-15

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: 70.30  E-value: 6.25e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 995957923 125 LQDLFDAARTDGVYPIVASGYRTTEKQQEIMDEKIAEYKA----------KGYTSAQAKAEA-ETWVAVPGTSEHQLGLA 193
Cdd:cd14847    9 FLALQAAAAKDGFDLQIASSFRSFERQLAIWNRKWSGERPvlddngqpldISSLSPEEKIHAiLRWSALPGASRHHWGTD 88

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 995957923 194 VDINA-------------------DGIhstGNEVYRWLDENSYRFGFIRRYPPDKteiTGVSNEPWHYRY 244
Cdd:cd14847   89 IDVYDanalpagyqlqltpseyeeGGP---FAKLYQWLDENAAKFGFFRPYTQDR---GGVAPEPWHLSY 152
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 ...
 115-197 1.09e-05

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: 43.89  E-value: 1.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 995957923 115 ERIDIRISPYLQDLFDAARTDGVYPIVASGYRTTEKQqeimdekiAEYKAKGytsAQAKAEAETWvAVPGTSEHQLGLAV 194
Cdd:cd14845    6 AGLHPEVRAVVKELIELAEEEGIDFRITEGYRSPARQ--------AALYAQG---RTKPGLIVTN-ARGGQSYHNYGLAV 73


                 ...
gi 995957923 195 DIN 197
Cdd:cd14845   74 DIV 76
 
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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