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Conserved domains on  [gi|446682049|ref|WP_000759395|]
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MULTISPECIES: D-Ala-D-Ala carboxypeptidase VanY [Bacillus]

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];
62-232 3.50e-55

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


:

Pssm-ID: 441480  Cd Length: 168  Bit Score: 175.84  E-value: 3.50e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446682049  62 LVNRDYPVkkdsirsdiinvnHNSELVrgyVIFDRNLRLSKYVVKKFLNVVDAAGKDGVqHFLMSSGYRDFKEQSKLY-- 139
Cdd:COG1876    1 LVNKDHPL-------------PADDLV---PLPGGGHRLRKEAAAAFEAMQAAAKKDGI-DLVIVSGYRSYERQEALYnr 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446682049 140 --KEMGSDYAL----PAGYSEHNLGLSLDVGST------QKKMEKAPEGKWIEENVWKHGFVLRYPKNKSNITGIQYEPW 207
Cdd:COG1876   64 kvARYGIEAALrysaPPGTSEHHTGLAIDIGDPdpgtdlEEEFEETPAGKWLAANAAKYGFILRYPKGKEDITGYAYEPW 143

                        170       180
                 ....*....|....*....|....*
gi 446682049 208 HIRYVGLPHSAIMQKKNFTLEEYLE 232
Cdd:COG1876  144 HWRYVGVEAAKEIFEKGLTLEEYLG 168
 
Name Accession Description Interval E-value
LdcB COG1876
LD-carboxypeptidase LdcB, LAS superfamily [Cell wall/membrane/envelope biogenesis];
62-232 3.50e-55

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


Pssm-ID: 441480  Cd Length: 168  Bit Score: 175.84  E-value: 3.50e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446682049  62 LVNRDYPVkkdsirsdiinvnHNSELVrgyVIFDRNLRLSKYVVKKFLNVVDAAGKDGVqHFLMSSGYRDFKEQSKLY-- 139
Cdd:COG1876    1 LVNKDHPL-------------PADDLV---PLPGGGHRLRKEAAAAFEAMQAAAKKDGI-DLVIVSGYRSYERQEALYnr 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446682049 140 --KEMGSDYAL----PAGYSEHNLGLSLDVGST------QKKMEKAPEGKWIEENVWKHGFVLRYPKNKSNITGIQYEPW 207
Cdd:COG1876   64 kvARYGIEAALrysaPPGTSEHHTGLAIDIGDPdpgtdlEEEFEETPAGKWLAANAAKYGFILRYPKGKEDITGYAYEPW 143

                        170       180
                 ....*....|....*....|....*
gi 446682049 208 HIRYVGLPHSAIMQKKNFTLEEYLE 232
Cdd:COG1876  144 HWRYVGVEAAKEIFEKGLTLEEYLG 168
LD-carboxypeptidase cd14852
L,D-carboxypeptidase DacB and LdcB, and related proteins; This L,D-carboxypeptidase family ...
 61-220 1.09e-52

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: 169.35  E-value: 1.09e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446682049  61 LLVNRDYPVKKDSIRSDIINvnhnselvrgYVIFDRNLRLSKYVVKKFLNVVDAAGKDGVqHFLMSSGYRDFKEQSKLY- 139
Cdd:cd14852    1 VLVNKDHPLPEDYVPEDLVP----------YVLLDNGLYLRKEAAEALEEMFDAAKKDGI-DLTIVSGYRSYEYQQELYn 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446682049 140 -------KEMGSDYALPAGYSEHNLGLSLDVGSTQ-----KKMEKAPEGKWIEENVWKHGFVLRYPKNKSNITGIQYEPW 207
Cdd:cd14852   70 nyvarygKEEADRYSARPGYSEHQTGLAVDIGSTDgpcleESFEDTPAGKWLAENAHKYGFILRYPKGKENITGYSYEPW 149

                        170
                 ....*....|...
gi 446682049 208 HIRYVGLPHSAIM 220
Cdd:cd14852  150 HFRYVGKEAAKKI 162
VanY pfam02557
D-alanyl-D-alanine carboxypeptidase;
97-214 3.15e-39

D-alanyl-D-alanine carboxypeptidase;


Pssm-ID: 426830 [Multi-domain]  Cd Length: 131  Bit Score: 133.90  E-value: 3.15e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446682049   97 NLRLSKYVVKKFLNVVDAAGKDGVQHFLmSSGYRDFKEQSKLYKEMGSDYALPA--------GYSEHNLGLSLDVGSTQK 168
Cdd:pfam02557   1 GIYLRKEAAEALEELFAAAKKEGINLRA-ISGFRSYEYQEALFKKYVKGEGKKAilrwsappGTSEHHTGLAIDIGDPDN 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 446682049  169 KM------EKAPEGKWIEENVWKHGFVLRYPKNKSNITGIQYEPWHIRYVGL 214
Cdd:pfam02557  80 PWeleesfEDTAAFKWLQANAHKYGFVLRYPKGKEQITGVSYEPWHWRYVGI 131
 
Name Accession Description Interval E-value
LdcB COG1876
LD-carboxypeptidase LdcB, LAS superfamily [Cell wall/membrane/envelope biogenesis];
62-232 3.50e-55

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


Pssm-ID: 441480  Cd Length: 168  Bit Score: 175.84  E-value: 3.50e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446682049  62 LVNRDYPVkkdsirsdiinvnHNSELVrgyVIFDRNLRLSKYVVKKFLNVVDAAGKDGVqHFLMSSGYRDFKEQSKLY-- 139
Cdd:COG1876    1 LVNKDHPL-------------PADDLV---PLPGGGHRLRKEAAAAFEAMQAAAKKDGI-DLVIVSGYRSYERQEALYnr 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446682049 140 --KEMGSDYAL----PAGYSEHNLGLSLDVGST------QKKMEKAPEGKWIEENVWKHGFVLRYPKNKSNITGIQYEPW 207
Cdd:COG1876   64 kvARYGIEAALrysaPPGTSEHHTGLAIDIGDPdpgtdlEEEFEETPAGKWLAANAAKYGFILRYPKGKEDITGYAYEPW 143

                        170       180
                 ....*....|....*....|....*
gi 446682049 208 HIRYVGLPHSAIMQKKNFTLEEYLE 232
Cdd:COG1876  144 HWRYVGVEAAKEIFEKGLTLEEYLG 168
LD-carboxypeptidase cd14852
L,D-carboxypeptidase DacB and LdcB, and related proteins; This L,D-carboxypeptidase family ...
 61-220 1.09e-52

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: 169.35  E-value: 1.09e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446682049  61 LLVNRDYPVKKDSIRSDIINvnhnselvrgYVIFDRNLRLSKYVVKKFLNVVDAAGKDGVqHFLMSSGYRDFKEQSKLY- 139
Cdd:cd14852    1 VLVNKDHPLPEDYVPEDLVP----------YVLLDNGLYLRKEAAEALEEMFDAAKKDGI-DLTIVSGYRSYEYQQELYn 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446682049 140 -------KEMGSDYALPAGYSEHNLGLSLDVGSTQ-----KKMEKAPEGKWIEENVWKHGFVLRYPKNKSNITGIQYEPW 207
Cdd:cd14852   70 nyvarygKEEADRYSARPGYSEHQTGLAVDIGSTDgpcleESFEDTPAGKWLAENAHKYGFILRYPKGKENITGYSYEPW 149

                        170
                 ....*....|...
gi 446682049 208 HIRYVGLPHSAIM 220
Cdd:cd14852  150 HFRYVGKEAAKKI 162
VanY pfam02557
D-alanyl-D-alanine carboxypeptidase;
97-214 3.15e-39

D-alanyl-D-alanine carboxypeptidase;


Pssm-ID: 426830 [Multi-domain]  Cd Length: 131  Bit Score: 133.90  E-value: 3.15e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446682049   97 NLRLSKYVVKKFLNVVDAAGKDGVQHFLmSSGYRDFKEQSKLYKEMGSDYALPA--------GYSEHNLGLSLDVGSTQK 168
Cdd:pfam02557   1 GIYLRKEAAEALEELFAAAKKEGINLRA-ISGFRSYEYQEALFKKYVKGEGKKAilrwsappGTSEHHTGLAIDIGDPDN 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 446682049  169 KM------EKAPEGKWIEENVWKHGFVLRYPKNKSNITGIQYEPWHIRYVGL 214
Cdd:pfam02557  80 PWeleesfEDTAAFKWLQANAHKYGFVLRYPKGKEQITGVSYEPWHWRYVGI 131
DD-dipeptidase_VanXYc cd14849
D-Ala-D-Ala dipeptidase/D-Ala-D-Ala carboxypeptidase (VanXYc) and related proteins; VanXYc ...
 127-213 5.10e-22

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: 88.86  E-value: 5.10e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446682049 127 SGYRDFKEQSKLY----KEMGSDY-----ALPaGYSEHNLGLSLDVGSTQKKM-------EKAPEGKWIEENVWKHGFVL 190
Cdd:cd14849   26 SGYRSKEEQTAIYddslNENGEEFtekyvALP-GHSEHQTGLAIDLGLNKKDIdficpsfPDSGICDLFREQAADYGFIE 104

                         90       100
                 ....*....|....*....|...
gi 446682049 191 RYPKNKSNITGIQYEPWHIRYVG 213
Cdd:cd14849  105 RYPKDKEEITGISYEPWHFRYVG 127
Peptidase_M15 cd14814
Metalloproteases including zinc D-Ala-D-Ala carboxypeptidase, L-Ala-D-Glu peptidase, L, ...
 106-212 1.24e-16

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: 74.01  E-value: 1.24e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446682049 106 KKFLNVVDAAGKDGVqHFLMSSGYRDFKEQSKLYKEMGSDY-----ALPAGYSEHNLGLSLDVGSTQKKMEkAPEGKWIE 180
Cdd:cd14814    5 EALARMIAAAGAEGR-TLTINSGYRTYAQQLRLFAAKGKGSggrrwAAPPGTSNHQWGLAIDLGDGGGWRE-TQGYRWLK 82

                         90       100       110
                 ....*....|....*....|....*....|..
gi 446682049 181 ENVWKHGFVLRYPKNKsniTGIQYEPWHIRYV 212
Cdd:cd14814   83 ANAPRYGFDNPGGARR---GGAFQEPWHWEYV 111
DD-carboxypeptidase_like cd14847
Uncharacterized proteins of the MEROPS peptidase family M15, subfamily B; This family of ...
 104-222 9.51e-07

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: 47.57  E-value: 9.51e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446682049 104 VVKKFLNVVDAAGKDGVQHFLMSsGYRDFKEQS-----------KLYKEMG--------SDY----------ALPaGYSE 154
Cdd:cd14847    5 AAEAFLALQAAAAKDGFDLQIAS-SFRSFERQLaiwnrkwsgerPVLDDNGqpldisslSPEekihailrwsALP-GASR 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446682049 155 HNLGLSLDVGSTQKKMEK----------------APEGKWIEENVWKHGFVLRYpknKSNITGIQYEPWHIRYvgLPHSA 218
Cdd:cd14847   83 HHWGTDIDVYDANALPAGyqlqltpseyeeggpfAKLYQWLDENAAKFGFFRPY---TQDRGGVAPEPWHLSY--APLAQ 157


                 ....
gi 446682049 219 IMQK 222
Cdd:cd14847  158 KYLQ 161
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 ...
 95-186 1.12e-04

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: 41.19  E-value: 1.12e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446682049  95 DRNL-RLSKYVVKKFLNVVDAAGKDGVqHFLMSSGYRDFKEQSKLYK------EMGSDYAlPAGYSEHNLGLSLDVGSTQ 167
Cdd:cd14845    2 ERRIaGLHPEVRAVVKELIELAEEEGI-DFRITEGYRSPARQAALYAqgrtkpGLIVTNA-RGGQSYHNYGLAVDIVPLV 79

                         90
                 ....*....|....*....
gi 446682049 168 KKMEKAPEGKWIEENVWKH 186
Cdd:cd14845   80 NGKLSTGGADPWVSKAYQK 98
 
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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