NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|446164138|ref|WP_000241993|]
View 

MULTISPECIES: M15 family metallopeptidase [Bacillus]

Protein Classification

M15 family metallopeptidase( domain architecture ID 13000893)

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

EC:  3.4.17.-
Gene Ontology:  GO:0008233|GO:0016787|GO:0006508
PubMed:  15044722

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
LD-carboxypeptidase cd14852
L,D-carboxypeptidase DacB and LdcB, and related proteins; This L,D-carboxypeptidase family ...
 51-225 1.03e-68

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: 208.64  E-value: 1.03e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446164138  51 ILVNREHMLSKELGIELTSITQNAKPNMKIDSRIATSYQDMVAAAKKEGINLYLRSGYRAIKLQQTYYDASVKSYKSqgl 130
Cdd:cd14852    1 VLVNKDHPLPEDYVPEDLVPYVLLDNGLYLRKEAAEALEEMFDAAKKDGIDLTIVSGYRSYEYQQELYNNYVARYGK--- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446164138 131 sdkeasAKALEYLQYPGASEHHTGLALDIISVEWqntvEDLNAKFETTDAFKWLDKNAAEYGFTLRYPKDKENITGIKYE 210
Cdd:cd14852   78 ------EEADRYSARPGYSEHQTGLAVDIGSTDG----PCLEESFEDTPAGKWLAENAHKYGFILRYPKGKENITGYSYE 147

                        170
                 ....*....|....*
gi 446164138 211 PWHYRYVGKEVAVYL 225
Cdd:cd14852  148 PWHFRYVGKEAAKKI 162
 
Name Accession Description Interval E-value
LD-carboxypeptidase cd14852
L,D-carboxypeptidase DacB and LdcB, and related proteins; This L,D-carboxypeptidase family ...
 51-225 1.03e-68

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: 208.64  E-value: 1.03e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446164138  51 ILVNREHMLSKELGIELTSITQNAKPNMKIDSRIATSYQDMVAAAKKEGINLYLRSGYRAIKLQQTYYDASVKSYKSqgl 130
Cdd:cd14852    1 VLVNKDHPLPEDYVPEDLVPYVLLDNGLYLRKEAAEALEEMFDAAKKDGIDLTIVSGYRSYEYQQELYNNYVARYGK--- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446164138 131 sdkeasAKALEYLQYPGASEHHTGLALDIISVEWqntvEDLNAKFETTDAFKWLDKNAAEYGFTLRYPKDKENITGIKYE 210
Cdd:cd14852   78 ------EEADRYSARPGYSEHQTGLAVDIGSTDG----PCLEESFEDTPAGKWLAENAHKYGFILRYPKGKENITGYSYE 147

                        170
                 ....*....|....*
gi 446164138 211 PWHYRYVGKEVAVYL 225
Cdd:cd14852  148 PWHFRYVGKEAAKKI 162
LdcB COG1876
LD-carboxypeptidase LdcB, LAS superfamily [Cell wall/membrane/envelope biogenesis];
52-237 1.91e-68

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


Pssm-ID: 441480  Cd Length: 168  Bit Score: 208.20  E-value: 1.91e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446164138  52 LVNREHMLSKElgiELTSITQnakPNMKIDSRIATSYQDMVAAAKKEGINLYLRSGYRAIKLQQTYYDASVKSYksqGLs 131
Cdd:COG1876    1 LVNKDHPLPAD---DLVPLPG---GGHRLRKEAAAAFEAMQAAAKKDGIDLVIVSGYRSYERQEALYNRKVARY---GI- 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446164138 132 dkeasAKALEYLQYPGASEHHTGLALDIISVewqNTVEDLNAKFETTDAFKWLDKNAAEYGFTLRYPKDKENITGIKYEP 211
Cdd:COG1876   71 -----EAALRYSAPPGTSEHHTGLAIDIGDP---DPGTDLEEEFEETPAGKWLAANAAKYGFILRYPKGKEDITGYAYEP 142

                        170       180
                 ....*....|....*....|....*.
gi 446164138 212 WHYRYVGKEVAVYLKEKGLTLEEYNE 237
Cdd:COG1876  143 WHWRYVGVEAAKEIFEKGLTLEEYLG 168
VanY pfam02557
D-alanyl-D-alanine carboxypeptidase;
79-219 1.19e-51

D-alanyl-D-alanine carboxypeptidase;


Pssm-ID: 426830 [Multi-domain]  Cd Length: 131  Bit Score: 163.95  E-value: 1.19e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446164138   79 KIDSRIATSYQDMVAAAKKEGINLYLRSGYRAIKLQQTYYDASVKsyksqglsdKEASAKALEYLQYPGASEHHTGLALD 158
Cdd:pfam02557   3 YLRKEAAEALEELFAAAKKEGINLRAISGFRSYEYQEALFKKYVK---------GEGKKAILRWSAPPGTSEHHTGLAID 73

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446164138  159 IISVEWQNTVEDLnakFETTDAFKWLDKNAAEYGFTLRYPKDKENITGIKYEPWHYRYVGK 219
Cdd:pfam02557  74 IGDPDNPWELEES---FEDTAAFKWLQANAHKYGFVLRYPKGKEQITGVSYEPWHWRYVGI 131
 
Name Accession Description Interval E-value
LD-carboxypeptidase cd14852
L,D-carboxypeptidase DacB and LdcB, and related proteins; This L,D-carboxypeptidase family ...
 51-225 1.03e-68

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: 208.64  E-value: 1.03e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446164138  51 ILVNREHMLSKELGIELTSITQNAKPNMKIDSRIATSYQDMVAAAKKEGINLYLRSGYRAIKLQQTYYDASVKSYKSqgl 130
Cdd:cd14852    1 VLVNKDHPLPEDYVPEDLVPYVLLDNGLYLRKEAAEALEEMFDAAKKDGIDLTIVSGYRSYEYQQELYNNYVARYGK--- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446164138 131 sdkeasAKALEYLQYPGASEHHTGLALDIISVEWqntvEDLNAKFETTDAFKWLDKNAAEYGFTLRYPKDKENITGIKYE 210
Cdd:cd14852   78 ------EEADRYSARPGYSEHQTGLAVDIGSTDG----PCLEESFEDTPAGKWLAENAHKYGFILRYPKGKENITGYSYE 147

                        170
                 ....*....|....*
gi 446164138 211 PWHYRYVGKEVAVYL 225
Cdd:cd14852  148 PWHFRYVGKEAAKKI 162
LdcB COG1876
LD-carboxypeptidase LdcB, LAS superfamily [Cell wall/membrane/envelope biogenesis];
52-237 1.91e-68

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


Pssm-ID: 441480  Cd Length: 168  Bit Score: 208.20  E-value: 1.91e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446164138  52 LVNREHMLSKElgiELTSITQnakPNMKIDSRIATSYQDMVAAAKKEGINLYLRSGYRAIKLQQTYYDASVKSYksqGLs 131
Cdd:COG1876    1 LVNKDHPLPAD---DLVPLPG---GGHRLRKEAAAAFEAMQAAAKKDGIDLVIVSGYRSYERQEALYNRKVARY---GI- 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446164138 132 dkeasAKALEYLQYPGASEHHTGLALDIISVewqNTVEDLNAKFETTDAFKWLDKNAAEYGFTLRYPKDKENITGIKYEP 211
Cdd:COG1876   71 -----EAALRYSAPPGTSEHHTGLAIDIGDP---DPGTDLEEEFEETPAGKWLAANAAKYGFILRYPKGKEDITGYAYEP 142

                        170       180
                 ....*....|....*....|....*.
gi 446164138 212 WHYRYVGKEVAVYLKEKGLTLEEYNE 237
Cdd:COG1876  143 WHWRYVGVEAAKEIFEKGLTLEEYLG 168
VanY pfam02557
D-alanyl-D-alanine carboxypeptidase;
79-219 1.19e-51

D-alanyl-D-alanine carboxypeptidase;


Pssm-ID: 426830 [Multi-domain]  Cd Length: 131  Bit Score: 163.95  E-value: 1.19e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446164138   79 KIDSRIATSYQDMVAAAKKEGINLYLRSGYRAIKLQQTYYDASVKsyksqglsdKEASAKALEYLQYPGASEHHTGLALD 158
Cdd:pfam02557   3 YLRKEAAEALEELFAAAKKEGINLRAISGFRSYEYQEALFKKYVK---------GEGKKAILRWSAPPGTSEHHTGLAID 73

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446164138  159 IISVEWQNTVEDLnakFETTDAFKWLDKNAAEYGFTLRYPKDKENITGIKYEPWHYRYVGK 219
Cdd:pfam02557  74 IGDPDNPWELEES---FEDTAAFKWLQANAHKYGFVLRYPKGKEQITGVSYEPWHWRYVGI 131
DD-dipeptidase_VanXYc cd14849
D-Ala-D-Ala dipeptidase/D-Ala-D-Ala carboxypeptidase (VanXYc) and related proteins; VanXYc ...
 106-218 2.34e-26

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: 99.26  E-value: 2.34e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446164138 106 SGYRAIKLQQTYYDASVKSyKSQGLSDKeasakaleYLQYPGASEHHTGLALDIisVEWQNTVEDLNAKFETTDAFKWLD 185
Cdd:cd14849   26 SGYRSKEEQTAIYDDSLNE-NGEEFTEK--------YVALPGHSEHQTGLAIDL--GLNKKDIDFICPSFPDSGICDLFR 94

                         90       100       110
                 ....*....|....*....|....*....|...
gi 446164138 186 KNAAEYGFTLRYPKDKENITGIKYEPWHYRYVG 218
Cdd:cd14849   95 EQAADYGFIERYPKDKEEITGISYEPWHFRYVG 127
Peptidase_M15 cd14814
Metalloproteases including zinc D-Ala-D-Ala carboxypeptidase, L-Ala-D-Glu peptidase, L, ...
 85-217 3.38e-21

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: 85.19  E-value: 3.38e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446164138  85 ATSYQDMVAAAKKEGINLYLRSGYRAIKLQQTYYDASVKSYKSQGlsdkeASAKaleylqyPGASEHHTGLALDIisvew 164
Cdd:cd14814    4 AEALARMIAAAGAEGRTLTINSGYRTYAQQLRLFAAKGKGSGGRR-----WAAP-------PGTSNHQWGLAIDL----- 66

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446164138 165 qntveDLNAKFETTDAFKWLDKNAAEYGFTLRYPKDKeniTGIKYEPWHYRYV 217
Cdd:cd14814   67 -----GDGGGWRETQGYRWLKANAPRYGFDNPGGARR---GGAFQEPWHWEYV 111
DD-carboxypeptidase_like cd14847
Uncharacterized proteins of the MEROPS peptidase family M15, subfamily B; This family of ...
 84-216 9.04e-21

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: 85.32  E-value: 9.04e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446164138  84 IATSYQDMVAAAKKEGINLYLRSGYR------AI---KL--QQTYYDASVKSYKSQGLSDKEASAKALEYLQYPGASEHH 152
Cdd:cd14847    5 AAEAFLALQAAAAKDGFDLQIASSFRsferqlAIwnrKWsgERPVLDDNGQPLDISSLSPEEKIHAILRWSALPGASRHH 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446164138 153 TGLALDIIS---VEWQNTVEDLNAKFETTDAF----KWLDKNAAEYGFTLRYPKDKeniTGIKYEPWHYRY 216
Cdd:cd14847   85 WGTDIDVYDanaLPAGYQLQLTPSEYEEGGPFaklyQWLDENAAKFGFFRPYTQDR---GGVAPEPWHLSY 152
Peptidase_M15_like cd14846
Uncharacterized family of the peptidase family M15, subfamily B; This family of ...
 80-216 6.35e-11

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: 57.71  E-value: 6.35e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446164138  80 IDSRIATSYQDMVAAAKKEGINLYLRSGYRAIKLQQTYYDASVKSYKSQglsdkeasAKALEYLQYPGASEHHTGLALDI 159
Cdd:cd14846    1 LDPALLAALTAAATAAAADGVTLRITSGWRSPAEQQRLLDDAVRTYGSE--------EEARRWVAPPEDSAHVTGEAVDI 72

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446164138 160 isvewqntvedlnakfETTDAFKWLDKNAAEYGFTLRYpkdkENitgikyEPWHYRY 216
Cdd:cd14846   73 ----------------GPADAAQWLERHGARYGLCRIY----AN------EWWHFEL 103
D-Ala-D-Ala_dipeptidase_like cd14843
D-Ala-D-Ala dipeptidase, includes uncharacterized enzymes; This subfamily of D-Ala-D-Ala ...
 98-181 4.74e-03

D-Ala-D-Ala dipeptidase, includes uncharacterized enzymes; This subfamily of D-Ala-D-Ala dipeptidase (also known as D-alanyl-D-alanine dipeptidase vanX; VanX; EC 3.4.13.22) also includes several uncharacterized proteins. This is a Zn2+-dependent enzyme that mediates resistance to the antibiotic vancomycin in Enterococci and other bacteria (both Gram-positive and Gram-negative). It is part of a gene cluster that affects cell-wall biosynthesis. The operon triggers the termination of peptidoglycan precursors by D-Ala-(R)-lactate instead of D-Ala-D-Ala dipeptides. The enzyme is stereospecific, as L-Ala-L-Ala, D-Ala-L-Ala and L-Ala-D-Ala are not substrates. It belongs in the MEROPS peptidase family M15, subfamily D.


Pssm-ID: 350618 [Multi-domain]  Cd Length: 160  Bit Score: 36.50  E-value: 4.74e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446164138  98 EGINLYLRSGYRAIKLQQ----TYYDASVKSYKsqGLSDKEASAKALEYLQYPGASE-----HHTGLALDI-ISVEWQNT 167
Cdd:cd14843   18 KGLRLLIFDGYRPLAVQKflfeRYYQKIRKRHP--GRSPEELIEEVRKFVAPPSKDPltpppHSTGGAVDLtLADEDGKE 95

                         90
                 ....*....|....
gi 446164138 168 VEDLNAKFETTDAF 181
Cdd:cd14843   96 LDMGGPIDDDTEAS 109
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH