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Conserved domains on  [gi|1130939684|ref|WP_075704592|]
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C39 family peptidase [Intestinimonas butyriciproducens]

Protein Classification

cysteine peptidase family C39 domain-containing protein( domain architecture ID 2867)

cysteine peptidase family C39 domain-containing protein, similar to Niallia circulans butirosin biosynthesis protein H

PubMed:  11517925

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Peptidase_C39_like super family cl00296
Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The ...
 94-226 2.00e-09

Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in all sub-families.


The actual alignment was detected with superfamily member cd02549:

Pssm-ID: 469710 [Multi-domain]  Cd Length: 141  Bit Score: 54.72  E-value: 2.00e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1130939684  94 QQTSEWaCGVTSALMVLNWYGelgdwnektlaalrhplegelaeYPGTTLRQAMDIFDGVGGFTYTTTLDQP------EI 167
Cdd:cd02549     1 PQLENG-CGPTSLAMVLSYLG-----------------------VKVTKPQLAAEGNTYDFAKDGYGTYPKPivsaaaRK 56

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1130939684 168 WT---------EDIRGWLAEGTPVMVCWN-----DWGGHWQVIVGYDTMGTeseqddvILVADPYDTTDHNQD 226
Cdd:cd02549    57 YGlvvrpltglLALLRQLAAGHPVIVSVNlgvsiTPSGHAMVVIGYDRKGN-------VYVNDPGGGRRLVVS 122
 
Name Accession Description Interval E-value
Peptidase_C39A cd02549
A sub-family of peptidase family C39. Peptidase family C39 mostly contains ...
 94-226 2.00e-09

A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are lacking the nucleotide-binding transporter signature or have different domain architectures.


Pssm-ID: 239109 [Multi-domain]  Cd Length: 141  Bit Score: 54.72  E-value: 2.00e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1130939684  94 QQTSEWaCGVTSALMVLNWYGelgdwnektlaalrhplegelaeYPGTTLRQAMDIFDGVGGFTYTTTLDQP------EI 167
Cdd:cd02549     1 PQLENG-CGPTSLAMVLSYLG-----------------------VKVTKPQLAAEGNTYDFAKDGYGTYPKPivsaaaRK 56

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1130939684 168 WT---------EDIRGWLAEGTPVMVCWN-----DWGGHWQVIVGYDTMGTeseqddvILVADPYDTTDHNQD 226
Cdd:cd02549    57 YGlvvrpltglLALLRQLAAGHPVIVSVNlgvsiTPSGHAMVVIGYDRKGN-------VYVNDPGGGRRLVVS 122
Peptidase_C39_2 pfam13529
Peptidase_C39 like family;
101-217 9.11e-05

Peptidase_C39 like family;


Pssm-ID: 379241 [Multi-domain]  Cd Length: 139  Bit Score: 41.28  E-value: 9.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1130939684 101 CGVTSALMVLNWYGElgDWNEKTLAAlrhplegELAEYP--GTTLRQAMDIFDGVGGFTYTTTLDQ------PEIWT--- 169
Cdd:pfam13529  15 CGPTSLAMVLSYLGI--TVTQDELAK-------EIGTNPdgNPNTGFVGNPYDKSGYGVYNPPIVAlaekygLKVTDitg 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1130939684 170 ---EDIRGWLAEGTPVmVCWNDW----------GGHWQVIVGYDtmgtesEQDDVILVADP 217
Cdd:pfam13529  86 ssfDEVIRLLDAGIPV-VVSTTTfgplnyyftsSGHLVVIVGYD------DKGDYVYVNDP 139
 
Name Accession Description Interval E-value
Peptidase_C39A cd02549
A sub-family of peptidase family C39. Peptidase family C39 mostly contains ...
 94-226 2.00e-09

A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are lacking the nucleotide-binding transporter signature or have different domain architectures.


Pssm-ID: 239109 [Multi-domain]  Cd Length: 141  Bit Score: 54.72  E-value: 2.00e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1130939684  94 QQTSEWaCGVTSALMVLNWYGelgdwnektlaalrhplegelaeYPGTTLRQAMDIFDGVGGFTYTTTLDQP------EI 167
Cdd:cd02549     1 PQLENG-CGPTSLAMVLSYLG-----------------------VKVTKPQLAAEGNTYDFAKDGYGTYPKPivsaaaRK 56

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1130939684 168 WT---------EDIRGWLAEGTPVMVCWN-----DWGGHWQVIVGYDTMGTeseqddvILVADPYDTTDHNQD 226
Cdd:cd02549    57 YGlvvrpltglLALLRQLAAGHPVIVSVNlgvsiTPSGHAMVVIGYDRKGN-------VYVNDPGGGRRLVVS 122
Peptidase_C39_2 pfam13529
Peptidase_C39 like family;
101-217 9.11e-05

Peptidase_C39 like family;


Pssm-ID: 379241 [Multi-domain]  Cd Length: 139  Bit Score: 41.28  E-value: 9.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1130939684 101 CGVTSALMVLNWYGElgDWNEKTLAAlrhplegELAEYP--GTTLRQAMDIFDGVGGFTYTTTLDQ------PEIWT--- 169
Cdd:pfam13529  15 CGPTSLAMVLSYLGI--TVTQDELAK-------EIGTNPdgNPNTGFVGNPYDKSGYGVYNPPIVAlaekygLKVTDitg 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1130939684 170 ---EDIRGWLAEGTPVmVCWNDW----------GGHWQVIVGYDtmgtesEQDDVILVADP 217
Cdd:pfam13529  86 ssfDEVIRLLDAGIPV-VVSTTTfgplnyyftsSGHLVVIVGYD------DKGDYVYVNDP 139
Peptidase_C70 pfam12385
Papain-like cysteine protease AvrRpt2; This is a family of cysteine proteases, found in ...
 94-205 6.16e-03

Papain-like cysteine protease AvrRpt2; This is a family of cysteine proteases, found in actinobacteria, protobacteria and firmicutes. Papain-like cysteine proteases play a crucial role in plant-pathogen/pest interactions. On entering the host they act on non-self substrates, thereby manipulating the host to evade proteolysis. AvrRpt2 from Pseudomonas syringae pv. tomato DC3000 triggers resistance to P. syringae-2-dependent defence responses, including hypersensitive cell death, by cleaving the Arabidopsis RIN4 protein which is monitored by the cognate resistance protein RPS2.


Pssm-ID: 403550 [Multi-domain]  Cd Length: 143  Bit Score: 36.28  E-value: 6.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1130939684  94 QQTSEWACGVTSALMVLNWYGELGdWNEKTLAALrhpLEGELAEYPGTTLRQAMDIFDGVGGFTYTTTLDQPEIWteDIR 173
Cdd:pfam12385  11 VQQAAMGCWAASASMIAGYRGQKP-IDPSEIAAL---VPGWSQYDTGLNGPEDIALAEKWGLGNVPEPPQSYSID--ALV 84

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1130939684 174 GWLAEGTPVMVCW---NDWGGHWQVIVGYDTMGTE 205
Cdd:pfam12385  85 KLLRAYGPLWCAIawpGGFVGHAIVLTGIDEDGTP 119
Peptidase_C39 pfam03412
Peptidase C39 family; Lantibiotic and non-lantibiotic bacteriocins are synthesized as ...
 89-217 8.32e-03

Peptidase C39 family; Lantibiotic and non-lantibiotic bacteriocins are synthesized as precursor peptides containing N-terminal extensions (leader peptides) which are cleaved off during maturation. Most non-lantibiotics and also some lantibiotics have leader peptides of the so-called double-glycine type. These leader peptides share consensus sequences and also a common processing site with two conserved glycine residues in positions -1 and -2. The double- glycine-type leader peptides are unrelated to the N-terminal signal sequences which direct proteins across the cytoplasmic membrane via the sec pathway. Their processing sites are also different from typical signal peptidase cleavage sites, suggesting that a different processing enzyme is involved. Peptide bacteriocins are exported across the cytoplasmic membrane by a dedicated ATP-binding cassette (ABC) transporter. The ABC transporter is the maturation protease and its proteolytic domain resides in the N-terminal part of the protein. This peptidase domain is found in a wide range of ABC transporters, however the presumed catalytic cysteine and histidine are not conserved in all members of this family.


Pssm-ID: 367483 [Multi-domain]  Cd Length: 133  Bit Score: 35.66  E-value: 8.32e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1130939684  89 RFQTMQQTSEWACGVTSALMVLNWYGelgdwNEKTLAALRHpLEGELAEypGTTLRQAMDIFDGVGgftYTTTLDQPeiw 168
Cdd:pfam03412   1 KYKIVLQVDENDCGLACLAMILKYYG-----SNVSLEELRE-LAGTPAE--GTSLLGLKKAAEKLG---FKAKAIKA--- 66

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1130939684 169 teDIRGWLAEGTPVMVCWNDWGGHWQVIVGYDtmgteseqDDVILVADP 217
Cdd:pfam03412  67 --DLSELKELPLPFIAHWDGNGGHFVVVYGIK--------KNKVLIADP 105
 
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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