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Protein

Sirohydrochlorin cobaltochelatase CbiKP

Gene

cbiKp

Organism
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the insertion of Co2+ into sirohydrochlorin. To a lesser extent, is also able to insert Fe2+ into sirohydrochlorin, yielding siroheme. Its periplasmic location means that it cannot participate in cobalamin biosynthesis and its genomic environment suggests it is likely to be associated with a heme or metal transport system.1 Publication

Catalytic activityi

Cobalt-sirohydrochlorin + 2 H+ = sirohydrochlorin + Co2+.1 Publication
Siroheme + 2 H+ = sirohydrochlorin + Fe2+.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei45SubstrateBy similarity1
Metal bindingi124Iron (heme axial ligand); shared with dimeric partner1
Active sitei182Proton acceptorSequence analysis1
Metal bindingi182Cobalt1
Metal bindingi212Cobalt1
Metal bindingi244Cobalt1
Binding sitei244SubstrateBy similarity1

GO - Molecular functioni

  • cobalt ion binding Source: UniProtKB
  • heme binding Source: UniProtKB
  • sirohydrochlorin cobaltochelatase activity Source: UniProtKB
  • sirohydrochlorin ferrochelatase activity Source: UniProtKB

GO - Biological processi

  • anaerobic cobalamin biosynthetic process Source: InterPro
  • protein tetramerization Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

Heme, Iron, Metal-binding

Enzyme and pathway databases

BRENDAi4.99.1.3. 1914.

Names & Taxonomyi

Protein namesi
Recommended name:
Sirohydrochlorin cobaltochelatase CbiKP (EC:4.99.1.3)
Alternative name(s):
Sirohydrochlorin ferrochelatase CbiKP (EC:4.99.1.4)
Gene namesi
Name:cbiKp
Ordered Locus Names:DVU_0650
OrganismiDesulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)
Taxonomic identifieri882 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
Proteomesi
  • UP000002194 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

  • periplasmic space Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 28PROSITE-ProRule annotation1 PublicationAdd BLAST28
ChainiPRO_000040798529 – 297Sirohydrochlorin cobaltochelatase CbiKPAdd BLAST269

Proteomic databases

PaxDbiQ72EC8.

Interactioni

Subunit structurei

Homotetramer; dimer of dimers.1 Publication

Protein-protein interaction databases

DIPiDIP-59587N.
STRINGi882.DVU0650.

Structurei

Secondary structure

1297
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi38 – 44Combined sources7
Turni50 – 53Combined sources4
Helixi54 – 66Combined sources13
Beta strandi72 – 77Combined sources6
Helixi79 – 87Combined sources9
Helixi95 – 104Combined sources10
Beta strandi109 – 114Combined sources6
Beta strandi117 – 120Combined sources4
Helixi121 – 133Combined sources13
Beta strandi141 – 146Combined sources6
Helixi153 – 166Combined sources14
Beta strandi177 – 181Combined sources5
Helixi187 – 190Combined sources4
Helixi191 – 200Combined sources10
Beta strandi206 – 215Combined sources10
Helixi217 – 227Combined sources11
Beta strandi230 – 240Combined sources11
Helixi243 – 246Combined sources4
Turni247 – 250Combined sources4
Helixi257 – 263Combined sources7
Beta strandi267 – 270Combined sources4
Helixi275 – 277Combined sources3
Helixi279 – 294Combined sources16

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2XVXX-ray1.90A29-297[»]
2XVYX-ray1.70A29-297[»]
2XVZX-ray2.40A29-297[»]
ProteinModelPortaliQ72EC8.
SMRiQ72EC8.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ72EC8.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni117 – 125Substrate bindingBy similarity9
Regioni239 – 240Substrate bindingBy similarity2

Sequence similaritiesi

Belongs to the CbiK family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4107PPM. Bacteria.
COG4822. LUCA.
KOiK02190.
OMAiIEACEKR.
OrthoDBiPOG091H01X9.
PhylomeDBiQ72EC8.

Family and domain databases

InterProiIPR010388. Anaerobic_Co-chelatase.
[Graphical view]
PfamiPF06180. CbiK. 1 hit.
[Graphical view]
PIRSFiPIRSF033579. Anaer_Co_chel. 1 hit.
PROSITEiPS51257. PROKAR_LIPOPROTEIN. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q72EC8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSRHPMVTRL LCLVFSCLII LACSPAFAGH GAPKAQKTGI LLVAFGTSVE
60 70 80 90 100
EARPALDKMG DRVRAAHPDI PVRWAYTAKM IRAKLRAEGI AAPSPAEALA
110 120 130 140 150
GMAEEGFTHV AVQSLHTIPG EEFHGLLETA HAFQGLPKGL TRVSVGLPLI
160 170 180 190 200
GTTADAEAVA EALVASLPAD RKPGEPVVFM GHGTPHPADI CYPGLQYYLW
210 220 230 240 250
RLDPDLLVGT VEGSPSFDNV MAELDVRKAK RVWLMPLMAV AGDHARNDMA
260 270 280 290
GDEDDSWTSQ LARRGIEAKP VLHGTAESDA VAAIWLRHLD DALARLN
Length:297
Mass (Da):31,807
Last modified:July 5, 2004 - v1
Checksum:iEB6947A9C176295A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE017285 Genomic DNA. Translation: AAS95131.1.
RefSeqiWP_010937953.1. NC_002937.3.
YP_009872.1. NC_002937.3.

Genome annotation databases

EnsemblBacteriaiAAS95131; AAS95131; DVU_0650.
GeneIDi2795040.
KEGGidvu:DVU0650.
PATRICi32061234. VBIDesVul119526_0607.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE017285 Genomic DNA. Translation: AAS95131.1.
RefSeqiWP_010937953.1. NC_002937.3.
YP_009872.1. NC_002937.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2XVXX-ray1.90A29-297[»]
2XVYX-ray1.70A29-297[»]
2XVZX-ray2.40A29-297[»]
ProteinModelPortaliQ72EC8.
SMRiQ72EC8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-59587N.
STRINGi882.DVU0650.

Proteomic databases

PaxDbiQ72EC8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAS95131; AAS95131; DVU_0650.
GeneIDi2795040.
KEGGidvu:DVU0650.
PATRICi32061234. VBIDesVul119526_0607.

Phylogenomic databases

eggNOGiENOG4107PPM. Bacteria.
COG4822. LUCA.
KOiK02190.
OMAiIEACEKR.
OrthoDBiPOG091H01X9.
PhylomeDBiQ72EC8.

Enzyme and pathway databases

BRENDAi4.99.1.3. 1914.

Miscellaneous databases

EvolutionaryTraceiQ72EC8.

Family and domain databases

InterProiIPR010388. Anaerobic_Co-chelatase.
[Graphical view]
PfamiPF06180. CbiK. 1 hit.
[Graphical view]
PIRSFiPIRSF033579. Anaer_Co_chel. 1 hit.
PROSITEiPS51257. PROKAR_LIPOPROTEIN. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiCBIKP_DESVH
AccessioniPrimary (citable) accession number: Q72EC8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 3, 2011
Last sequence update: July 5, 2004
Last modified: November 2, 2016
This is version 72 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Binds 1 heme b (iron-protoporphyrin IX) group per dimer, which is not required for chelatase activity but may be linked to the putative transport function.
Desulfovibrio vulgaris possesses two versions of CbiK encoded within the genome, one cytoplasmic (CbiKC) and one periplasmic (CbiKP).

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.