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Protein

Sirohydrochlorin cobaltochelatase

Gene

cbiX

Organism
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the insertion of Co2+ into sirohydrochlorin as part of the anaerobic pathway to cobalamin biosynthesis.1 Publication

Catalytic activityi

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

Pathwayi: adenosylcobalamin biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes cob(II)yrinate a,c-diamide from sirohydrochlorin (anaerobic route).
Proteins known to be involved in the 10 steps of the subpathway in this organism are:
  1. Sirohydrochlorin cobaltochelatase (cbiX)
  2. no protein annotated in this organism
  3. Cobalamin biosynthesis protein CbiHC (cbiHC)
  4. no protein annotated in this organism
  5. no protein annotated in this organism
  6. Cobalt-precorrin-5B C(1)-methyltransferase (cbiD)
  7. no protein annotated in this organism
  8. Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) (cbiT)
  9. Cobalamin biosynthesis protein CbiHC (cbiHC)
  10. Cobyrinate a,c-diamide synthase (cbiA)
This subpathway is part of the pathway adenosylcobalamin biosynthesis, which is itself part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes cob(II)yrinate a,c-diamide from sirohydrochlorin (anaerobic route), the pathway adenosylcobalamin biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei10 – 101Proton acceptorSequence analysis
Metal bindingi10 – 101Cobalt
Binding sitei46 – 461Substrate
Metal bindingi74 – 741CobaltCurated

GO - Molecular functioni

  • cobalt ion binding Source: UniProtKB
  • sirohydrochlorin cobaltochelatase activity Source: UniProtKB
  • tetrapyrrole binding Source: UniProtKB

GO - Biological processi

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

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Cobalamin biosynthesis

Keywords - Ligandi

Cobalt, Metal-binding

Enzyme and pathway databases

BioCyciAFUL224325:GJBC-737-MONOMER.
BRENDAi4.99.1.3. 414.
UniPathwayiUPA00148; UER00223.

Names & Taxonomyi

Protein namesi
Recommended name:
Sirohydrochlorin cobaltochelatase (EC:4.99.1.3)
Alternative name(s):
CbiXS
Gene namesi
Name:cbiX
Ordered Locus Names:AF_0721
OrganismiArchaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Taxonomic identifieri224325 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaArchaeoglobiArchaeoglobalesArchaeoglobaceaeArchaeoglobus
Proteomesi
  • UP000002199 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 132132Sirohydrochlorin cobaltochelatasePRO_0000150353Add
BLAST

Interactioni

Subunit structurei

Homodimer or homotetramer.1 Publication

Protein-protein interaction databases

DIPiDIP-59586N.
STRINGi224325.AF0721.

Structurei

Secondary structure

1
132
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 97Combined sources
Helixi15 – 3117Combined sources
Beta strandi33 – 4311Combined sources
Helixi50 – 567Combined sources
Beta strandi60 – 667Combined sources
Beta strandi68 – 714Combined sources
Helixi73 – 764Combined sources
Helixi78 – 836Combined sources
Beta strandi88 – 903Combined sources
Beta strandi92 – 965Combined sources
Beta strandi99 – 1035Combined sources
Helixi111 – 12212Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1TJNX-ray2.01A1-132[»]
2DJ5X-ray2.55A/B1-132[»]
2XWQX-ray2.01A/B/C/D1-132[»]
2XWSX-ray1.60A1-132[»]
ProteinModelPortaliO29537.
SMRiO29537. Positions 1-125.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO29537.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni69 – 746Substrate binding

Sequence similaritiesi

Belongs to the CbiX family. CbiXS subfamily.Curated

Phylogenomic databases

eggNOGiarCOG02246. Archaea.
COG2138. LUCA.
KOiK03795.
OMAiVICDPIG.

Family and domain databases

HAMAPiMF_00785. CbiX.
InterProiIPR002762. Cbl_biosynth_CbiX.
IPR023652. SiroHydchlorin_Cochelatase.
[Graphical view]
PfamiPF01903. CbiX. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O29537-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRRGLVIVGH GSQLNHYREV MELHRKRIEE SGAFDEVKIA FAARKRRPMP
60 70 80 90 100
DEAIREMNCD IIYVVPLFIS YGLHVTEDLP DLLGFPRGRG IKEGEFEGKK
110 120 130
VVICEPIGED YFVTYAILNS VFRIGRDGKG EE
Length:132
Mass (Da):15,109
Last modified:January 1, 1998 - v1
Checksum:i61B97A773EC78BB7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000782 Genomic DNA. Translation: AAB90530.1.
PIRiA69340.
RefSeqiWP_010878224.1. NC_000917.1.

Genome annotation databases

EnsemblBacteriaiAAB90530; AAB90530; AF_0721.
GeneIDi24794319.
KEGGiafu:AF_0721.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000782 Genomic DNA. Translation: AAB90530.1.
PIRiA69340.
RefSeqiWP_010878224.1. NC_000917.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1TJNX-ray2.01A1-132[»]
2DJ5X-ray2.55A/B1-132[»]
2XWQX-ray2.01A/B/C/D1-132[»]
2XWSX-ray1.60A1-132[»]
ProteinModelPortaliO29537.
SMRiO29537. Positions 1-125.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-59586N.
STRINGi224325.AF0721.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB90530; AAB90530; AF_0721.
GeneIDi24794319.
KEGGiafu:AF_0721.

Phylogenomic databases

eggNOGiarCOG02246. Archaea.
COG2138. LUCA.
KOiK03795.
OMAiVICDPIG.

Enzyme and pathway databases

UniPathwayiUPA00148; UER00223.
BioCyciAFUL224325:GJBC-737-MONOMER.
BRENDAi4.99.1.3. 414.

Miscellaneous databases

EvolutionaryTraceiO29537.

Family and domain databases

HAMAPiMF_00785. CbiX.
InterProiIPR002762. Cbl_biosynth_CbiX.
IPR023652. SiroHydchlorin_Cochelatase.
[Graphical view]
PfamiPF01903. CbiX. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus."
    Klenk H.-P., Clayton R.A., Tomb J.-F., White O., Nelson K.E., Ketchum K.A., Dodson R.J., Gwinn M.L., Hickey E.K., Peterson J.D., Richardson D.L., Kerlavage A.R., Graham D.E., Kyrpides N.C., Fleischmann R.D., Quackenbush J., Lee N.H., Sutton G.G.
    , Gill S.R., Kirkness E.F., Dougherty B.A., McKenney K., Adams M.D., Loftus B.J., Peterson S.N., Reich C.I., McNeil L.K., Badger J.H., Glodek A., Zhou L., Overbeek R., Gocayne J.D., Weidman J.F., McDonald L.A., Utterback T.R., Cotton M.D., Spriggs T., Artiach P., Kaine B.P., Sykes S.M., Sadow P.W., D'Andrea K.P., Bowman C., Fujii C., Garland S.A., Mason T.M., Olsen G.J., Fraser C.M., Smith H.O., Woese C.R., Venter J.C.
    Nature 390:364-370(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126.
  2. "Crystal structure of the vitamin B12 biosynthetic cobaltochelatase, CbiXS, from Archaeoglobus fulgidus."
    Yin J., Xu L.X., Cherney M.M., Raux-Deery E., Bindley A.A., Savchenko A., Walker J.R., Cuff M.E., Warren M.J., James M.N.
    J. Struct. Funct. Genomics 7:37-50(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.01 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY, SUBUNIT.
  3. "Evolution in a family of chelatases facilitated by the introduction of active site asymmetry and protein oligomerization."
    Romao C.V., Ladakis D., Lobo S.A., Carrondo M.A., Brindley A.A., Deery E., Matias P.M., Pickersgill R.W., Saraiva L.M., Warren M.J.
    Proc. Natl. Acad. Sci. U.S.A. 108:97-102(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF NATIVE PROTEIN AND COMPLEX WITH COBALT-SIROHYDROCHLORIN.

Entry informationi

Entry nameiCBIX_ARCFU
AccessioniPrimary (citable) accession number: O29537
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2004
Last sequence update: January 1, 1998
Last modified: December 9, 2015
This is version 92 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.