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Protein

Cobalt-precorrin-4 C(11)-methyltransferase

Gene

cbiF

Organism
Bacillus megaterium
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the methylation of C-11 in cobalt-precorrin-4 to form cobalt-precorrin-5A.1 Publication

Catalytic activityi

S-adenosyl-L-methionine + cobalt-precorrin-4 = S-adenosyl-L-homocysteine + cobalt-precorrin-5A.1 Publication

Pathwayi: adenosylcobalamin biosynthesis

This protein is involved in step 4 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. no protein annotated in this organism
  4. Cobalt-precorrin-4 C(11)-methyltransferase (cbiF)
  5. Cobalt-precorrin-5A hydrolase (cbiG)
  6. Cobalt-precorrin-5B C(1)-methyltransferase (cbiD), Cobalt-precorrin-5B C(1)-methyltransferase (cbiD)
  7. Cobalt-precorrin-6A reductase (cbiJ)
  8. Cobalamin biosynthesis bifunctional protein CbiET (cbiET)
  9. Cobalt-precorrin-8 methylmutase (cbiC)
  10. Cobyrinate a,c-diamide synthase (cbiA), 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.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

Cobalamin biosynthesis

Keywords - Ligandi

S-adenosyl-L-methionine

Enzyme and pathway databases

BRENDAi2.1.1.271. 656.
UniPathwayiUPA00148; UER00226.

Names & Taxonomyi

Protein namesi
Recommended name:
Cobalt-precorrin-4 C(11)-methyltransferase (EC:2.1.1.271)
Alternative name(s):
Cobalt-precorrin-3 methylase
Gene namesi
Name:cbiF
OrganismiBacillus megaterium
Taxonomic identifieri1404 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 258258Cobalt-precorrin-4 C(11)-methyltransferasePRO_0000150392Add
BLAST

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

STRINGi545693.BMQ_2612.

Structurei

Secondary structure

258
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi1 – 77Combined sources
Beta strandi9 – 113Combined sources
Helixi13 – 153Combined sources
Helixi18 – 269Combined sources
Beta strandi28 – 325Combined sources
Turni34 – 363Combined sources
Helixi39 – 424Combined sources
Beta strandi50 – 534Combined sources
Helixi59 – 7012Combined sources
Turni71 – 733Combined sources
Beta strandi76 – 827Combined sources
Turni84 – 874Combined sources
Helixi91 – 999Combined sources
Beta strandi103 – 1075Combined sources
Helixi112 – 1198Combined sources
Turni127 – 1293Combined sources
Beta strandi133 – 1375Combined sources
Beta strandi140 – 1423Combined sources
Helixi146 – 1483Combined sources
Helixi150 – 1545Combined sources
Beta strandi158 – 1647Combined sources
Helixi166 – 1683Combined sources
Helixi169 – 17810Combined sources
Beta strandi186 – 1927Combined sources
Beta strandi199 – 2046Combined sources
Helixi205 – 2073Combined sources
Helixi208 – 2147Combined sources
Beta strandi219 – 2268Combined sources
Helixi227 – 2293Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CBFX-ray2.40A1-250[»]
2CBFX-ray3.10A1-231[»]
ProteinModelPortaliO87696.
SMRiO87696. Positions 1-231.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO87696.

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi115 – 1228Poly-Ala
Compositional biasi187 – 1904Poly-Val

Sequence similaritiesi

Belongs to the precorrin methyltransferase family.Curated

Phylogenomic databases

eggNOGiENOG4105CIA. Bacteria.
COG2875. LUCA.

Family and domain databases

Gene3Di3.30.950.10. 1 hit.
3.40.1010.10. 1 hit.
InterProiIPR000878. 4pyrrol_Mease.
IPR014777. 4pyrrole_Mease_sub1.
IPR014776. 4pyrrole_Mease_sub2.
IPR006362. Cbl_synth_CobM/CibF.
IPR003043. Uropor_MeTrfase_CS.
[Graphical view]
PfamiPF00590. TP_methylase. 1 hit.
[Graphical view]
SUPFAMiSSF53790. SSF53790. 1 hit.
TIGRFAMsiTIGR01465. cobM_cbiF. 1 hit.
PROSITEiPS00839. SUMT_1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O87696-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKLYIIGAGP GDPDLITVKG LKLLQQADVV LYADSLVSQD LIAKSKPGAE
60 70 80 90 100
VLKTAGMHLE EMVGTMLDRM REGKMVVRVH TGDPAMYGAI MEQMVLLKRE
110 120 130 140 150
GVDIEIVPGV TSVFAAAAAA EAELTIPDLT QTVILTRAEG RTPVPEFEKL
160 170 180 190 200
TDLAKHKCTI ALFLSATLTK KVMKEFINAG WSEDTPVVVV YKATWPDEKI
210 220 230 240 250
VRTTVKDLDD AMRTNGIRKQ AMILAGWALD PHIHDKDYRS KLYDKTFTHG

FRKGVKSE
Length:258
Mass (Da):28,452
Last modified:November 1, 1998 - v1
Checksum:i59C2E7FF9FAF1D03
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ000758 Genomic DNA. Translation: CAA04314.1.
PIRiT44690.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ000758 Genomic DNA. Translation: CAA04314.1.
PIRiT44690.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CBFX-ray2.40A1-250[»]
2CBFX-ray3.10A1-231[»]
ProteinModelPortaliO87696.
SMRiO87696. Positions 1-231.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi545693.BMQ_2612.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4105CIA. Bacteria.
COG2875. LUCA.

Enzyme and pathway databases

UniPathwayiUPA00148; UER00226.
BRENDAi2.1.1.271. 656.

Miscellaneous databases

EvolutionaryTraceiO87696.

Family and domain databases

Gene3Di3.30.950.10. 1 hit.
3.40.1010.10. 1 hit.
InterProiIPR000878. 4pyrrol_Mease.
IPR014777. 4pyrrole_Mease_sub1.
IPR014776. 4pyrrole_Mease_sub2.
IPR006362. Cbl_synth_CobM/CibF.
IPR003043. Uropor_MeTrfase_CS.
[Graphical view]
PfamiPF00590. TP_methylase. 1 hit.
[Graphical view]
SUPFAMiSSF53790. SSF53790. 1 hit.
TIGRFAMsiTIGR01465. cobM_cbiF. 1 hit.
PROSITEiPS00839. SUMT_1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Cobalamin (vitamin B12) biosynthesis: identification and characterization of a Bacillus megaterium cobI operon."
    Raux E., Lanois A., Warren M.J., Rambach A., Thermes C.
    Biochem. J. 335:159-166(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: DSM 509 / NBRC 12109.
  2. "Elucidation of the anaerobic pathway for the corrin component of cobalamin (vitamin B12)."
    Moore S.J., Lawrence A.D., Biedendieck R., Deery E., Frank S., Howard M.J., Rigby S.E., Warren M.J.
    Proc. Natl. Acad. Sci. U.S.A. 110:14906-14911(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY.
  3. "Cobalamin (vitamin B12) biosynthesis -- cloning, expression and crystallisation of the Bacillus megaterium S-adenosyl-L-methionine-dependent cobalt-precorrin-4 transmethylase CbiF."
    Raux E., Schubert H.L., Woodcock S.C., Wilson K.S., Warren M.J.
    Eur. J. Biochem. 254:341-346(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).

Entry informationi

Entry nameiCBIF_BACME
AccessioniPrimary (citable) accession number: O87696
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2004
Last sequence update: November 1, 1998
Last modified: November 11, 2015
This is version 82 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

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.