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Protein

Cobyrinate a,c-diamide synthase

Gene

cbiA

Organism
Pelobacter carbinolicus (strain DSM 2380 / Gra Bd 1)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Catalyzes the ATP-dependent amidation of the two carboxylate groups at positions a and c of cobyrinate, using either L-glutamine or ammonia as the nitrogen source.UniRule annotation

Catalytic activityi

2 ATP + cobyrinate + 2 L-glutamine + 2 H2O = 2 ADP + 2 phosphate + cobyrinate a,c-diamide + 2 L-glutamate.UniRule annotation

Cofactori

Mg2+UniRule annotation

Pathwayi: adenosylcobalamin biosynthesis

This protein is involved in step 10 of the subpathway that synthesizes cob(II)yrinate a,c-diamide from sirohydrochlorin (anaerobic route).UniRule annotation
Proteins known to be involved in the 10 steps of the subpathway in this organism are:
  1. no protein annotated in this organism
  2. no protein annotated in this organism
  3. no protein annotated in this organism
  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. no protein annotated in this organism
  9. no protein annotated in this organism
  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 sitei332 – 3321NucleophileUniRule annotation
Sitei438 – 4381Increases nucleophilicity of active site CysUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Cobalamin biosynthesis

Keywords - Ligandi

ATP-binding, Magnesium, Nucleotide-binding

Enzyme and pathway databases

BioCyciPCAR338963:GKDU-544-MONOMER.
UniPathwayiUPA00148; UER00231.

Names & Taxonomyi

Protein namesi
Recommended name:
Cobyrinate a,c-diamide synthaseUniRule annotation (EC:6.3.5.11UniRule annotation)
Alternative name(s):
Cobyrinic acid a,c-diamide synthetaseUniRule annotation
Gene namesi
Name:cbiAUniRule annotation
Ordered Locus Names:Pcar_0481
OrganismiPelobacter carbinolicus (strain DSM 2380 / Gra Bd 1)
Taxonomic identifieri338963 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfuromonadalesDesulfuromonadaceaePelobacter
Proteomesi
  • UP000002534 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 459459Cobyrinate a,c-diamide synthasePRO_1000002295Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi338963.Pcar_0481.

Structurei

3D structure databases

ProteinModelPortaliQ3A7A3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini249 – 446198GATase cobBQ-typeUniRule annotationAdd
BLAST

Domaini

Comprises of two domains. The C-terminal domain contains the binding site for glutamine and catalyzes the hydrolysis of this substrate to glutamate and ammonia. The N-terminal domain is anticipated to bind ATP and cobyrinate and catalyzes the ultimate synthesis of the diamide product. The ammonia produced via the glutaminase domain is probably translocated to the adjacent domain via a molecular tunnel, where it reacts with an activated intermediate.UniRule annotation

Sequence similaritiesi

Belongs to the CobB/CbiA family.UniRule annotation
Contains 1 GATase cobBQ-type domain.UniRule annotation

Keywords - Domaini

Glutamine amidotransferase

Phylogenomic databases

eggNOGiENOG4105C0Y. Bacteria.
COG1797. LUCA.
HOGENOMiHOG000289959.
KOiK02224.
OMAiCWLPGGY.
OrthoDBiEOG6X6R8V.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
3.40.50.880. 1 hit.
HAMAPiMF_00027. CobB_CbiA.
InterProiIPR004484. CbiA_synth.
IPR029062. Class_I_gatase-like.
IPR017929. CobB/CobQ_GATase.
IPR002586. CobQ/CobB/MinD/ParA_Nub-bd_dom.
IPR011698. GATase_3.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF01656. CbiA. 1 hit.
PF07685. GATase_3. 1 hit.
[Graphical view]
SUPFAMiSSF52317. SSF52317. 1 hit.
SSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00379. cobB. 1 hit.
PROSITEiPS51274. GATASE_COBBQ. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q3A7A3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSCPRLVIAG TSSGAGKTSL TLGLTAALRR RGLKVQTFKV GPDFLDPTWL
60 70 80 90 100
SLASERPCIN LDGWMCGERY VRDRFATATA DADIAIVEGV MGLFDGADPA
110 120 130 140 150
AAAGSTAEIA RWLDAPVLLV VNAHGMARSL AALVKGYAEF DPDLHLAGVI
160 170 180 190 200
ANRCGSTRHG DWLSEALCAA GMPPLTGTVI RDSLPPLPSR HLGLVTADRQ
210 220 230 240 250
HLTSEALNTL ADAVERQLDM PRILDLAEKV PATPGVAATA SSTEGRPVRI
260 270 280 290 300
GMAFDEAFHF YYPDNLQALE DAGATLVRFS PMHDDTLPAD LDALLLGGGY
310 320 330 340 350
PEEYADTLET NQTMRQAVAD FAAADRPIYA ECGGLMYLSE GIELRDGSRH
360 370 380 390 400
AMTGALPFAT RMLATRKRLG YAEVRHLAHG PFGPAGTCLR GHEFHYSEAI
410 420 430 440 450
AEPAAPGWQS AWQVSYRRSN KPVAEGYQRG RLFASYVHTH FASRPGAARA

FVDFCRGES
Length:459
Mass (Da):49,296
Last modified:November 22, 2005 - v1
Checksum:i11707DAADC429945
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000142 Genomic DNA. Translation: ABA87741.1.
RefSeqiWP_011340166.1. NC_007498.2.

Genome annotation databases

EnsemblBacteriaiABA87741; ABA87741; Pcar_0481.
KEGGipca:Pcar_0481.
PATRICi22886910. VBIPelCar86875_0530.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000142 Genomic DNA. Translation: ABA87741.1.
RefSeqiWP_011340166.1. NC_007498.2.

3D structure databases

ProteinModelPortaliQ3A7A3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi338963.Pcar_0481.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABA87741; ABA87741; Pcar_0481.
KEGGipca:Pcar_0481.
PATRICi22886910. VBIPelCar86875_0530.

Phylogenomic databases

eggNOGiENOG4105C0Y. Bacteria.
COG1797. LUCA.
HOGENOMiHOG000289959.
KOiK02224.
OMAiCWLPGGY.
OrthoDBiEOG6X6R8V.

Enzyme and pathway databases

UniPathwayiUPA00148; UER00231.
BioCyciPCAR338963:GKDU-544-MONOMER.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
3.40.50.880. 1 hit.
HAMAPiMF_00027. CobB_CbiA.
InterProiIPR004484. CbiA_synth.
IPR029062. Class_I_gatase-like.
IPR017929. CobB/CobQ_GATase.
IPR002586. CobQ/CobB/MinD/ParA_Nub-bd_dom.
IPR011698. GATase_3.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF01656. CbiA. 1 hit.
PF07685. GATase_3. 1 hit.
[Graphical view]
SUPFAMiSSF52317. SSF52317. 1 hit.
SSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00379. cobB. 1 hit.
PROSITEiPS51274. GATASE_COBBQ. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Complete sequence of Pelobacter carbinolicus DSM 2380."
    Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T., Hammon N., Israni S., Pitluck S., Chertkov O., Schmutz J., Larimer F., Land M., Kyrpides N., Ivanova N., Richardson P.
    Submitted (OCT-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DSM 2380 / Gra Bd 1.

Entry informationi

Entry nameiCBIA_PELCD
AccessioniPrimary (citable) accession number: Q3A7A3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: November 22, 2005
Last modified: June 8, 2016
This is version 70 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The a and c carboxylates of cobyrinate are activated for nucleophilic attack via formation of a phosphorylated intermediate by ATP. CbiA catalyzes first the amidation of the c-carboxylate, and then that of the a-carboxylate.UniRule annotation

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  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.