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Protein

Hydrogenobyrinate a,c-diamide synthase

Gene

cobB

Organism
Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094)
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 hydrogenobyrinate, using either L-glutamine or ammonia as the nitrogen source.

Miscellaneous

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

Catalytic activityi

2 ATP + hydrogenobyrinic acid + 2 L-glutamine + 2 H2O = 2 ADP + 2 phosphate + hydrogenobyrinic acid a,c-diamide + 2 L-glutamate.

Cofactori

Mg2+

Pathwayi: adenosylcobalamin biosynthesis

This protein is involved in step 9 of the subpathway that synthesizes cob(II)yrinate a,c-diamide from precorrin-2 (aerobic route).
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. no protein annotated in this organism
  7. no protein annotated in this organism
  8. no protein annotated in this organism
  9. Hydrogenobyrinate a,c-diamide synthase (cobB)
  10. no protein annotated in this organism
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 precorrin-2 (aerobic route), the pathway adenosylcobalamin biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei327Nucleophile1
Sitei427Increases nucleophilicity of active site Cys1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionLigase
Biological processCobalamin biosynthesis
LigandATP-binding, Magnesium, Nucleotide-binding

Enzyme and pathway databases

UniPathwayiUPA00148; UER00220.

Names & Taxonomyi

Protein namesi
Recommended name:
Hydrogenobyrinate a,c-diamide synthase (EC:6.3.5.9)
Alternative name(s):
Hydrogenobyrinic acid a,c-diamide synthase
Gene namesi
Name:cobB
Ordered Locus Names:BMEI0705
OrganismiBrucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094)
Taxonomic identifieri224914 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBrucellaceaeBrucella
Proteomesi
  • UP000000419 Componenti: Chromosome I

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001412551 – 436Hydrogenobyrinate a,c-diamide synthaseAdd BLAST436

Interactioni

Protein-protein interaction databases

STRINGi224914.BAWG_2678.

Structurei

3D structure databases

ProteinModelPortaliQ8YHU1.
SMRiQ8YHU1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini244 – 435GATase cobBQ-typeAdd BLAST192

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 hydrogenobyrinate 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.

Sequence similaritiesi

Belongs to the CobB/CbiA family.

Keywords - Domaini

Glutamine amidotransferase

Phylogenomic databases

eggNOGiENOG4105C0Y. Bacteria.
COG1797. LUCA.
HOGENOMiHOG000289959.
KOiK02224.
OMAiQPFKCGP.

Family and domain databases

Gene3Di3.40.50.880. 1 hit.
HAMAPiMF_00027. CobB_CbiA. 1 hit.
InterProiView protein in InterPro
IPR004484. CbiA_synth.
IPR029062. Class_I_gatase-like.
IPR017929. CobB/CobQ_GATase.
IPR011698. GATase_3.
IPR027417. P-loop_NTPase.
PANTHERiPTHR43873. PTHR43873. 1 hit.
PfamiView protein in Pfam
PF07685. GATase_3. 1 hit.
SUPFAMiSSF52317. SSF52317. 1 hit.
SSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00379. cobB. 1 hit.
PROSITEiView protein in PROSITE
PS51274. GATASE_COBBQ. 1 hit.

Sequencei

Sequence statusi: Complete.

Q8YHU1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKGFMIAAPA SGSGKTTVTL GLLRALKRRG EVLAPVKAGP DYIDPAYHRA
60 70 80 90 100
ASGVDCFNLD PWAMRPELIS ALSSRMTESG ARVLVAEGMM GLFDGAIDGK
110 120 130 140 150
GSSADLARLL DLPVVLVVDC ARQSHSIAAL VWGFSQFRKD VLIEGVILNR
160 170 180 190 200
VGSPRHEAML RGALAPLGVP VLGALPRDPA LSLPERHLGL VQADEHAGLE
210 220 230 240 250
SFLEQAADVM EAHIDMDALQ TIWLRPKRYD AMANVARLKP LGNRIAVARD
260 270 280 290 300
DAFAFAYMHL FEGWRRRGAE ISFFSPLADE APKADADAIY LPGGYPELHA
310 320 330 340 350
QRLAGASRFR TAIGDAAARG VTVYGECGGY MVLGKTLEDA AGVHHPMLGL
360 370 380 390 400
LPLETSFARR KLHLGYRLLE PLGGLPWDMP LKAHEFHYAS IVREEKADRL
410 420 430
FRVRDASGEN LGEAGLRVGS VSGSFMHVID FSGEAA
Length:436
Mass (Da):47,034
Last modified:March 1, 2002 - v1
Checksum:iAED85D8A1549862B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE008917 Genomic DNA. Translation: AAL51886.1.
PIRiAC3340.
RefSeqiWP_002964414.1. NZ_GG703780.1.

Genome annotation databases

EnsemblBacteriaiAAL51886; AAL51886; BMEI0705.
GeneIDi29593498.
KEGGibme:BMEI0705.
bmel:DK63_722.
PATRICifig|224914.52.peg.755.

Similar proteinsi

Entry informationi

Entry nameiCOBB_BRUME
AccessioniPrimary (citable) accession number: Q8YHU1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 23, 2003
Last sequence update: March 1, 2002
Last modified: June 7, 2017
This is version 86 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome

Documents

  1. Brucella melitensis
    Brucella melitensis (strain 16M): entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families