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Protein

Hydrogenobyrinate a,c-diamide synthase

Gene

cobB

Organism
Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
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.UniRule annotation

Catalytic activityi

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

Cofactori

Mg2+UniRule annotation

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).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. 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 sitei372NucleophileUniRule annotation1
Sitei466Increases nucleophilicity of active site CysUniRule annotation1

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

UniPathwayiUPA00148; UER00220.

Names & Taxonomyi

Protein namesi
Recommended name:
Hydrogenobyrinate a,c-diamide synthaseUniRule annotation (EC:6.3.5.9UniRule annotation)
Alternative name(s):
Hydrogenobyrinic acid a,c-diamide synthaseUniRule annotation
Gene namesi
Name:cobBUniRule annotation
Ordered Locus Names:SCO1852
ORF Names:SCI8.37
OrganismiStreptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
Taxonomic identifieri100226 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaStreptomycetalesStreptomycetaceaeStreptomycesStreptomyces albidoflavus group
Proteomesi
  • UP000001973 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001412701 – 486Hydrogenobyrinate a,c-diamide synthaseAdd BLAST486

Interactioni

Protein-protein interaction databases

STRINGi100226.SCO1852.

Structurei

3D structure databases

ProteinModelPortaliQ9RJ16.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini289 – 474GATase cobBQ-typeUniRule annotationAdd BLAST186

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.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.
HOGENOMiHOG000289958.
InParanoidiQ9RJ16.
KOiK02224.
OMAiCWLPGGY.
OrthoDBiPOG091H0042.
PhylomeDBiQ9RJ16.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
3.40.50.880. 1 hit.
HAMAPiMF_00027. CobB_CbiA. 1 hit.
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.
PROSITEiPS51274. GATASE_COBBQ. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9RJ16-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTSSDSGSAV PRLVIAAPSS GSGKTTVATG LMAALTARGL AVSPHKVGPD
60 70 80 90 100
YIDPGYHALA TGRVGRNLDA YLCGPELVGP LFLHGARGCD IAVVEGVMGL
110 120 130 140 150
YDGAAGEGEL ASTAQVAKLL RAPVVLVVDA SSQSRSVAAL VHGFVSWDPE
160 170 180 190 200
VRIGGVILNK VASDRHEALL REAVDSVGVP VLGVLRRAAP VETPSRHLGL
210 220 230 240 250
VPVAERGSDA VDAVAAMGAR VADGCDLEAL VGLARSTGAL SCAAWDAGEA
260 270 280 290 300
LVSSPPPPLP VPSPGAAPPD PLVRPGRPRP QAPDGLRRRV AMASGAAFTF
310 320 330 340 350
SYAEHTELLA AAGAEVVTFD PLRDEELPEG TQGLVIGGGF PEVYASELSA
360 370 380 390 400
NEGLRKSVAE LAFSGAPVAA ECAGLLYLCR ELDGLPMCGV LDAAARMSKR
410 420 430 440 450
LTLGYRDAVA VSDSALAVAG TRMRGHEFHR TVVEPGAGAA PAWGMRAPER
460 470 480
RVEGFVERGV HASYLHTHWA AEPGVARRFV ERCRTS
Length:486
Mass (Da):50,069
Last modified:May 1, 2000 - v1
Checksum:iDB9F4343780CD2B0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL939110 Genomic DNA. Translation: CAB59468.1.
RefSeqiNP_626120.1. NC_003888.3.
WP_011028009.1. NC_003888.3.

Genome annotation databases

EnsemblBacteriaiCAB59468; CAB59468; CAB59468.
GeneIDi1097286.
KEGGisco:SCO1852.
PATRICi23733332. VBIStrCoe124346_1876.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL939110 Genomic DNA. Translation: CAB59468.1.
RefSeqiNP_626120.1. NC_003888.3.
WP_011028009.1. NC_003888.3.

3D structure databases

ProteinModelPortaliQ9RJ16.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi100226.SCO1852.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB59468; CAB59468; CAB59468.
GeneIDi1097286.
KEGGisco:SCO1852.
PATRICi23733332. VBIStrCoe124346_1876.

Phylogenomic databases

eggNOGiENOG4105C0Y. Bacteria.
COG1797. LUCA.
HOGENOMiHOG000289958.
InParanoidiQ9RJ16.
KOiK02224.
OMAiCWLPGGY.
OrthoDBiPOG091H0042.
PhylomeDBiQ9RJ16.

Enzyme and pathway databases

UniPathwayiUPA00148; UER00220.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
3.40.50.880. 1 hit.
HAMAPiMF_00027. CobB_CbiA. 1 hit.
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.
PROSITEiPS51274. GATASE_COBBQ. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiCOBB_STRCO
AccessioniPrimary (citable) accession number: Q9RJ16
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 23, 2003
Last sequence update: May 1, 2000
Last modified: September 7, 2016
This is version 86 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 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.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.