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P29946

- CBIA_SALTY

UniProt

P29946 - CBIA_SALTY

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Protein

Cobyrinate a,c-diamide synthase

Gene

cbiA

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

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. Is able to use other nucleotide triphosphates as substrate, such as GTP or UTP, although less efficiently than ATP.1 PublicationUniRule annotation

Catalytic activityi

2 ATP + cobyrinate + 2 L-glutamine + 2 H2O = 2 ADP + 2 phosphate + cobyrinate a,c-diamide + 2 L-glutamate.1 PublicationUniRule annotation

Cofactori

Mg2+UniRule annotation

Kineticsi

kcat is 0.16 sec(-1)1 Publication

  1. KM=0.74 µM for cobyrinate1 Publication
  2. KM=2.7 µM for ATP1 Publication
  3. KM=53 µM for glutamine1 Publication
  4. KM=26200 µM for ammonia1 Publication

pH dependencei

The catalytic activity is essentially constant between pH 6.8 and 8.0.1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei334 – 3341NucleophileUniRule annotation
Sitei438 – 4381Increases nucleophilicity of active site CysUniRule annotation

GO - Molecular functioni

  1. cobalamin-transporting ATPase activity Source: UniProtKB-HAMAP
  2. cobyrinic acid a,c-diamide synthase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. cobalamin biosynthetic process Source: UniProtKB-HAMAP
  2. glutamine metabolic process Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Cobalamin biosynthesis

Keywords - Ligandi

ATP-binding, Magnesium, Nucleotide-binding

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-13217.
SENT99287:GCTI-2047-MONOMER.
SABIO-RKP29946.
UniPathwayiUPA00148; UER00231.

Names & Taxonomyi

Protein namesi
Recommended name:
Cobyrinate a,c-diamide synthaseCuratedUniRule annotation (EC:6.3.5.111 PublicationUniRule annotation)
Alternative name(s):
Cobyrinic acid a,c-diamide synthetase1 PublicationUniRule annotation
Cleaved into the following chain:
Gene namesi
Name:cbiA1 PublicationUniRule annotation
Ordered Locus Names:STM2035
OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Taxonomic identifieri99287 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
ProteomesiUP000001014: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi45 – 451D → N: Loss of amidation activity when glutamine is used as substrate, and 750-fold reduction in amidation activity whith ammonia as substrate. 1 Publication
Mutagenesisi46 – 461Y → A: 26-fold reduction in amidation activity with glutamine as substrate. The affinity for cobyrinate is nearly not affected whereas that for the c-monoamide intermediate decreases by 27-fold. 1 Publication
Mutagenesisi47 – 471L → A: 10-fold reduction in amidation activity with glutamine as substrate. The affinity for cobyrinate is nearly not affected whereas that for the c-monoamide intermediate decreases by 6-fold. 1 Publication
Mutagenesisi48 – 481D → N: 500-fold reduction in amidation activity with either glutamine or ammonia as substrate. 1 Publication
Mutagenesisi90 – 901E → Q: Loss of amidation activity with either glutamine or ammonia as substrate. 1 Publication
Mutagenesisi97 – 971D → N: 3-fold reduction in amidation activity with glutamine as substrate. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 459459Cobyrinate a,c-diamide synthasePRO_0000141269Add
BLAST
Initiator methioninei1 – 11Removed; alternate1 Publication
Chaini2 – 459458Cobyrinate a,c-diamide synthase, N-terminally processedPRO_0000430805Add
BLAST

Proteomic databases

PaxDbiP29946.
PRIDEiP29946.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

STRINGi99287.STM2035.

Structurei

3D structure databases

ProteinModelPortaliP29946.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini252 – 446195GATase 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.1 PublicationUniRule 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

eggNOGiCOG1797.
HOGENOMiHOG000289958.
KOiK02224.
OMAiVATYMHM.
OrthoDBiEOG6X6R8V.
PhylomeDBiP29946.

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.

Sequence processingi: The displayed sequence is further processed into a mature form.

P29946-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAARHHAFIL AGTGSGCGKT TVTLGLLRLL QKRALRVQPF KVGPDYLDTG
60 70 80 90 100
WHTAICGVAS RNLDSFMLPP PVLNALFCEQ MRQADIAVIE GVMGLYDGYG
110 120 130 140 150
VDPNYCSTAA MAKQLGCPVI LLVDGKAVST SLAATVMGFQ HFDPTLNLAG
160 170 180 190 200
VIVNRVTSDA HYQLLKNAIE HYCSLPVLGY VPPCDGVALP ERHLGLITAR
210 220 230 240 250
ESLVNQQSWH DFAATLEQTV DVDALLSLSV LSALPAGMWP ERPDNTAGAG
260 270 280 290 300
LTLALADDEA FNFYYPDNID LLERAGVNIV RFSPLHDRAL PDCQMIWLGG
310 320 330 340 350
GYPELYAADL AANTVMLKHL RAAHQRGVAI YAECGGLMYL GSTLEDSGGE
360 370 380 390 400
IHQMANIIPG HSKMGKRLTR FGYCEAQAMQ PTLLAAPGEI VRGHEFHYSD
410 420 430 440 450
FIPETPAVMA CRKVRDGRVL QEWTGGWQTG NTFASYLHVH FAQRPEMLQH

WLAAARRVL
Length:459
Mass (Da):50,037
Last modified:January 23, 2002 - v3
Checksum:iE1FEF1B5A37F5C14
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti36 – 361R → P in AAA27252. (PubMed:8501034)Curated
Sequence conflicti111 – 1111M → I in AAA27252. (PubMed:8501034)Curated
Sequence conflicti128 – 1281V → I in AAA27252. (PubMed:8501034)Curated
Sequence conflicti133 – 1331A → T in AAA27252. (PubMed:8501034)Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L12006 Genomic DNA. Translation: AAA27252.1.
AE006468 Genomic DNA. Translation: AAL20939.1.
X63012 Genomic DNA. Translation: CAA44740.1.
PIRiS20553.
RefSeqiNP_460980.1. NC_003197.1.

Genome annotation databases

EnsemblBacteriaiAAL20939; AAL20939; STM2035.
GeneIDi1253556.
KEGGistm:STM2035.
PATRICi32382653. VBISalEnt20916_2157.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L12006 Genomic DNA. Translation: AAA27252.1 .
AE006468 Genomic DNA. Translation: AAL20939.1 .
X63012 Genomic DNA. Translation: CAA44740.1 .
PIRi S20553.
RefSeqi NP_460980.1. NC_003197.1.

3D structure databases

ProteinModelPortali P29946.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 99287.STM2035.

Proteomic databases

PaxDbi P29946.
PRIDEi P29946.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAL20939 ; AAL20939 ; STM2035 .
GeneIDi 1253556.
KEGGi stm:STM2035.
PATRICi 32382653. VBISalEnt20916_2157.

Phylogenomic databases

eggNOGi COG1797.
HOGENOMi HOG000289958.
KOi K02224.
OMAi VATYMHM.
OrthoDBi EOG6X6R8V.
PhylomeDBi P29946.

Enzyme and pathway databases

UniPathwayi UPA00148 ; UER00231 .
BioCyci MetaCyc:MONOMER-13217.
SENT99287:GCTI-2047-MONOMER.
SABIO-RK P29946.

Family and domain databases

Gene3Di 3.40.50.300. 1 hit.
3.40.50.880. 1 hit.
HAMAPi MF_00027. CobB_CbiA.
InterProi IPR004484. 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 ]
Pfami PF01656. CbiA. 1 hit.
PF07685. GATase_3. 1 hit.
[Graphical view ]
SUPFAMi SSF52317. SSF52317. 1 hit.
SSF52540. SSF52540. 1 hit.
TIGRFAMsi TIGR00379. cobB. 1 hit.
PROSITEi PS51274. GATASE_COBBQ. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium."
    Roth J.R., Lawrence J.G., Rubenfield M., Kieffer-Higgins S., Church G.M.
    J. Bacteriol. 175:3303-3316(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: LT2.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: LT2 / SGSC1412 / ATCC 700720.
  3. "Cobalamin (vitamin B12) repression of the Cob operon in Salmonella typhimurium requires sequences within the leader and the first translated open reading frame."
    Richter-Dahlfors A.A., Andersson D.I.
    Mol. Microbiol. 6:743-749(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-106.
    Strain: LT2.
  4. "Mechanism of cobyrinic acid a,c-diamide synthetase from Salmonella typhimurium LT2."
    Fresquet V., Williams L., Raushel F.M.
    Biochemistry 43:10619-10627(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-7, FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, DOMAIN, REACTION MECHANISM, MUTAGENESIS OF ASP-45; TYR-46; LEU-47; ASP-48; GLU-90 AND ASP-97.
    Strain: LT2 / SGSC1412 / ATCC 700720.

Entry informationi

Entry nameiCBIA_SALTY
AccessioniPrimary (citable) accession number: P29946
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1993
Last sequence update: January 23, 2002
Last modified: November 26, 2014
This is version 105 of the entry and version 3 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.1 PublicationUniRule annotation

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3