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P80859

- 6PGD_BACSU

UniProt

P80859 - 6PGD_BACSU

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Protein
6-phosphogluconate dehydrogenase, NADP(+)-dependent, decarboxylating
Gene
gndA, yqjI, BSU23860
Organism
Bacillus subtilis (strain 168)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and CO2, with concomitant reduction of NADP to NADPH. Is the predominant 6-P-gluconate dehydrogenase isoenzyme in B.subtilis during growth on glucose and gluconate.1 Publication

Catalytic activityi

6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH.1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei102 – 1021NADP By similarity
Binding sitei102 – 1021Substrate By similarity
Active sitei182 – 1821Proton acceptor By similarity
Active sitei189 – 1891Proton donor By similarity
Binding sitei190 – 1901Substrate By similarity
Binding sitei260 – 2601Substrate; via amide nitrogen By similarity
Binding sitei287 – 2871Substrate By similarity
Binding sitei446 – 4461Substrate; shared with dimeric partner By similarity
Binding sitei452 – 4521Substrate; shared with dimeric partner By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi10 – 156NADP By similarity
Nucleotide bindingi33 – 353NADP By similarity
Nucleotide bindingi74 – 763NADP By similarity

GO - Molecular functioni

  1. NADP binding Source: InterPro
  2. phosphogluconate dehydrogenase (decarboxylating) activity Source: UniProtKB-EC

GO - Biological processi

  1. D-gluconate metabolic process Source: UniProtKB-KW
  2. pentose-phosphate shunt Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Gluconate utilization, Pentose shunt

Keywords - Ligandi

NADP

Enzyme and pathway databases

BioCyciBSUB:BSU23860-MONOMER.
MetaCyc:MONOMER-6842.
RETL1328306-WGS:GSTH-2489-MONOMER.
BRENDAi1.1.1.44. 700.
UniPathwayiUPA00115; UER00410.

Names & Taxonomyi

Protein namesi
Recommended name:
6-phosphogluconate dehydrogenase, NADP(+)-dependent, decarboxylating (EC:1.1.1.44)
Alternative name(s):
GNTZII
Gene namesi
Name:gndA
Synonyms:yqjI
Ordered Locus Names:BSU23860
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
ProteomesiUP000001570: Chromosome

Organism-specific databases

GenoListiBSU23860. [Micado]

Pathology & Biotechi

Disruption phenotypei

Cells lacking this gene exhibit a reduced growth on glucose as the sole carbon source, and they do not use the pentose phosphate (PP) pathway at all.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 4694686-phosphogluconate dehydrogenase, NADP(+)-dependent, decarboxylating
PRO_0000090027Add
BLAST

Proteomic databases

PaxDbiP80859.

Interactioni

Subunit structurei

Homodimer By similarity.

Protein-protein interaction databases

IntActiP80859. 1 interaction.
MINTiMINT-8364930.
STRINGi224308.BSU23860.

Structurei

3D structure databases

ProteinModelPortaliP80859.
SMRiP80859. Positions 1-469.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni128 – 1303Substrate binding By similarity
Regioni185 – 1862Substrate binding By similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0362.
HOGENOMiHOG000255147.
KOiK00033.
OMAiDKDGVFH.
OrthoDBiEOG6MSS4W.
PhylomeDBiP80859.

Family and domain databases

Gene3Di1.10.1040.10. 1 hit.
1.20.5.320. 1 hit.
3.40.50.720. 1 hit.
InterProiIPR008927. 6-PGluconate_DH_C-like.
IPR006114. 6PGDH_C.
IPR006113. 6PGDH_decarbox.
IPR006115. 6PGDH_NADP-bd.
IPR006184. 6PGdom_BS.
IPR013328. DH_multihelical.
IPR012284. Fibritin/6PGD_C-extension.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF00393. 6PGD. 1 hit.
PF03446. NAD_binding_2. 1 hit.
[Graphical view]
PIRSFiPIRSF000109. 6PGD. 1 hit.
SUPFAMiSSF48179. SSF48179. 1 hit.
TIGRFAMsiTIGR00873. gnd. 1 hit.
PROSITEiPS00461. 6PGD. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P80859-1 [UniParc]FASTAAdd to Basket

« Hide

MSKQQIGVIG LAVMGKNLAL NIESRGFSVS VYNRSSSKTE EFLQEAKGKN    50
VVGTYSIEEF VQSLETPRKI LLMVKAGTAT DATIQSLLPH LEKDDILIDG 100
GNTYYKDTQR RNKELAESGI HFIGTGVSGG EEGALKGPSI MPGGQKEAHE 150
LVKPILEAIS AKVDGEPCTT YIGPDGAGHY VKMVHNGIEY GDMQLISESY 200
FILKQVLGLS ADELHEVFAE WNKGELDSYL IEITADIFTK KDEETGKPLV 250
DVILDKAGQK GTGKWTSQSA LDLGVPLPII TESVFARFIS AMKEERVKAS 300
GLLSGPEVKP VTENKEELIE AVRKALFMSK ICSYAQGFAQ MKAASEEYNW 350
DLKYGEIAMI FRGGCIIRAA FLQKIKEAYD REPELDNLLL DSYFKNIVES 400
YQGALRQVIS LAVAQGVPVP SFSSALAYYD SYRTAVLPAN LIQAQRDYFG 450
AHTYERTDKE GIFHTEWMK 469
Length:469
Mass (Da):51,775
Last modified:January 23, 2007 - v4
Checksum:iD0A94E0B4F2250EF
GO

Sequence cautioni

The sequence BAA12615.1 differs from that shown. Reason: Frameshift at position 42.

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti11 – 111L → W AA sequence 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
D84432 Genomic DNA. Translation: BAA12615.1. Frameshift.
AL009126 Genomic DNA. Translation: CAB14318.2.
PIRiA69964.
RefSeqiNP_390267.2. NC_000964.3.

Genome annotation databases

EnsemblBacteriaiCAB14318; CAB14318; BSU23860.
GeneIDi938695.
KEGGibsu:BSU23860.
PATRICi18976597. VBIBacSub10457_2489.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
D84432 Genomic DNA. Translation: BAA12615.1 . Frameshift.
AL009126 Genomic DNA. Translation: CAB14318.2 .
PIRi A69964.
RefSeqi NP_390267.2. NC_000964.3.

3D structure databases

ProteinModelPortali P80859.
SMRi P80859. Positions 1-469.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

IntActi P80859. 1 interaction.
MINTi MINT-8364930.
STRINGi 224308.BSU23860.

Proteomic databases

PaxDbi P80859.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai CAB14318 ; CAB14318 ; BSU23860 .
GeneIDi 938695.
KEGGi bsu:BSU23860.
PATRICi 18976597. VBIBacSub10457_2489.

Organism-specific databases

GenoListi BSU23860. [Micado ]

Phylogenomic databases

eggNOGi COG0362.
HOGENOMi HOG000255147.
KOi K00033.
OMAi DKDGVFH.
OrthoDBi EOG6MSS4W.
PhylomeDBi P80859.

Enzyme and pathway databases

UniPathwayi UPA00115 ; UER00410 .
BioCyci BSUB:BSU23860-MONOMER.
MetaCyc:MONOMER-6842.
RETL1328306-WGS:GSTH-2489-MONOMER.
BRENDAi 1.1.1.44. 700.

Family and domain databases

Gene3Di 1.10.1040.10. 1 hit.
1.20.5.320. 1 hit.
3.40.50.720. 1 hit.
InterProi IPR008927. 6-PGluconate_DH_C-like.
IPR006114. 6PGDH_C.
IPR006113. 6PGDH_decarbox.
IPR006115. 6PGDH_NADP-bd.
IPR006184. 6PGdom_BS.
IPR013328. DH_multihelical.
IPR012284. Fibritin/6PGD_C-extension.
IPR016040. NAD(P)-bd_dom.
[Graphical view ]
Pfami PF00393. 6PGD. 1 hit.
PF03446. NAD_binding_2. 1 hit.
[Graphical view ]
PIRSFi PIRSF000109. 6PGD. 1 hit.
SUPFAMi SSF48179. SSF48179. 1 hit.
TIGRFAMsi TIGR00873. gnd. 1 hit.
PROSITEi PS00461. 6PGD. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Systematic sequencing of the 283 kb 210 degrees-232 degrees region of the Bacillus subtilis genome containing the skin element and many sporulation genes."
    Mizuno M., Masuda S., Takemaru K., Hosono S., Sato T., Takeuchi M., Kobayashi Y.
    Microbiology 142:3103-3111(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168 / JH642.
  2. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
    Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
    , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
    Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 168.
  3. "Detecting and analyzing DNA sequencing errors: toward a higher quality of the Bacillus subtilis genome sequence."
    Medigue C., Rose M., Viari A., Danchin A.
    Genome Res. 9:1116-1127(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: SEQUENCE REVISION.
  4. "First steps from a two-dimensional protein index towards a response-regulation map for Bacillus subtilis."
    Antelmann H., Bernhardt J., Schmid R., Mach H., Voelker U., Hecker M.
    Electrophoresis 18:1451-1463(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-14.
    Strain: 168 / IS58.
  5. "The Bacillus subtilis yqjI gene encodes the NADP+-dependent 6-P-gluconate dehydrogenase in the pentose phosphate pathway."
    Zamboni N., Fischer E., Laudert D., Aymerich S., Hohmann H.P., Sauer U.
    J. Bacteriol. 186:4528-4534(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, ROLE IN PP PATHWAY, GENE NAME, DISRUPTION PHENOTYPE.
    Strain: 168.

Entry informationi

Entry namei6PGD_BACSU
AccessioniPrimary (citable) accession number: P80859
Secondary accession number(s): P54546
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: January 23, 2007
Last modified: July 9, 2014
This is version 110 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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