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Protein

6-phosphogluconate dehydrogenase, decarboxylating

Gene

gnd

Organism
Synechococcus sp. (strain JA-2-3B'a(2-13)) (Cyanobacteria bacterium Yellowstone B-Prime)
Status
Unreviewed-Annotation score: -Protein inferred from homologyi

Functioni

Catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and CO2, with concomitant reduction of NADP to NADPH.UniRule annotation

Catalytic activityi

6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH.UniRule annotation

Pathwayi: pentose phosphate pathway

This protein is involved in step 3 of the subpathway that synthesizes D-ribulose 5-phosphate from D-glucose 6-phosphate (oxidative stage).UniRule annotation
Proteins known to be involved in the 3 steps of the subpathway in this organism are:
  1. Glucose-6-phosphate 1-dehydrogenase (zwf)
  2. no protein annotated in this organism
  3. 6-phosphogluconate dehydrogenase, decarboxylating (gnd)
This subpathway is part of the pathway pentose phosphate pathway, which is itself part of Carbohydrate degradation.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes D-ribulose 5-phosphate from D-glucose 6-phosphate (oxidative stage), the pathway pentose phosphate pathway and in Carbohydrate degradation.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei103NADPUniRule annotation1
Binding sitei103SubstrateUniRule annotation1
Active sitei183Proton acceptorUniRule annotation1
Active sitei190Proton donorUniRule annotation1
Binding sitei191SubstrateUniRule annotation1
Binding sitei261Substrate; via amide nitrogenUniRule annotation1
Binding sitei288SubstrateUniRule annotation1
Binding sitei446Substrate; shared with dimeric partnerUniRule annotation1
Binding sitei452Substrate; shared with dimeric partnerUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi10 – 15NADPUniRule annotation6
Nucleotide bindingi33 – 35NADPUniRule annotation3
Nucleotide bindingi75 – 77NADPUniRule annotation3

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionOxidoreductaseUniRule annotationImported
Biological processGluconate utilizationUniRule annotation, Pentose shuntUniRule annotation
LigandNADPUniRule annotation

Enzyme and pathway databases

BioCyciSSP321332:G1G5P-2374-MONOMER
UniPathwayiUPA00115; UER00410

Names & Taxonomyi

Protein namesi
Recommended name:
6-phosphogluconate dehydrogenase, decarboxylatingUniRule annotation (EC:1.1.1.44UniRule annotation)
Gene namesi
Name:gndImported
Ordered Locus Names:CYB_2481Imported
OrganismiSynechococcus sp. (strain JA-2-3B'a(2-13)) (Cyanobacteria bacterium Yellowstone B-Prime)Imported
Taxonomic identifieri321332 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaSynechococcalesSynechococcaceaeSynechococcus
Proteomesi
  • UP000001938 Componenti: Chromosome

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi321332.CYB_2481

Structurei

3D structure databases

ProteinModelPortaliQ2JIY1
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini179 – 4686PGDInterPro annotationAdd BLAST290

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni129 – 131Substrate bindingUniRule annotation3
Regioni186 – 187Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the 6-phosphogluconate dehydrogenase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C7Q Bacteria
COG0362 LUCA
HOGENOMiHOG000255147
KOiK00033
OMAiNSHYPDS
OrthoDBiPOG091H01QF

Family and domain databases

Gene3Di1.10.1040.10, 1 hit
InterProiView protein in InterPro
IPR008927 6-PGluconate_DH-like_C_sf
IPR013328 6PGD_dom2
IPR006114 6PGDH_C
IPR006113 6PGDH_Gnd/GntZ
IPR006115 6PGDH_NADP-bd
IPR006184 6PGdom_BS
IPR036291 NAD(P)-bd_dom_sf
IPR006183 Pgluconate_DH
PfamiView protein in Pfam
PF00393 6PGD, 1 hit
PF03446 NAD_binding_2, 1 hit
PIRSFiPIRSF000109 6PGD, 1 hit
PRINTSiPR00076 6PGDHDRGNASE
SMARTiView protein in SMART
SM01350 6PGD, 1 hit
SUPFAMiSSF48179 SSF48179, 1 hit
SSF51735 SSF51735, 1 hit
TIGRFAMsiTIGR00873 gnd, 1 hit
PROSITEiView protein in PROSITE
PS00461 6PGD, 1 hit

Sequencei

Sequence statusi: Complete.

Q2JIY1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKPSFAVIG LAVMGENLAL NVERNGFPVA VYNRTSSKTD QFMRERAQGK
60 70 80 90 100
RITPAYSLPE LVQLMERPRK FLIMVKAGAP VDAVIDELKP LLDPGDIIID
110 120 130 140 150
GGNSLYTDTD RRAEALAPTG IHFVGMGVSG GEEGALNGPS LMPGCSPEAY
160 170 180 190 200
QQLEPILAKI AAQVPDGPCV TYLGPKGGGH YVKMVHNGIE YGDMQLIAEV
210 220 230 240 250
YDLMRRALKL SASQMQEIFQ AWNETELESF LIEITAKIFQ TLDPETGKPL
260 270 280 290 300
VDLILDKAGQ KGTGLWTVKD ALDLGVPVPT IEAAVQARIL SSMKEERVAA
310 320 330 340 350
SAQLKGPDAT FAGDPDCFIQ DLRAALYCSK ICSYAQGMAL LKRATVAHGY
360 370 380 390 400
VYTFSEIPRI WKGGCIIRAR FLGEIQSAYK RDPELVNLLL DEEFEQAIRE
410 420 430 440 450
RQGSWRRVVS TAAALGIPIP AISASLAYYD SYRTANLPQN LTQAQRDFFG
460 470
AHTFERIDRP GVFHHEWNAC CR
Length:472
Mass (Da):51,844
Last modified:March 7, 2006 - v1
Checksum:iD1C7C9A64FC4C2CF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000240 Genomic DNA Translation: ABD03413.1
RefSeqiWP_011434040.1, NC_007776.1

Genome annotation databases

EnsemblBacteriaiABD03413; ABD03413; CYB_2481
KEGGicyb:CYB_2481

Similar proteinsi

Entry informationi

Entry nameiQ2JIY1_SYNJB
AccessioniPrimary (citable) accession number: Q2JIY1
Entry historyiIntegrated into UniProtKB/TrEMBL: March 7, 2006
Last sequence update: March 7, 2006
Last modified: March 28, 2018
This is version 96 of the entry and version 1 of the sequence. See complete history.
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteomeImported
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Main funding by: National Institutes of Health