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Protein

6-phosphogluconate dehydrogenase, decarboxylating

Gene

GND

Organism
Trypanosoma brucei brucei
Status
Reviewed-Annotation score: Annotation score: 3 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.By similarity

Catalytic activityi

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

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).
Proteins known to be involved in the 3 steps of the subpathway in this organism are:
  1. no protein annotated in this organism
  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 sitei105NADPBy similarity1
Binding sitei105SubstrateBy similarity1
Active sitei186Proton acceptorBy similarity1
Active sitei193Proton donorBy similarity1
Binding sitei194SubstrateBy similarity1
Binding sitei263Substrate; via amide nitrogenBy similarity1
Binding sitei290SubstrateBy similarity1
Binding sitei454Substrate; shared with dimeric partnerBy similarity1
Binding sitei460Substrate; shared with dimeric partnerBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi9 – 14NADPBy similarity6
Nucleotide bindingi32 – 34NADPBy similarity3
Nucleotide bindingi77 – 79NADPBy similarity3

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Gluconate utilization, Pentose shunt

Keywords - Ligandi

NADP

Enzyme and pathway databases

BRENDAi1.1.1.44. 6519.
UniPathwayiUPA00115; UER00410.

Names & Taxonomyi

Protein namesi
Recommended name:
6-phosphogluconate dehydrogenase, decarboxylating (EC:1.1.1.44)
Gene namesi
Name:GND
OrganismiTrypanosoma brucei brucei
Taxonomic identifieri5702 [NCBI]
Taxonomic lineageiEukaryotaEuglenozoaKinetoplastidaTrypanosomatidaeTrypanosoma

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: GeneDB
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000900711 – 4796-phosphogluconate dehydrogenase, decarboxylatingAdd BLAST479

Interactioni

Subunit structurei

Homodimer.1 Publication

Structurei

Secondary structure

1479
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 8Combined sources6
Helixi12 – 23Combined sources12
Beta strandi28 – 31Combined sources4
Helixi35 – 44Combined sources10
Turni45 – 47Combined sources3
Helixi51 – 53Combined sources3
Beta strandi54 – 56Combined sources3
Helixi60 – 66Combined sources7
Beta strandi72 – 75Combined sources4
Helixi81 – 93Combined sources13
Beta strandi99 – 102Combined sources4
Helixi108 – 119Combined sources12
Turni120 – 122Combined sources3
Beta strandi124 – 132Combined sources9
Helixi133 – 139Combined sources7
Beta strandi142 – 147Combined sources6
Helixi149 – 162Combined sources14
Helixi181 – 209Combined sources29
Helixi214 – 226Combined sources13
Helixi233 – 243Combined sources11
Beta strandi249 – 251Combined sources3
Helixi252 – 255Combined sources4
Helixi265 – 276Combined sources12
Helixi281 – 294Combined sources14
Helixi296 – 305Combined sources10
Turni307 – 310Combined sources4
Helixi325 – 356Combined sources32
Helixi362 – 367Combined sources6
Beta strandi370 – 373Combined sources4
Helixi380 – 389Combined sources10
Helixi398 – 400Combined sources3
Helixi401 – 421Combined sources21
Helixi427 – 439Combined sources13
Helixi446 – 458Combined sources13
Beta strandi462 – 471Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1PGJX-ray2.82A/B2-479[»]
ProteinModelPortaliP31072.
SMRiP31072.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP31072.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni131 – 133Substrate bindingBy similarity3
Regioni189 – 190Substrate bindingBy similarity2

Sequence similaritiesi

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.
IPR013328. 6PGD_dom_2.
IPR012284. 6PGD_dom_3.
IPR006114. 6PGDH_C.
IPR006113. 6PGDH_Gnd/GntZ.
IPR006115. 6PGDH_NADP-bd.
IPR006184. 6PGdom_BS.
IPR016040. NAD(P)-bd_dom.
IPR006183. Pgluconate_DH.
[Graphical view]
PfamiPF00393. 6PGD. 1 hit.
PF03446. NAD_binding_2. 1 hit.
[Graphical view]
PIRSFiPIRSF000109. 6PGD. 1 hit.
PRINTSiPR00076. 6PGDHDRGNASE.
SMARTiSM01350. 6PGD. 1 hit.
[Graphical view]
SUPFAMiSSF48179. SSF48179. 1 hit.
SSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR00873. gnd. 1 hit.
PROSITEiPS00461. 6PGD. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P31072-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSMDVGVVGL GVMGANLALN IAEKGFKVAV FNRTYSKSEE FMKANASAPF
60 70 80 90 100
AGNLKAFETM EAFAASLKKP RKALILVQAG AATDSTTEQL KKVFEKGDIL
110 120 130 140 150
VDTGNAHFKD QGRRAQQLEA AGLRFLGMGI SGGEEGARKG PAFFPGGTLS
160 170 180 190 200
VWEEIRPIVE AAAAKADDGR PCVTMNGSGG AGSCVKMYHN SGEYAILQIW
210 220 230 240 250
GEVFDILRAM GLNNDEVAAV LEDWKSKNFL KSYMLDISIA AARAKDKDGS
260 270 280 290 300
YLTEHVMDRI GSKGTGLWSA QEALEIGVPA PSLNMAVVSR QFTMYKTERQ
310 320 330 340 350
ANASNAPGIT QSPGYTLKNK SPSGPEIKQL YDSVCIAIIS CYAQMFQCLR
360 370 380 390 400
EMDKVHNFGL NLPATIATFR AGCILQGYLL KPMTEAFEKN PNISNLMCAF
410 420 430 440 450
QTEIRAGLQN YRDMVALITS KLEVSIPVLS ASLNYVTAMF TPTLKYGQLV
460 470
SLQRDVFGRH GYERVDKDGR ESFQWPELQ
Length:479
Mass (Da):52,154
Last modified:July 1, 1993 - v1
Checksum:i64FED260915ABC2F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X65623 Genomic DNA. Translation: CAA46577.1.
PIRiA48565.

Genome annotation databases

GeneDBiTb927.9.12110:pep.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X65623 Genomic DNA. Translation: CAA46577.1.
PIRiA48565.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1PGJX-ray2.82A/B2-479[»]
ProteinModelPortaliP31072.
SMRiP31072.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneDBiTb927.9.12110:pep.

Enzyme and pathway databases

UniPathwayiUPA00115; UER00410.
BRENDAi1.1.1.44. 6519.

Miscellaneous databases

EvolutionaryTraceiP31072.

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.
IPR013328. 6PGD_dom_2.
IPR012284. 6PGD_dom_3.
IPR006114. 6PGDH_C.
IPR006113. 6PGDH_Gnd/GntZ.
IPR006115. 6PGDH_NADP-bd.
IPR006184. 6PGdom_BS.
IPR016040. NAD(P)-bd_dom.
IPR006183. Pgluconate_DH.
[Graphical view]
PfamiPF00393. 6PGD. 1 hit.
PF03446. NAD_binding_2. 1 hit.
[Graphical view]
PIRSFiPIRSF000109. 6PGD. 1 hit.
PRINTSiPR00076. 6PGDHDRGNASE.
SMARTiSM01350. 6PGD. 1 hit.
[Graphical view]
SUPFAMiSSF48179. SSF48179. 1 hit.
SSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR00873. gnd. 1 hit.
PROSITEiPS00461. 6PGD. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry namei6PGD_TRYBB
AccessioniPrimary (citable) accession number: P31072
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: July 1, 1993
Last modified: November 2, 2016
This is version 102 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)

Miscellaneousi

Keywords - Technical termi

3D-structure

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.