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Protein

6-phosphogluconate dehydrogenase, decarboxylating

Gene

gnd

Organism
Lactococcus lactis subsp. cremoris (strain MG1363)
Status
Reviewed-Annotation score: Annotation score: 4 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. 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 sitei102NADP1 Publication1
Binding sitei102Substrate1 Publication1
Active sitei184Proton acceptor1 Publication1
Active sitei191Proton donor1 Publication1
Binding sitei192Substrate1 Publication1
Binding sitei262Substrate; via amide nitrogen1 Publication1
Binding sitei289Substrate1 Publication1
Binding sitei447Substrate; shared with dimeric partner1 Publication1
Binding sitei453Substrate; shared with dimeric partner1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi10 – 15NADP1 Publication6
Nucleotide bindingi33 – 35NADP1 Publication3
Nucleotide bindingi74 – 76NADP1 Publication3

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. 2903.
SABIO-RKP96789.
UniPathwayiUPA00115; UER00410.

Names & Taxonomyi

Protein namesi
Recommended name:
6-phosphogluconate dehydrogenase, decarboxylating (EC:1.1.1.44)
Gene namesi
Name:gnd
Ordered Locus Names:llmg_0586
OrganismiLactococcus lactis subsp. cremoris (strain MG1363)
Taxonomic identifieri416870 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeLactococcus
Proteomesi
  • UP000000364 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000900461 – 4726-phosphogluconate dehydrogenase, decarboxylatingAdd BLAST472

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi416870.llmg_0586.

Structurei

Secondary structure

1472
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 9Combined sources6
Helixi13 – 24Combined sources12
Beta strandi29 – 32Combined sources4
Helixi36 – 45Combined sources10
Turni46 – 48Combined sources3
Beta strandi51 – 53Combined sources3
Helixi57 – 62Combined sources6
Beta strandi69 – 72Combined sources4
Helixi78 – 87Combined sources10
Helixi88 – 90Combined sources3
Beta strandi96 – 99Combined sources4
Helixi105 – 114Combined sources10
Turni115 – 117Combined sources3
Beta strandi121 – 127Combined sources7
Helixi130 – 136Combined sources7
Beta strandi140 – 144Combined sources5
Helixi146 – 159Combined sources14
Turni164 – 166Combined sources3
Beta strandi169 – 171Combined sources3
Helixi179 – 207Combined sources29
Helixi213 – 223Combined sources11
Turni224 – 228Combined sources5
Helixi231 – 239Combined sources9
Beta strandi245 – 250Combined sources6
Helixi251 – 254Combined sources4
Helixi264 – 275Combined sources12
Helixi280 – 293Combined sources14
Helixi295 – 304Combined sources10
Helixi316 – 349Combined sources34
Helixi355 – 361Combined sources7
Beta strandi363 – 365Combined sources3
Helixi373 – 382Combined sources10
Helixi389 – 391Combined sources3
Helixi393 – 416Combined sources24
Helixi421 – 433Combined sources13
Helixi440 – 451Combined sources12
Beta strandi457 – 462Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2IYOX-ray2.40A1-472[»]
2IYPX-ray2.79A/B/C1-472[»]
2IZ0X-ray2.60A/B/C1-472[»]
2IZ1X-ray2.30A/B/C1-472[»]
ProteinModelPortaliP96789.
SMRiP96789.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP96789.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni128 – 130Substrate binding1 Publication3
Regioni187 – 188Substrate binding1 Publication2

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105C7Q. Bacteria.
COG0362. LUCA.
HOGENOMiHOG000255147.
KOiK00033.
OMAiEGEPCVT.

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.

P96789-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAQANFGVVG MAVMGKNLAL NVESRGYTVA IYNRTTSKTE EVYKEHQDKN
60 70 80 90 100
LVFTKTLEEF VGSLEKPRRI MLMVQAGAAT DATIKSLLPL LDIGDILIDG
110 120 130 140 150
GNTHFPDTMR RNAELADSGI NFIGTGVSGG EKGALLGPSM MPGGQKEAYD
160 170 180 190 200
LVAPIFEQIA AKAPQDGKPC VAYMGANGAG HYVKMVHNGI EYGDMQLIAE
210 220 230 240 250
SYDLLKRILG LSNAEIQAIF EEWNEGELDS YLIEITKEVL KRKDDEGEGY
260 270 280 290 300
IVDKILDKAG NKGTGKWTSE SALDLGVPLP LITESVFARY ISTYKDERVK
310 320 330 340 350
ASKVLSGPAL DFSGDKKEVI EKIRKALYFS KIMSYAQGFA QLRKASEEFD
360 370 380 390 400
WDLPYGTIAQ IWRAGCIIRA EFLQNITDAF DKDSELENLL LDDYFVDITK
410 420 430 440 450
RYQEAVRDVV SLAVQAGTPI PTFTSAISYY DSYRSENLPA NLIQAQRDYF
460 470
GAHTYERTDK AGIFHYDWYT ED
Length:472
Mass (Da):52,460
Last modified:May 1, 2007 - v3
Checksum:iA0075C9F46171F1C
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti43Y → F in AAC12804 (PubMed:9931298).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U74322 Genomic DNA. Translation: AAC12804.1.
AM406671 Genomic DNA. Translation: CAL97186.1.
RefSeqiWP_011834606.1. NC_009004.1.

Genome annotation databases

EnsemblBacteriaiCAL97186; CAL97186; llmg_0586.
KEGGillm:llmg_0586.
PATRICi22282257. VBILacLac4574_0596.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U74322 Genomic DNA. Translation: AAC12804.1.
AM406671 Genomic DNA. Translation: CAL97186.1.
RefSeqiWP_011834606.1. NC_009004.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2IYOX-ray2.40A1-472[»]
2IYPX-ray2.79A/B/C1-472[»]
2IZ0X-ray2.60A/B/C1-472[»]
2IZ1X-ray2.30A/B/C1-472[»]
ProteinModelPortaliP96789.
SMRiP96789.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi416870.llmg_0586.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAL97186; CAL97186; llmg_0586.
KEGGillm:llmg_0586.
PATRICi22282257. VBILacLac4574_0596.

Phylogenomic databases

eggNOGiENOG4105C7Q. Bacteria.
COG0362. LUCA.
HOGENOMiHOG000255147.
KOiK00033.
OMAiEGEPCVT.

Enzyme and pathway databases

UniPathwayiUPA00115; UER00410.
BRENDAi1.1.1.44. 2903.
SABIO-RKP96789.

Miscellaneous databases

EvolutionaryTraceiP96789.

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_LACLM
AccessioniPrimary (citable) accession number: P96789
Secondary accession number(s): A2RIU0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: May 1, 2007
Last modified: November 2, 2016
This is version 117 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome

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.