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P96789

- 6PGD_LACLM

UniProt

P96789 - 6PGD_LACLM

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Protein

6-phosphogluconate dehydrogenase, decarboxylating

Gene

gnd

Organism
Lactococcus lactis subsp. cremoris (strain MG1363)
Status
Reviewed - 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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei102 – 1021NADPBy similarity
Binding sitei102 – 1021Substrate
Active sitei184 – 1841Proton acceptor1 Publication
Active sitei191 – 1911Proton donor1 Publication
Binding sitei192 – 1921Substrate
Binding sitei262 – 2621Substrate; via amide nitrogen
Binding sitei289 – 2891Substrate
Binding sitei447 – 4471Substrate; shared with dimeric partner
Binding sitei453 – 4531Substrate; shared with dimeric partner

Regions

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

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

BioCyciLLAC416870:GCDT-613-MONOMER.
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
ProteomesiUP000000364: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 4724726-phosphogluconate dehydrogenase, decarboxylatingPRO_0000090046Add
BLAST

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi416870.llmg_0586.

Structurei

Secondary structure

1
472
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 96
Helixi13 – 2412
Beta strandi29 – 324
Helixi36 – 4510
Turni46 – 483
Beta strandi51 – 533
Helixi57 – 626
Beta strandi69 – 724
Helixi78 – 8710
Helixi88 – 903
Beta strandi96 – 994
Helixi105 – 11410
Turni115 – 1173
Beta strandi121 – 1277
Helixi130 – 1367
Beta strandi140 – 1445
Helixi146 – 15914
Turni164 – 1663
Beta strandi169 – 1713
Helixi179 – 20729
Helixi213 – 22311
Turni224 – 2285
Helixi231 – 2399
Beta strandi245 – 2506
Helixi251 – 2544
Helixi264 – 27512
Helixi280 – 29314
Helixi295 – 30410
Helixi316 – 34934
Helixi355 – 3617
Beta strandi363 – 3653
Helixi373 – 38210
Helixi389 – 3913
Helixi393 – 41624
Helixi421 – 43313
Helixi440 – 45112
Beta strandi457 – 4626

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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. Positions 1-470.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP96789.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni128 – 1303Substrate binding
Regioni187 – 1882Substrate binding

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0362.
HOGENOMiHOG000255147.
KOiK00033.
OMAiDKDGVFH.
OrthoDBiEOG6MSS4W.

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.

P96789 [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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti43 – 431Y → F in AAC12804. (PubMed:9931298)Curated

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U74322 Genomic DNA. Translation: AAC12804.1.
AM406671 Genomic DNA. Translation: CAL97186.1.
RefSeqiWP_011834606.1. NC_009004.1.
YP_001031931.1. NC_009004.1.

Genome annotation databases

EnsemblBacteriaiCAL97186; CAL97186; llmg_0586.
GeneIDi4798708.
KEGGillm:llmg_0586.
PATRICi22282257. VBILacLac4574_0596.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U74322 Genomic DNA. Translation: AAC12804.1 .
AM406671 Genomic DNA. Translation: CAL97186.1 .
RefSeqi WP_011834606.1. NC_009004.1.
YP_001031931.1. NC_009004.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2IYO X-ray 2.40 A 1-472 [» ]
2IYP X-ray 2.79 A/B/C 1-472 [» ]
2IZ0 X-ray 2.60 A/B/C 1-472 [» ]
2IZ1 X-ray 2.30 A/B/C 1-472 [» ]
ProteinModelPortali P96789.
SMRi P96789. Positions 1-470.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 416870.llmg_0586.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai CAL97186 ; CAL97186 ; llmg_0586 .
GeneIDi 4798708.
KEGGi llm:llmg_0586.
PATRICi 22282257. VBILacLac4574_0596.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00115 ; UER00410 .
BioCyci LLAC416870:GCDT-613-MONOMER.
SABIO-RK P96789.

Miscellaneous databases

EvolutionaryTracei P96789.

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. "6-phosphogluconate dehydrogenase from Lactococcus lactis: a role for arginine residues in binding substrate and coenzyme."
    Tetaud E., Hanau S., Wells J.M., Le Page R.W.F., Adams M.J., Arkison S., Barrett M.P.
    Biochem. J. 338:55-60(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "The complete genome sequence of the lactic acid bacterial paradigm Lactococcus lactis subsp. cremoris MG1363."
    Wegmann U., O'Connell-Motherway M., Zomer A., Buist G., Shearman C., Canchaya C., Ventura M., Goesmann A., Gasson M.J., Kuipers O.P., van Sinderen D., Kok J.
    J. Bacteriol. 189:3256-3270(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: MG1363.
  3. "Crystal structures of a bacterial 6-phosphogluconate dehydrogenase reveal aspects of specificity, mechanism and mode of inhibition by analogues of high-energy reaction intermediates."
    Sundaramoorthy R., Iulek J., Barrett M.P., Bidet O., Ruda G.F., Gilbert I.H., Hunter W.N.
    FEBS J. 274:275-286(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEXES WITH SUBSTRATE; PRODUCT; INHIBITORS AND NADP, SUBUNIT, ACTIVE SITE.

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: October 29, 2014
This is version 99 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

External Data

Dasty 3