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Protein

Glycerol-3-phosphate dehydrogenase [NAD(+)], glycosomal

Gene

GPD

Organism
Leishmania mexicana
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

sn-glycerol 3-phosphate + NAD+ = glycerone phosphate + NADH.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei97 – 971NADBy similarity
Binding sitei125 – 1251NAD; via amide nitrogen2 Publications
Binding sitei125 – 1251Substrate1 Publication
Binding sitei157 – 1571NAD; via amide nitrogen2 Publications
Active sitei210 – 2101Proton acceptorCurated
Binding sitei274 – 2741NADBy similarity
Binding sitei298 – 2981NAD; via amide nitrogen2 Publications
Binding sitei300 – 3001NAD2 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi22 – 276NAD2 Publications

GO - Molecular functioni

  1. glycerol-3-phosphate dehydrogenase [NAD+] activity Source: UniProtKB-EC
  2. NAD binding Source: InterPro

GO - Biological processi

  1. carbohydrate metabolic process Source: InterPro
  2. glycerol-3-phosphate catabolic process Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

NAD

Enzyme and pathway databases

SABIO-RKP90551.

Names & Taxonomyi

Protein namesi
Recommended name:
Glycerol-3-phosphate dehydrogenase [NAD(+)], glycosomal (EC:1.1.1.8)
Gene namesi
Name:GPD
OrganismiLeishmania mexicana
Taxonomic identifieri5665 [NCBI]
Taxonomic lineageiEukaryotaEuglenozoaKinetoplastidaTrypanosomatidaeLeishmaniinaeLeishmania

Subcellular locationi

  1. Glycosome 1 Publication

GO - Cellular componenti

  1. glycerol-3-phosphate dehydrogenase complex Source: InterPro
  2. glycosome Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Glycosome, Peroxisome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi125 – 1251K → A or M: Loss of activity. 1 Publication
Mutagenesisi210 – 2101K → A or M: Loss of activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 366366Glycerol-3-phosphate dehydrogenase [NAD(+)], glycosomalPRO_0000262292Add
BLAST

Interactioni

Subunit structurei

Homodimer.3 Publications

Structurei

Secondary structure

1
366
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi15 – 217Combined sources
Helixi25 – 3410Combined sources
Turni35 – 373Combined sources
Beta strandi38 – 447Combined sources
Helixi48 – 5710Combined sources
Turni61 – 633Combined sources
Beta strandi73 – 775Combined sources
Helixi79 – 835Combined sources
Beta strandi87 – 915Combined sources
Helixi95 – 10511Combined sources
Helixi107 – 11610Combined sources
Beta strandi120 – 1223Combined sources
Turni129 – 1313Combined sources
Helixi135 – 1395Combined sources
Turni140 – 1423Combined sources
Helixi145 – 1473Combined sources
Beta strandi148 – 1547Combined sources
Helixi157 – 1615Combined sources
Beta strandi166 – 1716Combined sources
Helixi175 – 18511Combined sources
Beta strandi190 – 1989Combined sources
Helixi200 – 22223Combined sources
Helixi227 – 24721Combined sources
Turni253 – 2564Combined sources
Turni258 – 2603Combined sources
Helixi261 – 2688Combined sources
Helixi274 – 28310Combined sources
Helixi288 – 2925Combined sources
Helixi300 – 31516Combined sources
Helixi320 – 33011Combined sources
Helixi335 – 3428Combined sources
Helixi343 – 3453Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1EVYX-ray1.75A1-366[»]
1EVZX-ray2.80A1-366[»]
1JDJX-ray2.20A1-366[»]
1M66X-ray1.90A1-366[»]
1M67X-ray2.50A1-366[»]
1N1EX-ray1.90A/B1-366[»]
1N1GX-ray2.50A1-366[»]
ProteinModelPortaliP90551.
SMRiP90551. Positions 9-357.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP90551.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni274 – 2752Substrate binding

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi364 – 3663Microbody targeting signalSequence Analysis

Sequence similaritiesi

Family and domain databases

Gene3Di1.10.1040.10. 1 hit.
3.40.50.720. 1 hit.
HAMAPiMF_00394. NAD_Glyc3P_dehydrog.
InterProiIPR008927. 6-PGluconate_DH_C-like.
IPR013328. 6PGD_dom_2.
IPR006168. G3P_DH_NAD-dep.
IPR006109. G3P_DH_NAD-dep_C.
IPR011128. G3P_DH_NAD-dep_N.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PANTHERiPTHR11728. PTHR11728. 1 hit.
PfamiPF07479. NAD_Gly3P_dh_C. 1 hit.
PF01210. NAD_Gly3P_dh_N. 1 hit.
[Graphical view]
PIRSFiPIRSF000114. Glycerol-3-P_dh. 1 hit.
PRINTSiPR00077. GPDHDRGNASE.
SUPFAMiSSF48179. SSF48179. 1 hit.
PROSITEiPS00957. NAD_G3PDH. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P90551-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTKQHSAKD ELLYLNKAVV FGSGAFGTAL AMVLSKKCRE VCVWHMNEEE
60 70 80 90 100
VRLVNEKREN VLFLKGVQLA SNITFTSDVE KAYNGAEIIL FVIPTQFLRG
110 120 130 140 150
FFEKSGGNLI AYAKEKQVPV LVCTKGIERS TLKFPAEIIG EFLPSPLLSV
160 170 180 190 200
LAGPSFAIEV ATGVFTCVSI ASADINVARR LQRIMSTGDR SFVCWATTDT
210 220 230 240 250
VGCEVASAVK NVLAIGSGVA NGLGMGLNAR AALIMRGLLE IRDLTAALGG
260 270 280 290 300
DGSAVFGLAG LGDLQLTCSS ELSRNFTVGK KLGKGLPIEE IQRTSKAVAE
310 320 330 340 350
GVATADPLMR LAKQLKVKMP LCHQIYEIVY KKKNPRDALA DLLSCGLQDE
360
GLPPLFKRSA STPSKL
Length:366
Mass (Da):39,272
Last modified:May 1, 1997 - v1
Checksum:iE47594525FC0CF44
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X89739 Genomic DNA. Translation: CAA61891.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X89739 Genomic DNA. Translation: CAA61891.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1EVYX-ray1.75A1-366[»]
1EVZX-ray2.80A1-366[»]
1JDJX-ray2.20A1-366[»]
1M66X-ray1.90A1-366[»]
1M67X-ray2.50A1-366[»]
1N1EX-ray1.90A/B1-366[»]
1N1GX-ray2.50A1-366[»]
ProteinModelPortaliP90551.
SMRiP90551. Positions 9-357.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

SABIO-RKP90551.

Miscellaneous databases

EvolutionaryTraceiP90551.

Family and domain databases

Gene3Di1.10.1040.10. 1 hit.
3.40.50.720. 1 hit.
HAMAPiMF_00394. NAD_Glyc3P_dehydrog.
InterProiIPR008927. 6-PGluconate_DH_C-like.
IPR013328. 6PGD_dom_2.
IPR006168. G3P_DH_NAD-dep.
IPR006109. G3P_DH_NAD-dep_C.
IPR011128. G3P_DH_NAD-dep_N.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PANTHERiPTHR11728. PTHR11728. 1 hit.
PfamiPF07479. NAD_Gly3P_dh_C. 1 hit.
PF01210. NAD_Gly3P_dh_N. 1 hit.
[Graphical view]
PIRSFiPIRSF000114. Glycerol-3-P_dh. 1 hit.
PRINTSiPR00077. GPDHDRGNASE.
SUPFAMiSSF48179. SSF48179. 1 hit.
PROSITEiPS00957. NAD_G3PDH. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Cloning and characterization of the NAD-linked glycerol-3-phosphate dehydrogenases of Trypanosoma brucei brucei and Leishmania mexicana mexicana and expression of the trypanosome enzyme in Escherichia coli."
    Kohl L., Drmota T., Thi C.-D., Callens M., van Beeumen J., Opperdoes F.R., Michels P.A.M.
    Mol. Biochem. Parasitol. 76:159-173(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], SUBCELLULAR LOCATION.
  2. "A potential target enzyme for trypanocidal drugs revealed by the crystal structure of NAD-dependent glycerol-3-phosphate dehydrogenase from Leishmania mexicana."
    Suresh S., Turley S., Opperdoes F.R., Michels P.A.M., Hol W.G.J.
    Structure 8:541-552(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) IN COMPLEX WITH NAD AND SUBSTRATE ANALOG, SUBUNIT.
  3. "Anomalous differences of light elements in determining precise binding modes of ligands to glycerol-3-phosphate dehydrogenase."
    Choe J., Suresh S., Wisedchaisri G., Kennedy K.J., Gelb M.H., Hol W.G.J.
    Chem. Biol. 9:1189-1197(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH NAD ANALOG.
  4. "Leishmania mexicana glycerol-3-phosphate dehydrogenase showed conformational changes upon binding a bi-substrate adduct."
    Choe J., Guerra D., Michels P.A.M., Hol W.G.J.
    J. Mol. Biol. 329:335-349(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND NAD, MUTAGENESIS OF LYS-125 AND LYS-210.

Entry informationi

Entry nameiGPDA_LEIME
AccessioniPrimary (citable) accession number: P90551
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 28, 2006
Last sequence update: May 1, 1997
Last modified: April 29, 2015
This is version 88 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)

Miscellaneousi

Keywords - Technical termi

3D-structure

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.