P90551 (GPDA_LEIME) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Glycerol-3-phosphate dehydrogenase [NAD(+)], glycosomal
EC=1.1.1.8

Gene names

Name:

GPD

Organism

Leishmania mexicana

Taxonomic identifier

5665 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Euglenozoa › Kinetoplastida › Trypanosomatidae › Leishmaniinae › Leishmania › Leishmania › Leishmania mexicana species complex

Protein attributes

Sequence length	366 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Catalytic activity	sn-glycerol 3-phosphate + NAD+ = glycerone phosphate + NADH.
Subunit structure	Homodimer. Ref.2
Subcellular location	Glycosome Ref.1.
Sequence similarities	Belongs to the NAD-dependent glycerol-3-phosphate dehydrogenase family.

Ontologies

Keywords
Cellular component	Glycosome Peroxisome
Ligand	NAD
Molecular function	Oxidoreductase
Technical term	3D-structure
Gene Ontology (GO)
Biological_process	carbohydrate metabolic process Inferred from electronic annotation. Source: InterPro glycerol-3-phosphate catabolic process Inferred from electronic annotation. Source: InterPro
Cellular_component	glycerol-3-phosphate dehydrogenase complex Inferred from electronic annotation. Source: InterPro glycosome Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	NAD binding Inferred from electronic annotation. Source: InterPro glycerol-3-phosphate dehydrogenase [NAD+] activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 366

366

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

PRO_0000262292

Regions

Nucleotide binding

22 – 27

6

NAD

Region

274 – 275

2

Substrate binding

Motif

364 – 366

3

Microbody targeting signal Potential

Sites

Active site

210

1

Proton acceptor Probable

Binding site

97

1

NAD By similarity

Binding site

125

1

NAD; via amide nitrogen

Binding site

125

1

Substrate

Binding site

157

1

NAD; via amide nitrogen

Binding site

274

1

NAD By similarity

Binding site

298

1

NAD; via amide nitrogen

Binding site

300

1

NAD

Experimental info

Mutagenesis

125

1

K → A or M: Loss of activity. Ref.4

Mutagenesis

210

1

K → A or M: Loss of activity. Ref.4

Secondary structure

1

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366

Helix Strand Turn

Details...

Beta strand

15 – 21

7

Helix

25 – 34

10

Turn

35 – 37

3

Beta strand

38 – 44

7

Helix

48 – 57

10

Turn

61 – 63

3

Beta strand

73 – 77

5

Helix

79 – 83

5

Beta strand

87 – 91

5

Helix

95 – 105

11

Helix

107 – 116

10

Beta strand

120 – 122

3

Turn

129 – 131

3

Helix

135 – 139

5

Turn

140 – 142

3

Helix

145 – 147

3

Beta strand

148 – 154

7

Helix

157 – 161

5

Beta strand

166 – 171

6

Helix

175 – 185

11

Beta strand

190 – 198

9

Helix

200 – 222

23

Helix

227 – 247

21

Turn

253 – 256

4

Turn

258 – 260

3

Helix

261 – 268

8

Helix

274 – 283

10

Helix

288 – 292

5

Helix

300 – 315

16

Helix

320 – 330

11

Helix

335 – 342

8

Helix

343 – 345

3

Sequences

	Sequence		Length	Mass (Da)
	P90551 [UniParc]. Last modified May 1, 1997. Version 1. Checksum: E47594525FC0CF44	FASTA	366	39,272
	10 20 30 40 50 60 MSTKQHSAKD ELLYLNKAVV FGSGAFGTAL AMVLSKKCRE VCVWHMNEEE VRLVNEKREN 70 80 90 100 110 120 VLFLKGVQLA SNITFTSDVE KAYNGAEIIL FVIPTQFLRG FFEKSGGNLI AYAKEKQVPV 130 140 150 160 170 180 LVCTKGIERS TLKFPAEIIG EFLPSPLLSV LAGPSFAIEV ATGVFTCVSI ASADINVARR 190 200 210 220 230 240 LQRIMSTGDR SFVCWATTDT VGCEVASAVK NVLAIGSGVA NGLGMGLNAR AALIMRGLLE 250 260 270 280 290 300 IRDLTAALGG DGSAVFGLAG LGDLQLTCSS ELSRNFTVGK KLGKGLPIEE IQRTSKAVAE 310 320 330 340 350 360 GVATADPLMR LAKQLKVKMP LCHQIYEIVY KKKNPRDALA DLLSCGLQDE GLPPLFKRSA STPSKL

References

[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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X89739 Genomic DNA. Translation: CAA61891.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1EVY	X-ray	1.75	A	1-366	[»]
1EVZ	X-ray	2.80	A	1-366	[»]
1JDJ	X-ray	2.20	A	1-366	[»]
1M66	X-ray	1.90	A	1-366	[»]
1M67	X-ray	2.50	A	1-366	[»]
1N1E	X-ray	1.90	A/B	1-366	[»]
1N1G	X-ray	2.50	A	1-366	[»]

ProteinModelPortal

P90551.

SMR

P90551. Positions 9-357.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Enzyme and pathway databases

SABIO-RK

P90551.

Family and domain databases

Gene3D

1.10.1040.10. 1 hit.
3.40.50.720. 1 hit.

InterPro

IPR008927. 6-PGluconate_DH_C-like.
IPR013328. DH_multihelical.
IPR006168. G3P_DH_NAD-dep.
IPR006109. G3P_DH_NAD-dep_C.
IPR011128. G3P_DH_NAD-dep_N.
IPR016040. NAD(P)-bd_dom.
[Graphical view]

PANTHER

PTHR11728. PTHR11728. 1 hit.

Pfam

PF07479. NAD_Gly3P_dh_C. 1 hit.
PF01210. NAD_Gly3P_dh_N. 1 hit.
[Graphical view]

PIRSF

PIRSF000114. Glycerol-3-P_dh. 1 hit.

PRINTS

PR00077. GPDHDRGNASE.

SUPFAM

SSF48179. 6DGDH_C_like. 1 hit.

PROSITE

PS00957. NAD_G3PDH. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P90551.

Entry information

Entry name

GPDA_LEIME

Accession

Primary (citable) accession number: P90551

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 28, 2006
Last sequence update:	May 1, 1997
Last modified:	April 3, 2013
This is version 81 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)