P36234 (DHGY_HYPME) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names	Recommended name: Glycerate dehydrogenase Short name=GDH EC=1.1.1.29 Alternative name(s): Glyoxylate reductase Hydroxypyruvate dehydrogenase NADH-dependent hydroxypyruvate reductase Short name=HPR
Organism	Hyphomicrobium methylovorum
Taxonomic identifier	84 [NCBI]
Taxonomic lineage	cellular organisms › Bacteria › Proteobacteria › Alphaproteobacteria › Rhizobiales › Hyphomicrobiaceae › Hyphomicrobium

Protein attributes

Sequence length	322 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Active on hydroxypyruvate and glyoxylate.
Catalytic activity	D-glycerate + NAD+ = hydroxypyruvate + NADH.
Pathway	One-carbon metabolism; formaldehyde assimilation via serine pathway.
Subunit structure	Homodimer.
Induction	By methanol.
Sequence similarities	Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family.
Biophysicochemical properties	pH dependence: Optimum pH is 6.8. Temperature dependence: Optimum temperature is 45 degrees Celsius.

Ontologies

Keywords
Ligand	NAD
Molecular function	Oxidoreductase
Technical term	3D-structure
Gene Ontology (GO)
Molecular_function	NAD binding Inferred from electronic annotation. Source: InterPro glycerate dehydrogenase 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

Initiator methionine

1

1

Removed

Chain

2 – 322

321

Glycerate dehydrogenase

PRO_0000075942

Regions

Nucleotide binding

158 – 159

2

NAD By similarity

Nucleotide binding

239 – 241

3

NAD By similarity

Nucleotide binding

288 – 291

4

NAD By similarity

Region

2 – 100

99

Catalytic

Region

101 – 291

191

Coenzyme-binding

Region

292 – 322

31

Catalytic

Sites

Active site

241

1

Active site

270

1

Active site

288

1

Proton donor

Binding site

178

1

NAD By similarity

Binding site

265

1

NAD By similarity

Secondary structure

1

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322

Helix Strand Turn

Details...

Beta strand

5 – 10

6

Helix

14 – 21

8

Beta strand

24 – 28

5

Helix

37 – 44

8

Beta strand

48 – 53

6

Helix

60 – 65

6

Beta strand

72 – 78

7

Helix

85 – 90

6

Beta strand

94 – 96

3

Helix

103 – 118

16

Helix

121 – 129

9

Turn

138 – 141

4

Beta strand

150 – 154

5

Helix

158 – 168

11

Turn

169 – 171

3

Beta strand

173 – 177

5

Helix

184 – 189

6

Helix

198 – 204

7

Beta strand

206 – 210

5

Turn

216 – 220

5

Helix

224 – 227

4

Beta strand

234 – 238

5

Helix

242 – 244

3

Helix

247 – 255

9

Beta strand

258 – 265

8

Turn

268 – 271

4

Helix

277 – 279

3

Beta strand

283 – 285

3

Helix

294 – 312

19

Beta strand

320 – 322

3

Sequences

	Sequence		Length	Mass (Da)
	P36234 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: CA5E39C1617AF2FE	FASTA	322	35,115
	10 20 30 40 50 60 MSKKKILITW PLPEAAMARA RESYDVIAHG DDPKITIDEM IETAKSVDAL LITLNEKCRK 70 80 90 100 110 120 EVIDRIPENI KCISTYSIGF DHIDLDACKA RGIKVGNAPH GVTVATAEIA MLLLLGSARR 130 140 150 160 170 180 AGEGEKMIRT RSWPGWEPLE LVGEKLDNKT LGIYGFGSIG QALAKRAQGF DMDIDYFDTH 190 200 210 220 230 240 RASSSDEASY QATFHDSLDS LLSVSQFFSL NAPSTPETRY FFNKATIKSL PQGAIVVNTA 250 260 270 280 290 300 RGDLVDNELV VAALEAGRLA YAGFDVFAGE PNINEGYYDL PNTFLFPHIG SAATQAREDM 310 320 AHQANDLIDA LFGGADMSYA LA

References

[1]	"Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4-A resolution." Goldberg J.D., Yoshida T., Brick P. J. Mol. Biol. 236:1123-1140(1994) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
[2]	"Purification and characterization of hydroxypyruvate reductase from a serine-producing methylotroph, Hyphomicrobium methylovorum GM2." Izumi Y., Yoshida T., Kanzaki H., Toki S., Miyazaki S.S., Yamada H. Eur. J. Biochem. 190:279-284(1990) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION. Strain: KM146 / GM2.

Cross-references

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1GDH	X-ray	2.40	A/B	3-322	[»]

ProteinModelPortal

P36234.

SMR

P36234. Positions 3-322.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Enzyme and pathway databases

BioCyc

MetaCyc:MONOMER-4245.

UniPathway

UPA00927.

Family and domain databases

Gene3D

3.40.50.720. 2 hits.

InterPro

IPR006139. D-isomer_2_OHA_DH_cat_dom.
IPR006140. D-isomer_2_OHA_DH_NAD-bd.
IPR016040. NAD(P)-bd_dom.
[Graphical view]

Pfam

PF00389. 2-Hacid_dh. 1 hit.
PF02826. 2-Hacid_dh_C. 1 hit.
[Graphical view]

PROSITE

PS00065. D_2_HYDROXYACID_DH_1. 1 hit.
PS00670. D_2_HYDROXYACID_DH_2. 1 hit.
PS00671. D_2_HYDROXYACID_DH_3. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P36234.

Entry information

Entry name

DHGY_HYPME

Accession

Primary (citable) accession number: P36234

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 1, 1994
Last sequence update:	January 23, 2007
Last modified:	April 3, 2013
This is version 89 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program