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P36234 (DHGY_HYPME) Reviewed, UniProtKB/Swiss-Prot

Last modified October 16, 2013. Version 90. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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
OrganismHyphomicrobium methylovorum
Taxonomic identifier84 [NCBI]
Taxonomic lineageBacteriaProteobacteriaAlphaproteobacteriaRhizobialesHyphomicrobiaceaeHyphomicrobium

Protein attributes

Sequence length322 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence 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
   LigandNAD
   Molecular functionOxidoreductase
   Technical term3D-structure
Gene Ontology (GO)
   Molecular_functionNAD binding

Inferred from electronic annotation. Source: InterPro

glycerate dehydrogenase activity

Inferred from electronic annotation. Source: UniProtKB-EC

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed
Chain2 – 322321Glycerate dehydrogenase
PRO_0000075942

Regions

Nucleotide binding158 – 1592NAD By similarity
Nucleotide binding239 – 2413NAD By similarity
Nucleotide binding288 – 2914NAD By similarity
Region2 – 10099Catalytic
Region101 – 291191Coenzyme-binding
Region292 – 32231Catalytic

Sites

Active site2411
Active site2701
Active site2881Proton donor
Binding site1781NAD By similarity
Binding site2651NAD By similarity

Secondary structure

........................................................... 322
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P36234 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: CA5E39C1617AF2FE

FASTA32235,115
        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 

« Hide

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
EntryMethodResolution (Å)ChainPositionsPDBsum
1GDHX-ray2.40A/B3-322[»]
ProteinModelPortalP36234.
SMRP36234. Positions 3-322.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Enzyme and pathway databases

BioCycMetaCyc:MONOMER-4245.
UniPathwayUPA00927.

Family and domain databases

Gene3D3.40.50.720. 2 hits.
InterProIPR006139. D-isomer_2_OHA_DH_cat_dom.
IPR006140. D-isomer_2_OHA_DH_NAD-bd.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamPF00389. 2-Hacid_dh. 1 hit.
PF02826. 2-Hacid_dh_C. 1 hit.
[Graphical view]
PROSITEPS00065. 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]
ProtoNetSearch...

Other

EvolutionaryTraceP36234.

Entry information

Entry nameDHGY_HYPME
AccessionPrimary (citable) accession number: P36234
Entry history
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: January 23, 2007
Last modified: October 16, 2013
This is version 90 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways