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P36234

- DHGY_HYPME

UniProt

P36234 - DHGY_HYPME

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Protein
Glycerate dehydrogenase
Gene
N/A
Organism
Hyphomicrobium methylovorum
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Active on hydroxypyruvate and glyoxylate.

Catalytic activityi

D-glycerate + NAD+ = hydroxypyruvate + NADH.

pH dependencei

Optimum pH is 6.8.

Temperature dependencei

Optimum temperature is 45 degrees Celsius.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei178 – 1781NAD By similarity
Active sitei241 – 2411
Binding sitei265 – 2651NAD By similarity
Active sitei270 – 2701
Active sitei288 – 2881Proton donor

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi158 – 1592NAD By similarity
Nucleotide bindingi239 – 2413NAD By similarity
Nucleotide bindingi288 – 2914NAD By similarity

GO - Molecular functioni

  1. NAD binding Source: InterPro
  2. glycerate dehydrogenase activity Source: UniProtKB-EC
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

NAD

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-4245.
UniPathwayiUPA00927.

Names & Taxonomyi

Protein namesi
Recommended name:
Glycerate dehydrogenase (EC:1.1.1.29)
Short name:
GDH
Alternative name(s):
Glyoxylate reductase
Hydroxypyruvate dehydrogenase
NADH-dependent hydroxypyruvate reductase
Short name:
HPR
OrganismiHyphomicrobium methylovorum
Taxonomic identifieri84 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesHyphomicrobiaceaeHyphomicrobium

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed
Chaini2 – 322321Glycerate dehydrogenase
PRO_0000075942Add
BLAST

Expressioni

Inductioni

By methanol.

Interactioni

Subunit structurei

Homodimer.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 106
Helixi14 – 218
Beta strandi24 – 285
Helixi37 – 448
Beta strandi48 – 536
Helixi60 – 656
Beta strandi72 – 787
Helixi85 – 906
Beta strandi94 – 963
Helixi103 – 11816
Helixi121 – 1299
Turni138 – 1414
Beta strandi150 – 1545
Helixi158 – 16811
Turni169 – 1713
Beta strandi173 – 1775
Helixi184 – 1896
Helixi198 – 2047
Beta strandi206 – 2105
Turni216 – 2205
Helixi224 – 2274
Beta strandi234 – 2385
Helixi242 – 2443
Helixi247 – 2559
Beta strandi258 – 2658
Turni268 – 2714
Helixi277 – 2793
Beta strandi283 – 2853
Helixi294 – 31219
Beta strandi320 – 3223

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1GDHX-ray2.40A/B3-322[»]
ProteinModelPortaliP36234.
SMRiP36234. Positions 3-322.

Miscellaneous databases

EvolutionaryTraceiP36234.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni2 – 10099Catalytic
Add
BLAST
Regioni101 – 291191Coenzyme-binding
Add
BLAST
Regioni292 – 32231Catalytic
Add
BLAST

Sequence similaritiesi

Family and domain databases

Gene3Di3.40.50.720. 2 hits.
InterProiIPR006139. D-isomer_2_OHA_DH_cat_dom.
IPR006140. D-isomer_DH_NAD-bd.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF00389. 2-Hacid_dh. 1 hit.
PF02826. 2-Hacid_dh_C. 1 hit.
[Graphical view]
PROSITEiPS00065. 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]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P36234-1 [UniParc]FASTAAdd to Basket

« Hide

MSKKKILITW PLPEAAMARA RESYDVIAHG DDPKITIDEM IETAKSVDAL    50
LITLNEKCRK EVIDRIPENI KCISTYSIGF DHIDLDACKA RGIKVGNAPH 100
GVTVATAEIA MLLLLGSARR AGEGEKMIRT RSWPGWEPLE LVGEKLDNKT 150
LGIYGFGSIG QALAKRAQGF DMDIDYFDTH RASSSDEASY QATFHDSLDS 200
LLSVSQFFSL NAPSTPETRY FFNKATIKSL PQGAIVVNTA RGDLVDNELV 250
VAALEAGRLA YAGFDVFAGE PNINEGYYDL PNTFLFPHIG SAATQAREDM 300
AHQANDLIDA LFGGADMSYA LA 322
Length:322
Mass (Da):35,115
Last modified:January 23, 2007 - v2
Checksum:iCA5E39C1617AF2FE
GO

Cross-referencesi

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1GDH X-ray 2.40 A/B 3-322 [» ]
ProteinModelPortali P36234.
SMRi P36234. Positions 3-322.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Enzyme and pathway databases

UniPathwayi UPA00927 .
BioCyci MetaCyc:MONOMER-4245.

Miscellaneous databases

EvolutionaryTracei P36234.

Family and domain databases

Gene3Di 3.40.50.720. 2 hits.
InterProi IPR006139. D-isomer_2_OHA_DH_cat_dom.
IPR006140. D-isomer_DH_NAD-bd.
IPR016040. NAD(P)-bd_dom.
[Graphical view ]
Pfami PF00389. 2-Hacid_dh. 1 hit.
PF02826. 2-Hacid_dh_C. 1 hit.
[Graphical view ]
PROSITEi 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 ]
ProtoNeti Search...

Publicationsi

  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.

Entry informationi

Entry nameiDHGY_HYPME
AccessioniPrimary (citable) accession number: P36234
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: January 23, 2007
Last modified: September 3, 2014
This is version 91 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure

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

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