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Protein

Glycerate dehydrogenase

Gene
N/A
Organism
Hyphomicrobium methylovorum
Status
Reviewed-Annotation score: 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: formaldehyde assimilation via serine pathway

This protein is involved in the pathway formaldehyde assimilation via serine pathway, which is part of One-carbon metabolism.
View all proteins of this organism that are known to be involved in the pathway formaldehyde assimilation via serine pathway and in One-carbon metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei178NADBy similarity1
Active sitei2411
Binding sitei265NADBy similarity1
Active sitei2701
Active sitei288Proton donor1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi158 – 159NADBy similarity2
Nucleotide bindingi239 – 241NADBy similarity3
Nucleotide bindingi288 – 291NADBy similarity4

GO - Molecular functioni

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)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved
ChainiPRO_00000759422 – 322Glycerate dehydrogenaseAdd BLAST321

Expressioni

Inductioni

By methanol.

Interactioni

Subunit structurei

Homodimer.

Structurei

Secondary structure

1322
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi5 – 10Combined sources6
Helixi14 – 21Combined sources8
Beta strandi24 – 28Combined sources5
Helixi37 – 44Combined sources8
Beta strandi48 – 53Combined sources6
Helixi60 – 65Combined sources6
Beta strandi72 – 78Combined sources7
Helixi85 – 90Combined sources6
Beta strandi94 – 96Combined sources3
Helixi103 – 118Combined sources16
Helixi121 – 129Combined sources9
Turni138 – 141Combined sources4
Beta strandi150 – 154Combined sources5
Helixi158 – 168Combined sources11
Turni169 – 171Combined sources3
Beta strandi173 – 177Combined sources5
Helixi184 – 189Combined sources6
Helixi198 – 204Combined sources7
Beta strandi206 – 210Combined sources5
Turni216 – 220Combined sources5
Helixi224 – 227Combined sources4
Beta strandi234 – 238Combined sources5
Helixi242 – 244Combined sources3
Helixi247 – 255Combined sources9
Beta strandi258 – 265Combined sources8
Turni268 – 271Combined sources4
Helixi277 – 279Combined sources3
Beta strandi283 – 285Combined sources3
Helixi294 – 312Combined sources19
Beta strandi320 – 322Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1GDHX-ray2.40A/B3-322[»]
ProteinModelPortaliP36234.
SMRiP36234.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP36234.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni2 – 100CatalyticAdd BLAST99
Regioni101 – 291Coenzyme-bindingAdd BLAST191
Regioni292 – 322CatalyticAdd BLAST31

Sequence similaritiesi

Family and domain databases

Gene3Di3.40.50.720. 2 hits.
InterProiIPR006139. D-isomer_2_OHA_DH_cat_dom.
IPR029753. D-isomer_DH_CS.
IPR029752. D-isomer_DH_CS1.
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]
SUPFAMiSSF51735. SSF51735. 1 hit.
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

        10         20         30         40         50
MSKKKILITW PLPEAAMARA RESYDVIAHG DDPKITIDEM IETAKSVDAL
60 70 80 90 100
LITLNEKCRK EVIDRIPENI KCISTYSIGF DHIDLDACKA RGIKVGNAPH
110 120 130 140 150
GVTVATAEIA MLLLLGSARR AGEGEKMIRT RSWPGWEPLE LVGEKLDNKT
160 170 180 190 200
LGIYGFGSIG QALAKRAQGF DMDIDYFDTH RASSSDEASY QATFHDSLDS
210 220 230 240 250
LLSVSQFFSL NAPSTPETRY FFNKATIKSL PQGAIVVNTA RGDLVDNELV
260 270 280 290 300
VAALEAGRLA YAGFDVFAGE PNINEGYYDL PNTFLFPHIG SAATQAREDM
310 320
AHQANDLIDA LFGGADMSYA LA
Length:322
Mass (Da):35,115
Last modified:January 23, 2007 - v2
Checksum:iCA5E39C1617AF2FE
GO

Cross-referencesi

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1GDHX-ray2.40A/B3-322[»]
ProteinModelPortaliP36234.
SMRiP36234.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayiUPA00927.
BioCyciMetaCyc:MONOMER-4245.

Miscellaneous databases

EvolutionaryTraceiP36234.

Family and domain databases

Gene3Di3.40.50.720. 2 hits.
InterProiIPR006139. D-isomer_2_OHA_DH_cat_dom.
IPR029753. D-isomer_DH_CS.
IPR029752. D-isomer_DH_CS1.
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]
SUPFAMiSSF51735. SSF51735. 1 hit.
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]
ProtoNetiSearch...

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: November 2, 2016
This is version 100 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

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 one 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.