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Protein

Glycerol kinase

Gene

glpK

Organism
Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Key enzyme in the regulation of glycerol uptake and metabolism. Catalyzes the phosphorylation of glycerol to yield sn-glycerol 3-phosphate.UniRule annotation

Catalytic activityi

ATP + glycerol = ADP + sn-glycerol 3-phosphate.UniRule annotation

Enzyme regulationi

Inhibited by fructose 1,6-bisphosphate (FBP).UniRule annotation

Pathwayi: glycerol degradation via glycerol kinase pathway

This protein is involved in step 1 of the subpathway that synthesizes sn-glycerol 3-phosphate from glycerol.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Glycerol kinase (glpK)
This subpathway is part of the pathway glycerol degradation via glycerol kinase pathway, which is itself part of Polyol metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes sn-glycerol 3-phosphate from glycerol, the pathway glycerol degradation via glycerol kinase pathway and in Polyol metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei12 – 121SubstrateUniRule annotation
Binding sitei16 – 161ATPUniRule annotation
Binding sitei134 – 1341Substrate
Binding sitei265 – 2651ATPUniRule annotation
Binding sitei308 – 3081ATP; via carbonyl oxygenUniRule annotation
Binding sitei312 – 3121ATP; via amide nitrogenUniRule annotation
Binding sitei327 – 3271ATPUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi12 – 143ATPUniRule annotation
Nucleotide bindingi411 – 4155ATPUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Biological processi

Glycerol metabolism

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciSMEL266834:GJF6-4568-MONOMER.
UniPathwayiUPA00618; UER00672.

Names & Taxonomyi

Protein namesi
Recommended name:
Glycerol kinaseUniRule annotation (EC:2.7.1.30UniRule annotation)
Alternative name(s):
ATP:glycerol 3-phosphotransferaseUniRule annotation
GlycerokinaseUniRule annotation
Short name:
GKUniRule annotation
Gene namesi
Name:glpKUniRule annotation
Ordered Locus Names:RB1135
ORF Names:SMb21009
Encoded oniPlasmid pSymB (megaplasmid 2)0 Publication
OrganismiRhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)
Taxonomic identifieri266834 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeSinorhizobium/Ensifer groupSinorhizobium
Proteomesi
  • UP000001976 Componenti: Plasmid pSymB

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 497497Glycerol kinasePRO_0000059483Add
BLAST

Structurei

Secondary structure

1
497
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 107Combined sources
Beta strandi12 – 209Combined sources
Beta strandi26 – 338Combined sources
Helixi48 – 6417Combined sources
Turni65 – 673Combined sources
Helixi70 – 723Combined sources
Beta strandi73 – 808Combined sources
Beta strandi85 – 895Combined sources
Turni90 – 923Combined sources
Beta strandi95 – 973Combined sources
Helixi108 – 1169Combined sources
Helixi120 – 1278Combined sources
Helixi136 – 14611Combined sources
Helixi150 – 1556Combined sources
Beta strandi159 – 1635Combined sources
Helixi164 – 1729Combined sources
Turni173 – 1753Combined sources
Beta strandi179 – 1813Combined sources
Helixi182 – 1854Combined sources
Beta strandi188 – 1925Combined sources
Turni193 – 1964Combined sources
Helixi200 – 2067Combined sources
Helixi210 – 2123Combined sources
Beta strandi215 – 2173Combined sources
Beta strandi219 – 2213Combined sources
Helixi228 – 2314Combined sources
Beta strandi236 – 2405Combined sources
Helixi243 – 2508Combined sources
Beta strandi259 – 27214Combined sources
Beta strandi281 – 2833Combined sources
Beta strandi285 – 2928Combined sources
Beta strandi295 – 30511Combined sources
Helixi308 – 3169Combined sources
Helixi328 – 3325Combined sources
Beta strandi341 – 3433Combined sources
Turni351 – 3533Combined sources
Beta strandi361 – 3655Combined sources
Helixi371 – 39626Combined sources
Beta strandi406 – 4105Combined sources
Helixi411 – 4144Combined sources
Helixi416 – 42611Combined sources
Beta strandi430 – 4345Combined sources
Helixi438 – 45114Combined sources
Helixi457 – 4626Combined sources
Beta strandi466 – 4705Combined sources
Helixi476 – 49419Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4E1JX-ray2.33A/B/C/D1-497[»]
ProteinModelPortaliO86033.
SMRiO86033. Positions 3-494.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni82 – 832Substrate binding
Regioni243 – 2442Substrate binding

Sequence similaritiesi

Belongs to the FGGY kinase family.UniRule annotation

Phylogenomic databases

KOiK00864.
OMAiGWVEHEP.
OrthoDBiEOG6RZB46.

Family and domain databases

HAMAPiMF_00186. Glycerol_kin.
InterProiIPR000577. Carb_kinase_FGGY.
IPR018485. Carb_kinase_FGGY_C.
IPR018483. Carb_kinase_FGGY_CS.
IPR018484. Carb_kinase_FGGY_N.
IPR005999. Glycerol_kin.
[Graphical view]
PfamiPF02782. FGGY_C. 1 hit.
PF00370. FGGY_N. 1 hit.
[Graphical view]
PIRSFiPIRSF000538. GlpK. 1 hit.
TIGRFAMsiTIGR01311. glycerol_kin. 1 hit.
PROSITEiPS00445. FGGY_KINASES_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O86033-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGGYILAIDQ GTTSTRAIVF DGNQKIAGVG QKEFKQHFPK SGWVEHDPEE
60 70 80 90 100
IWQTVVSTVK EAIEKSGITA NDIAAIGITN QRETVVVWDR ETGKPIHNAI
110 120 130 140 150
VWQDRRTAAF CDKLKKKGLE KTFVKKTGLL LDPYFSGTKL NWLLSNVKGA
160 170 180 190 200
QVRAAKGELC FGTIDTFLIW RLTGGECFCT DATNASRTLL YNIAENAWDD
210 220 230 240 250
ELTEVLRVPK EMLPEVKDCA ADFGVTDPSL FGAAIPILGV AGDQQAATIG
260 270 280 290 300
QACFKPGMLK STYGTGCFAL LNTGKDMVRS KNRLLTTIAY RLDGETTYAL
310 320 330 340 350
EGSIFVAGAA VQWLRDGLKV IKAAPDTGSL AESADPSQEV YLVPAFTGLG
360 370 380 390 400
APHWDPDARG AIFGMTRNTG PAEFARAALE AVCYQTRDLL EAMHKDWRRN
410 420 430 440 450
GNDTVLRVDG GMVASDWTMQ RLSDLLDAPV DRPVILETTA LGVAWLAGSR
460 470 480 490
AGVWPNQEAF AKSWARDRRF EPHMDEATRK VKLKGWRSAV KRTLIAA
Length:497
Mass (Da):54,419
Last modified:October 18, 2001 - v2
Checksum:i42D3428335ACC2B7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL591985 Genomic DNA. Translation: CAC49535.1.
AF080548 Genomic DNA. Translation: AAD12735.1.
PIRiG95983.
RefSeqiNP_437675.1. NC_003078.1.
WP_010975967.1. NC_003078.1.

Genome annotation databases

EnsemblBacteriaiCAC49535; CAC49535; SM_b21009.
GeneIDi1237466.
KEGGisme:SM_b21009.
PATRICi23638684. VBISinMel96828_6063.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL591985 Genomic DNA. Translation: CAC49535.1.
AF080548 Genomic DNA. Translation: AAD12735.1.
PIRiG95983.
RefSeqiNP_437675.1. NC_003078.1.
WP_010975967.1. NC_003078.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4E1JX-ray2.33A/B/C/D1-497[»]
ProteinModelPortaliO86033.
SMRiO86033. Positions 3-494.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAC49535; CAC49535; SM_b21009.
GeneIDi1237466.
KEGGisme:SM_b21009.
PATRICi23638684. VBISinMel96828_6063.

Phylogenomic databases

KOiK00864.
OMAiGWVEHEP.
OrthoDBiEOG6RZB46.

Enzyme and pathway databases

UniPathwayiUPA00618; UER00672.
BioCyciSMEL266834:GJF6-4568-MONOMER.

Family and domain databases

HAMAPiMF_00186. Glycerol_kin.
InterProiIPR000577. Carb_kinase_FGGY.
IPR018485. Carb_kinase_FGGY_C.
IPR018483. Carb_kinase_FGGY_CS.
IPR018484. Carb_kinase_FGGY_N.
IPR005999. Glycerol_kin.
[Graphical view]
PfamiPF02782. FGGY_C. 1 hit.
PF00370. FGGY_N. 1 hit.
[Graphical view]
PIRSFiPIRSF000538. GlpK. 1 hit.
TIGRFAMsiTIGR01311. glycerol_kin. 1 hit.
PROSITEiPS00445. FGGY_KINASES_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti."
    Finan T.M., Weidner S., Wong K., Buhrmester J., Chain P., Vorhoelter F.J., Hernandez-Lucas I., Becker A., Cowie A., Gouzy J., Golding B., Puehler A.
    Proc. Natl. Acad. Sci. U.S.A. 98:9889-9894(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 1021.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 1021.
  3. "Poly-3-hydroxybutyrate degradation in Rhizobium (Sinorhizobium) meliloti: isolation and characterization of a gene encoding 3-hydroxybutyrate dehydrogenase."
    Aneja P., Charles T.C.
    J. Bacteriol. 181:849-857(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-59.
    Strain: SU47 / 1021.
  4. "Crystal structure of glycerol kinase in complex with glycerol from Sinorhizobium meliloti 1021."
    New York structural genomics research consortium (NYSGRC)
    Submitted (MAR-2012) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.33 ANGSTROMS) IN COMPLEX WITH GLYCEROL.

Entry informationi

Entry nameiGLPK_RHIME
AccessioniPrimary (citable) accession number: O86033
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: October 18, 2001
Last modified: November 11, 2015
This is version 103 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, Complete proteome, Plasmid, Reference proteome

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.