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Protein

3-methyl-2-oxobutanoate hydroxymethyltransferase

Gene

panB

Organism
Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Catalyzes the reversible reaction in which hydroxymethyl group from 5,10-methylenetetrahydrofolate is tranferred onto alpha-ketoisovalerate to form ketopantoate.UniRule annotation

Catalytic activityi

5,10-methylenetetrahydrofolate + 3-methyl-2-oxobutanoate + H2O = tetrahydrofolate + 2-dehydropantoate.UniRule annotation

Cofactori

Mg2+UniRule annotationNote: Binds 1 Mg2+ ion per subunit.UniRule annotation

Pathwayi: (R)-pantothenate biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes (R)-pantoate from 3-methyl-2-oxobutanoate.UniRule annotation
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. 3-methyl-2-oxobutanoate hydroxymethyltransferase (panB)
  2. 2-dehydropantoate 2-reductase (VP2363)
This subpathway is part of the pathway (R)-pantothenate biosynthesis, which is itself part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes (R)-pantoate from 3-methyl-2-oxobutanoate, the pathway (R)-pantothenate biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi45 – 451MagnesiumUniRule annotation
Metal bindingi84 – 841MagnesiumUniRule annotation
Binding sitei84 – 841Alpha-ketoisovalerateUniRule annotation
Binding sitei112 – 1121Alpha-ketoisovalerateUniRule annotation
Metal bindingi114 – 1141MagnesiumUniRule annotation
Active sitei181 – 1811Proton acceptorUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Pantothenate biosynthesis

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciVPAR223926:GHK4-2565-MONOMER.
UniPathwayiUPA00028; UER00003.

Names & Taxonomyi

Protein namesi
Recommended name:
3-methyl-2-oxobutanoate hydroxymethyltransferaseUniRule annotation (EC:2.1.2.11UniRule annotation)
Alternative name(s):
Ketopantoate hydroxymethyltransferaseUniRule annotation
Short name:
KPHMTUniRule annotation
Gene namesi
Name:panBUniRule annotation
Ordered Locus Names:VP2506
OrganismiVibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Taxonomic identifieri223926 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
Proteomesi
  • UP000002493 Componenti: Chromosome 1

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 2642643-methyl-2-oxobutanoate hydroxymethyltransferasePRO_0000184904Add
BLAST

Interactioni

Subunit structurei

Homodecamer; pentamer of dimers.UniRule annotation

Protein-protein interaction databases

STRINGi223926.VP2506.

Structurei

3D structure databases

ProteinModelPortaliQ87LV2.
SMRiQ87LV2. Positions 5-262.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni45 – 462Alpha-ketoisovalerate bindingUniRule annotation

Sequence similaritiesi

Belongs to the PanB family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105CCG. Bacteria.
COG0413. LUCA.
HOGENOMiHOG000078427.
KOiK00606.
OMAiDMLGFFD.
OrthoDBiEOG63C0WN.

Family and domain databases

Gene3Di3.20.20.60. 1 hit.
HAMAPiMF_00156. PanB.
InterProiIPR003700. Pantoate_hydroxy_MeTrfase.
IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
[Graphical view]
PANTHERiPTHR20881. PTHR20881. 1 hit.
PfamiPF02548. Pantoate_transf. 1 hit.
[Graphical view]
PIRSFiPIRSF000388. Pantoate_hydroxy_MeTrfase. 1 hit.
SUPFAMiSSF51621. SSF51621. 1 hit.
TIGRFAMsiTIGR00222. panB. 1 hit.

Sequencei

Sequence statusi: Complete.

Q87LV2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKMTINDLI KWKQEGRKFA TSTAYDASFA QLFESQEMPV LLVGDSLGMV
60 70 80 90 100
LQGENDTLPV TVDDIVYHTR CVRAGSPNCL LMADMPFMSY ATPEQACENA
110 120 130 140 150
AKLMRAGANM VKIEGGDWLV DTVKMLTERA VPVCAHLGLT PQSVNIFGGY
160 170 180 190 200
KIQGRDQEKA DRMVKDALAL QEAGAQIVLL ECVPAELAER ITKVLDVPVI
210 220 230 240 250
GIGAGNVTDG QILVMHDMFG ISANYMPKFS KNFLAETGDM RKAVAKYIED
260
VANGVFPDDA HTIA
Length:264
Mass (Da):28,779
Last modified:May 23, 2003 - v1
Checksum:i51A087BC8468622E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000031 Genomic DNA. Translation: BAC60769.1.
RefSeqiNP_798885.1. NC_004603.1.
WP_005454450.1. NC_004603.1.

Genome annotation databases

EnsemblBacteriaiBAC60769; BAC60769; BAC60769.
GeneIDi1190021.
KEGGivpa:VP2506.
PATRICi20143156. VBIVibPar50997_2405.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000031 Genomic DNA. Translation: BAC60769.1.
RefSeqiNP_798885.1. NC_004603.1.
WP_005454450.1. NC_004603.1.

3D structure databases

ProteinModelPortaliQ87LV2.
SMRiQ87LV2. Positions 5-262.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi223926.VP2506.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC60769; BAC60769; BAC60769.
GeneIDi1190021.
KEGGivpa:VP2506.
PATRICi20143156. VBIVibPar50997_2405.

Phylogenomic databases

eggNOGiENOG4105CCG. Bacteria.
COG0413. LUCA.
HOGENOMiHOG000078427.
KOiK00606.
OMAiDMLGFFD.
OrthoDBiEOG63C0WN.

Enzyme and pathway databases

UniPathwayiUPA00028; UER00003.
BioCyciVPAR223926:GHK4-2565-MONOMER.

Family and domain databases

Gene3Di3.20.20.60. 1 hit.
HAMAPiMF_00156. PanB.
InterProiIPR003700. Pantoate_hydroxy_MeTrfase.
IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
[Graphical view]
PANTHERiPTHR20881. PTHR20881. 1 hit.
PfamiPF02548. Pantoate_transf. 1 hit.
[Graphical view]
PIRSFiPIRSF000388. Pantoate_hydroxy_MeTrfase. 1 hit.
SUPFAMiSSF51621. SSF51621. 1 hit.
TIGRFAMsiTIGR00222. panB. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V. cholerae."
    Makino K., Oshima K., Kurokawa K., Yokoyama K., Uda T., Tagomori K., Iijima Y., Najima M., Nakano M., Yamashita A., Kubota Y., Kimura S., Yasunaga T., Honda T., Shinagawa H., Hattori M., Iida T.
    Lancet 361:743-749(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: RIMD 2210633.

Entry informationi

Entry nameiPANB_VIBPA
AccessioniPrimary (citable) accession number: Q87LV2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 23, 2003
Last sequence update: May 23, 2003
Last modified: November 11, 2015
This is version 80 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.