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Protein

3-methyl-2-oxobutanoate hydroxymethyltransferase 1, mitochondrial

Gene

KPHMT1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the reversible reaction in which hydroxymethyl group from 5,10-methylenetetrahydrofolate is tranferred onto alpha-ketoisovalerate to form ketopantoate.1 Publication

Catalytic activityi

5,10-methylenetetrahydrofolate + 3-methyl-2-oxobutanoate + H2O = tetrahydrofolate + 2-dehydropantoate.1 Publication

Cofactori

Mg2+By similarityNote: Binds 1 Mg2+ ion per subunit.By similarity

Pathwayi: (R)-pantothenate biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes (R)-pantoate from 3-methyl-2-oxobutanoate.
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. 3-methyl-2-oxobutanoate hydroxymethyltransferase 1, mitochondrial (KPHMT1), 3-methyl-2-oxobutanoate hydroxymethyltransferase 2, mitochondrial (KPHMT2)
  2. Putative 2-dehydropantoate 2-reductase (KPR)
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 bindingi83 – 831MagnesiumBy similarity
Metal bindingi122 – 1221MagnesiumBy similarity
Binding sitei122 – 1221Alpha-ketoisovalerateBy similarity
Binding sitei152 – 1521Alpha-ketoisovalerateBy similarity
Metal bindingi154 – 1541MagnesiumBy similarity
Active sitei222 – 2221Proton acceptorBy similarity

GO - Molecular functioni

  • 3-methyl-2-oxobutanoate hydroxymethyltransferase activity Source: TAIR
  • metal ion binding Source: UniProtKB-KW
  • methyltransferase activity Source: UniProtKB-KW

GO - Biological processi

  • pantothenate biosynthetic process Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

Pantothenate biosynthesis

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciARA:AT2G46110-MONOMER.
MetaCyc:AT2G46110-MONOMER.
UniPathwayiUPA00028; UER00003.

Names & Taxonomyi

Protein namesi
Recommended name:
3-methyl-2-oxobutanoate hydroxymethyltransferase 1, mitochondrial (EC:2.1.2.11)
Alternative name(s):
Ketopantoate hydroxymethyltransferase 1
Gene namesi
Name:KPHMT1
Synonyms:PANB1
Ordered Locus Names:At2g46110
ORF Names:T3F17.24
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 2

Organism-specific databases

TAIRiAT2G46110.

Subcellular locationi

GO - Cellular componenti

  • mitochondrion Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 4848MitochondrionSequence analysisAdd
BLAST
Chaini49 – 3472993-methyl-2-oxobutanoate hydroxymethyltransferase 1, mitochondrialPRO_0000429566Add
BLAST

Proteomic databases

PaxDbiO82357.
PRIDEiO82357.

Expressioni

Gene expression databases

GenevisibleiO82357. AT.

Interactioni

Protein-protein interaction databases

BioGridi4554. 1 interaction.
STRINGi3702.AT2G46110.1.

Structurei

3D structure databases

ProteinModelPortaliO82357.
SMRiO82357. Positions 42-308.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni83 – 842Alpha-ketoisovalerate bindingBy similarity

Sequence similaritiesi

Belongs to the PanB family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG2949. Eukaryota.
COG0413. LUCA.
HOGENOMiHOG000078427.
InParanoidiO82357.
KOiK00606.
OMAiTEDMIGA.
PhylomeDBiO82357.

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]
SUPFAMiSSF51621. SSF51621. 1 hit.
TIGRFAMsiTIGR00222. panB. 1 hit.

Sequencei

Sequence statusi: Complete.

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

O82357-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MASSLTRNCS RFSKAISVRF MSNLPENTVY GGPKPQNPNQ RVTLTHLRQK
60 70 80 90 100
HRRGEPITVV TAYDYPSAVH LDTAGIDVCL VGDSASMVVH GHDTTLPISL
110 120 130 140 150
DEMLVHCRAV ARGAKRPLLV GDLPFGTYES SSSQAVDTAV RVLKEGGMDA
160 170 180 190 200
IKLEGGSASR ITAAKAIVEA GIAVIGHVGL TPQAISVLGG FRPQGRNIAS
210 220 230 240 250
AVKVVETAMA LQEAGCFSVV LECVPPPVAA AATSALKIPT IGIGAGPFCS
260 270 280 290 300
GQVLVYHDLL GMMQHPHHAK VTPKFCKQYA NVGEVINKAL MEYKEEVSKK
310 320 330 340
VFPGPSHSPY KITASELDGF LTELQKLGFD KAASAAALAA ENMEPSK
Length:347
Mass (Da):36,693
Last modified:November 1, 1998 - v1
Checksum:i1A37916DA6B97795
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC005397 Genomic DNA. Translation: AAC62893.1.
CP002685 Genomic DNA. Translation: AEC10645.1.
BT004820 mRNA. Translation: AAO44086.1.
AK227849 mRNA. Translation: BAE99826.1.
PIRiH84898.
RefSeqiNP_182135.1. NM_130174.4.
UniGeneiAt.48599.
At.66444.

Genome annotation databases

EnsemblPlantsiAT2G46110.1; AT2G46110.1; AT2G46110.
GeneIDi819219.
GrameneiAT2G46110.1; AT2G46110.1; AT2G46110.
KEGGiath:AT2G46110.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC005397 Genomic DNA. Translation: AAC62893.1.
CP002685 Genomic DNA. Translation: AEC10645.1.
BT004820 mRNA. Translation: AAO44086.1.
AK227849 mRNA. Translation: BAE99826.1.
PIRiH84898.
RefSeqiNP_182135.1. NM_130174.4.
UniGeneiAt.48599.
At.66444.

3D structure databases

ProteinModelPortaliO82357.
SMRiO82357. Positions 42-308.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4554. 1 interaction.
STRINGi3702.AT2G46110.1.

Proteomic databases

PaxDbiO82357.
PRIDEiO82357.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT2G46110.1; AT2G46110.1; AT2G46110.
GeneIDi819219.
GrameneiAT2G46110.1; AT2G46110.1; AT2G46110.
KEGGiath:AT2G46110.

Organism-specific databases

TAIRiAT2G46110.

Phylogenomic databases

eggNOGiKOG2949. Eukaryota.
COG0413. LUCA.
HOGENOMiHOG000078427.
InParanoidiO82357.
KOiK00606.
OMAiTEDMIGA.
PhylomeDBiO82357.

Enzyme and pathway databases

UniPathwayiUPA00028; UER00003.
BioCyciARA:AT2G46110-MONOMER.
MetaCyc:AT2G46110-MONOMER.

Miscellaneous databases

PROiO82357.

Gene expression databases

GenevisibleiO82357. AT.

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]
SUPFAMiSSF51621. SSF51621. 1 hit.
TIGRFAMsiTIGR00222. panB. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  2. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  3. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  4. "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs."
    Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.
    , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K.
    Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  5. "Organisation of the pantothenate (vitamin B5) biosynthesis pathway in higher plants."
    Ottenhof H.H., Ashurst J.L., Whitney H.M., Saldanha S.A., Schmitzberger F., Gweon H.S., Blundell T.L., Abell C., Smith A.G.
    Plant J. 37:61-72(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION.

Entry informationi

Entry nameiPANB1_ARATH
AccessioniPrimary (citable) accession number: O82357
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 9, 2014
Last sequence update: November 1, 1998
Last modified: February 17, 2016
This is version 108 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  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.