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Protein

3-methyl-2-oxobutanoate hydroxymethyltransferase

Gene

panB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 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.

Cofactori

Mg2+1 Publication, Mn2+1 Publication, Co2+1 Publication, Zn2+1 PublicationNote: Binds 1 Mg2+ ion per subunit. Can also use Mn2+, Co2+ and Zn2+ to a lesser extent.1 Publication

Enzyme regulationi

Inhibited by isovalerate, pyruvate, 3-methyl-2-butanone, and valine. Partially inhibited by formaldehyde and tetrahydrofolate below or near the KM value. Also inhibited by later intermediates pantoate, pantothenate and coenzyme A.1 Publication

Kineticsi

  1. KM=0.16 mM for ketopantoate1 Publication
  2. KM=0.18 mM for L-tetrahydrofolate1 Publication
  3. KM=1.0 mM for alpha-ketoisovalerate (at 37 degrees Celsius and pH 6.8)1 Publication
  4. KM=2.9 mM for alpha-ketobutyrate (at 37 degrees Celsius and pH 6.8)1 Publication
  5. KM=5.9 mM for formaldehyde1 Publication
  6. KM=5.9 mM for alpha-keto-beta-methylvalerate (at 37 degrees Celsius and pH 6.8)1 Publication
  7. KM=25 mM for alpha-ketovalerate (at 37 degrees Celsius and pH 6.8)1 Publication
  1. Vmax=8.25 µmol/min/mg enzyme for the forward reaction1 Publication
  2. Vmax=7.3 µmol/min/mg enzyme for the reverse reaction1 Publication
  3. Vmax=4 µmol/min/mg enzyme with alpha-ketobutyrate as substrate (at 37 degrees Celsius and pH 6.8)1 Publication
  4. Vmax=2.8 µmol/min/mg enzyme with alpha-ketoisovalerate as substrate (at 37 degrees Celsius and pH 6.8)1 Publication
  5. Vmax=2 µmol/min/mg enzyme with alpha-ketovalerate as substrate (at 37 degrees Celsius and pH 6.8)1 Publication
  6. Vmax=0.43 µmol/min/mg enzyme with alpha-keto-beta-methylvalerate as substrate (at 37 degrees Celsius and pH 6.8)1 Publication

pH dependencei

Optimum pH is 7.0-7.6. Stable from pH 5.0 to 10.0. Rapidly inactivated below pH 4.5.1 Publication

Temperature dependencei

Optimum temperature is 70-80 degrees Celsius.1 Publication

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 (panB)
  2. 2-dehydropantoate 2-reductase (panE)
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)DescriptionActionsGraphical viewLength
Metal bindingi45Magnesium1
Metal bindingi84Magnesium1
Binding sitei84Alpha-ketoisovalerate1
Binding sitei112Alpha-ketoisovalerate1
Metal bindingi114MagnesiumBy similarity1
Active sitei181Proton acceptor1

GO - Molecular functioni

  • 3-methyl-2-oxobutanoate hydroxymethyltransferase activity Source: EcoCyc
  • magnesium ion binding Source: EcoCyc

GO - Biological processi

  • pantothenate biosynthetic process from valine Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Pantothenate biosynthesis

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:3-CH3-2-OXOBUTANOATE-OH-CH3-XFER-MONOMER.
ECOL316407:JW0130-MONOMER.
MetaCyc:3-CH3-2-OXOBUTANOATE-OH-CH3-XFER-MONOMER.
BRENDAi2.1.2.11. 2026.
UniPathwayiUPA00028; UER00003.

Names & Taxonomyi

Protein namesi
Recommended name:
3-methyl-2-oxobutanoate hydroxymethyltransferase (EC:2.1.2.11)
Alternative name(s):
Ketopantoate hydroxymethyltransferase
Short name:
KPHMT
Gene namesi
Name:panB
Ordered Locus Names:b0134, JW0130
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11675. panB.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: UniProtKB
  • membrane Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001848411 – 2643-methyl-2-oxobutanoate hydroxymethyltransferaseAdd BLAST264

Proteomic databases

EPDiP31057.
PaxDbiP31057.
PRIDEiP31057.

Interactioni

Subunit structurei

Homodecamer; pentamer of dimers.2 Publications

Protein-protein interaction databases

BioGridi4261383. 245 interactors.
DIPiDIP-10436N.
IntActiP31057. 8 interactors.
MINTiMINT-1249247.
STRINGi511145.b0134.

Structurei

Secondary structure

1264
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi6 – 15Combined sources10
Beta strandi19 – 23Combined sources5
Helixi27 – 36Combined sources10
Beta strandi40 – 43Combined sources4
Helixi47 – 50Combined sources4
Beta strandi55 – 57Combined sources3
Helixi62 – 75Combined sources14
Beta strandi79 – 84Combined sources6
Beta strandi89 – 92Combined sources4
Helixi93 – 105Combined sources13
Beta strandi109 – 112Combined sources4
Helixi117 – 119Combined sources3
Helixi120 – 128Combined sources9
Beta strandi133 – 139Combined sources7
Helixi141 – 143Combined sources3
Helixi144 – 147Combined sources4
Helixi157 – 173Combined sources17
Beta strandi177 – 182Combined sources6
Helixi185 – 194Combined sources10
Beta strandi199 – 204Combined sources6
Beta strandi208 – 213Combined sources6
Helixi215 – 218Combined sources4
Turni235 – 237Combined sources3
Helixi240 – 252Combined sources13
Helixi259 – 261Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1M3UX-ray1.80A/B/C/D/E/F/G/H/I/J1-264[»]
ProteinModelPortaliP31057.
SMRiP31057.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP31057.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni45 – 46Alpha-ketoisovalerate binding2

Sequence similaritiesi

Belongs to the PanB family.Curated

Phylogenomic databases

eggNOGiENOG4105CCG. Bacteria.
COG0413. LUCA.
HOGENOMiHOG000078427.
InParanoidiP31057.
KOiK00606.
OMAiQMAYHTE.
PhylomeDBiP31057.

Family and domain databases

CDDicd06557. KPHMT-like. 1 hit.
Gene3Di3.20.20.60. 1 hit.
HAMAPiMF_00156. PanB. 1 hit.
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.

P31057-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKPTTISLLQ KYKQEKKRFA TITAYDYSFA KLFADEGLNV MLVGDSLGMT
60 70 80 90 100
VQGHDSTLPV TVADIAYHTA AVRRGAPNCL LLADLPFMAY ATPEQAFENA
110 120 130 140 150
ATVMRAGANM VKIEGGEWLV ETVQMLTERA VPVCGHLGLT PQSVNIFGGY
160 170 180 190 200
KVQGRGDEAG DQLLSDALAL EAAGAQLLVL ECVPVELAKR ITEALAIPVI
210 220 230 240 250
GIGAGNVTDG QILVMHDAFG ITGGHIPKFA KNFLAETGDI RAAVRQYMAE
260
VESGVYPGEE HSFH
Length:264
Mass (Da):28,237
Last modified:July 1, 1993 - v1
Checksum:i0437D6BB9EBF817B
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti7 – 8SL → AS in CAA46505 (PubMed:8096212).Curated2
Sequence conflicti12Y → C in CAA46505 (PubMed:8096212).Curated1
Sequence conflicti15E → D in CAA46505 (PubMed:8096212).Curated1
Sequence conflicti63A → E in CAA46505 (PubMed:8096212).Curated1
Sequence conflicti124Q → K in CAA46505 (PubMed:8096212).Curated1

Mass spectrometryi

Molecular mass is 28234 Da from positions 1 - 264. Determined by ESI. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L17086 Genomic DNA. Translation: AAA24271.1.
X65538 Genomic DNA. Translation: CAA46505.1.
U00096 Genomic DNA. Translation: AAC73245.1.
AP009048 Genomic DNA. Translation: BAB96711.1.
PIRiF64736.
RefSeqiNP_414676.1. NC_000913.3.
WP_000805497.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73245; AAC73245; b0134.
BAB96711; BAB96711; BAB96711.
GeneIDi944839.
KEGGiecj:JW0130.
eco:b0134.
PATRICi32115373. VBIEscCol129921_0138.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L17086 Genomic DNA. Translation: AAA24271.1.
X65538 Genomic DNA. Translation: CAA46505.1.
U00096 Genomic DNA. Translation: AAC73245.1.
AP009048 Genomic DNA. Translation: BAB96711.1.
PIRiF64736.
RefSeqiNP_414676.1. NC_000913.3.
WP_000805497.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1M3UX-ray1.80A/B/C/D/E/F/G/H/I/J1-264[»]
ProteinModelPortaliP31057.
SMRiP31057.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261383. 245 interactors.
DIPiDIP-10436N.
IntActiP31057. 8 interactors.
MINTiMINT-1249247.
STRINGi511145.b0134.

Proteomic databases

EPDiP31057.
PaxDbiP31057.
PRIDEiP31057.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73245; AAC73245; b0134.
BAB96711; BAB96711; BAB96711.
GeneIDi944839.
KEGGiecj:JW0130.
eco:b0134.
PATRICi32115373. VBIEscCol129921_0138.

Organism-specific databases

EchoBASEiEB1626.
EcoGeneiEG11675. panB.

Phylogenomic databases

eggNOGiENOG4105CCG. Bacteria.
COG0413. LUCA.
HOGENOMiHOG000078427.
InParanoidiP31057.
KOiK00606.
OMAiQMAYHTE.
PhylomeDBiP31057.

Enzyme and pathway databases

UniPathwayiUPA00028; UER00003.
BioCyciEcoCyc:3-CH3-2-OXOBUTANOATE-OH-CH3-XFER-MONOMER.
ECOL316407:JW0130-MONOMER.
MetaCyc:3-CH3-2-OXOBUTANOATE-OH-CH3-XFER-MONOMER.
BRENDAi2.1.2.11. 2026.

Miscellaneous databases

EvolutionaryTraceiP31057.
PROiP31057.

Family and domain databases

CDDicd06557. KPHMT-like. 1 hit.
Gene3Di3.20.20.60. 1 hit.
HAMAPiMF_00156. PanB. 1 hit.
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...

Entry informationi

Entry nameiPANB_ECOLI
AccessioniPrimary (citable) accession number: P31057
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: July 1, 1993
Last modified: November 2, 2016
This is version 147 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

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.