3-methyl-2-oxobutanoate hydroxymethyltransferase

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P31057 (PANB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 123. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
3-methyl-2-oxobutanoate hydroxymethyltransferase
EC=2.1.2.11

Alternative name(s):
Ketopantoate hydroxymethyltransferase
Short name=KPHMT

Gene names

Name:	panB
Ordered Locus Names:	b0134, JW0130

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	264 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the reversible reaction in which hydroxymethyl group from 5,10-methylenetetrahydrofolate is tranferred onto alpha-ketoisovalerate to form ketopantoate. Ref.7
Catalytic activity	5,10-methylenetetrahydrofolate + 3-methyl-2-oxobutanoate + H₂O = tetrahydrofolate + 2-dehydropantoate. HAMAP-Rule MF_00156
Cofactor	Binds 1 magnesium ion per subunit. Can also use manganese, cobalt and zinc to a lesser extent. Ref.8
Enzyme regulation	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. Ref.8
Pathway	Cofactor biosynthesis; (R)-pantothenate biosynthesis; (R)-pantoate from 3-methyl-2-oxobutanoate: step 1/2. HAMAP-Rule MF_00156
Subunit structure	Homodecamer; pentamer of dimers. Ref.8 Ref.9
Subcellular location	Cytoplasm Potential HAMAP-Rule MF_00156.
Sequence similarities	Belongs to the PanB family.
Biophysicochemical properties	Kinetic parameters: K_M=0.16 mM for ketopantoate Ref.8 K_M=0.18 mM for L-tetrahydrofolate K_M=1.0 mM for alpha-ketoisovalerate (at 37 degrees Celsius and pH 6.8) K_M=2.9 mM for alpha-ketobutyrate (at 37 degrees Celsius and pH 6.8) K_M=5.9 mM for formaldehyde K_M=5.9 mM for alpha-keto-beta-methylvalerate (at 37 degrees Celsius and pH 6.8) K_M=25 mM for alpha-ketovalerate (at 37 degrees Celsius and pH 6.8) V_max=8.25 µmol/min/mg enzyme for the forward reaction V_max=7.3 µmol/min/mg enzyme for the reverse reaction V_max=4 µmol/min/mg enzyme with alpha-ketobutyrate as substrate (at 37 degrees Celsius and pH 6.8) V_max=2.8 µmol/min/mg enzyme with alpha-ketoisovalerate as substrate (at 37 degrees Celsius and pH 6.8) V_max=2 µmol/min/mg enzyme with alpha-ketovalerate as substrate (at 37 degrees Celsius and pH 6.8) V_max=0.43 µmol/min/mg enzyme with alpha-keto-beta-methylvalerate as substrate (at 37 degrees Celsius and pH 6.8) pH dependence: Optimum pH is 7.0-7.6. Stable from pH 5.0 to 10.0. Rapidly inactivated below pH 4.5. Temperature dependence: Optimum temperature is 70-80 degrees Celsius.
Mass spectrometry	Molecular mass is 28234 Da from positions 1 - 264. Determined by ESI. Ref.9

Ontologies

Keywords
Biological process	Pantothenate biosynthesis
Cellular component	Cytoplasm
Ligand	Magnesium Metal-binding
Molecular function	Methyltransferase Transferase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	pantothenate biosynthetic process from valine Inferred from mutant phenotype Ref.7. Source: EcoCyc
Cellular_component	cytosol Inferred from direct assay PubMed 16858726. Source: UniProtKB membrane Inferred from direct assay PubMed 16858726. Source: UniProtKB
Molecular_function	3-methyl-2-oxobutanoate hydroxymethyltransferase activity Inferred from direct assay Ref.7. Source: EcoCyc magnesium ion binding Inferred from direct assay Ref.8. Source: EcoCyc methyltransferase activity Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 264

264

3-methyl-2-oxobutanoate hydroxymethyltransferase HAMAP-Rule MF_00156

PRO_0000184841

Regions

Region

45 – 46

Alpha-ketoisovalerate binding HAMAP-Rule MF_00156

Sites

Active site

181

Proton acceptor

Metal binding

Magnesium

Metal binding

Magnesium

Metal binding

114

Magnesium By similarity

Binding site

Alpha-ketoisovalerate

Binding site

112

Alpha-ketoisovalerate

Experimental info

Sequence conflict

7 – 8

SL → AS in CAA46505. Ref.2

Sequence conflict

Y → C in CAA46505. Ref.2

Sequence conflict

E → D in CAA46505. Ref.2

Sequence conflict

A → E in CAA46505. Ref.2

Sequence conflict

124

Q → K in CAA46505. Ref.2

Secondary structure

264

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P31057 [UniParc].

Last modified July 1, 1993. Version 1.
Checksum: 0437D6BB9EBF817B
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FASTA

264

28,237

        10         20         30         40         50         60 
MKPTTISLLQ KYKQEKKRFA TITAYDYSFA KLFADEGLNV MLVGDSLGMT VQGHDSTLPV 

        70         80         90        100        110        120 
TVADIAYHTA AVRRGAPNCL LLADLPFMAY ATPEQAFENA ATVMRAGANM VKIEGGEWLV 

       130        140        150        160        170        180 
ETVQMLTERA VPVCGHLGLT PQSVNIFGGY KVQGRGDEAG DQLLSDALAL EAAGAQLLVL 

       190        200        210        220        230        240 
ECVPVELAKR ITEALAIPVI GIGAGNVTDG QILVMHDAFG ITGGHIPKFA KNFLAETGDI 

       250        260 
RAAVRQYMAE VESGVYPGEE HSFH

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nucleotide sequence of the Escherichia coli panBCD gene cluster." Merkel W.K., Nichols B.P. Submitted (JUN-1993) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[2]	"Cloning and sequencing of the Escherichia coli panB gene, which encodes ketopantoate hydroxymethyltransferase, and overexpression of the enzyme." Jones C.E., Brook J.M., Buck D., Abell C., Smith A.G. J. Bacteriol. 175:2125-2130(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-15. Strain: K12.
[3]	"Systematic sequencing of the Escherichia coli genome: analysis of the 2.4-4.1 min (110,917-193,643 bp) region." Fujita N., Mori H., Yura T., Ishihama A. Nucleic Acids Res. 22:1637-1639(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[5]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]	"Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Link A.J., Robison K., Church G.M. Electrophoresis 18:1259-1313(1997) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-12. Strain: K12 / EMG2.
[7]	"Ketopantoate hydroxymethyltransferase. I. Purification and role in pantothenate biosynthesis." Teller J.H., Powers S.G., Snell E.E. J. Biol. Chem. 251:3780-3785(1976) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[8]	"Ketopantoate hydroxymethyltransferase. II. Physical, catalytic, and regulatory properties." Powers S.G., Snell E.E. J. Biol. Chem. 251:3786-3793(1976) [PubMed] [Europe PMC] [Abstract] Cited for: BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, COFACTOR, SUBUNIT.
[9]	"Structure of E. coli ketopantoate hydroxymethyl transferase complexed with ketopantoate and Mg2+, solved by locating 160 selenomethionine sites." von Delft F., Inoue T., Saldanha S.A., Ottenhof H.H., Schmitzberger F., Birch L.M., Dhanaraj V., Witty M., Smith A.G., Blundell T.L., Abell C. Structure 11:985-996(2003) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH ITS PRODUCT AND MAGNESIUM IONS, REACTION MECHANISM, MASS SPECTROMETRY, SUBUNIT.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

L17086 Genomic DNA. Translation: AAA24271.1.
X65538 Genomic DNA. Translation: CAA46505.1.
U00096 Genomic DNA. Translation: AAC73245.1.
AP009048 Genomic DNA. Translation: BAB96711.1.

PIR

F64736.

RefSeq

NP_414676.1. NC_000913.2.
YP_488437.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1M3U	X-ray	1.80	A/B/C/D/E/F/G/H/I/J	1-264	[»]

ProteinModelPortal

P31057.

SMR

P31057. Positions 3-264.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10436N.

IntAct

P31057. 8 interactions.

MINT

MINT-1249247.

STRING

511145.b0134.

Proteomic databases

PaxDb

P31057.

PRIDE

P31057.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC73245; AAC73245; b0134.
BAB96711; BAB96711; BAB96711.

GeneID

12932389.
944839.

KEGG

ecj:Y75_p0131.
eco:b0134.

PATRIC

32115373. VBIEscCol129921_0138.

Organism-specific databases

EchoBASE

EB1626.

EcoGene

EG11675. panB.

Phylogenomic databases

eggNOG

COG0413.

HOGENOM

HOG000078427.

K00606.

OMA

CYDASFA.

ProtClustDB

PRK00311.

Enzyme and pathway databases

BioCyc

EcoCyc:3-CH3-2-OXOBUTANOATE-OH-CH3-XFER-MONOMER.
ECOL316407:JW0130-MONOMER.
MetaCyc:3-CH3-2-OXOBUTANOATE-OH-CH3-XFER-MONOMER.

UniPathway

UPA00028; UER00003.

Gene expression databases

Genevestigator

P31057.

Family and domain databases

Gene3D

3.20.20.60. 1 hit.

HAMAP

MF_00156. PanB.

InterPro

IPR003700. Pantoate_hydroxy_MeTrfase.
IPR015813. Pyrv/PenolPyrv_Kinase.
[Graphical view]

PANTHER

PTHR20881. PTHR20881. 1 hit.

Pfam

PF02548. Pantoate_transf. 1 hit.
[Graphical view]

PIRSF

PIRSF000388. Pantoate_hydroxy_MeTrfase. 1 hit.

SUPFAM

SSF51621. Pyrv/PenolPyrv_Kinase_cat. 1 hit.

TIGRFAMs

TIGR00222. panB. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P31057.

Entry information

Entry name

PANB_ECOLI

Accession

Primary (citable) accession number: P31057

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1993
Last sequence update:	July 1, 1993
Last modified:	May 1, 2013
This is version 123 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents