Reviewed, UniProtKB/Swiss-Prot P31057 (PANB_ECOLI)

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) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	264 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
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 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 MF_00156
Subunit structure	Homodecamer; pentamer of dimers. Ref.8 Ref.9
Subcellular location	Cytoplasm Potential.
Sequence similarities	Belongs to the panB family.
Biophysicochemical properties	Kinetic parameters: KM=0.16 mM for ketopantoate HAMAP MF_00156 KM=0.18 mM for L-tetrahydrofolate KM=1.0 mM for alpha-ketoisovalerate (at 37 degrees Celsius and pH 6.8) KM=2.9 mM for alpha-ketobutyrate (at 37 degrees Celsius and pH 6.8) KM=5.9 mM for formaldehyde KM=5.9 mM for alpha-keto-beta-methylvalerate (at 37 degrees Celsius and pH 6.8) KM=25 mM for alpha-ketovalerate (at 37 degrees Celsius and pH 6.8) Vmax=8.25 µmol/min/mg enzyme for the forward reaction Vmax=7.3 µmol/min/mg enzyme for the reverse reaction Vmax=4 µmol/min/mg enzyme with alpha-ketobutyrate as substrate (at 37 degrees Celsius and pH 6.8) Vmax=2.8 µmol/min/mg enzyme with alpha-ketoisovalerate as substrate (at 37 degrees Celsius and pH 6.8) Vmax=2 µmol/min/mg enzyme with alpha-ketovalerate as substrate (at 37 degrees Celsius and pH 6.8) Vmax=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
Gene Ontology (GO)
Biological process	pantothenate biosynthetic process Inferred from electronic annotation. Source: HAMAP
Cellular component	cytosol Inferred from direct assay. Source: UniProtKB membrane Inferred from direct assay. Source: UniProtKB
Molecular function	3-methyl-2-oxobutanoate hydroxymethyltransferase activity Inferred from electronic annotation. Source: HAMAP magnesium ion binding 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 MF_00156

PRO_0000184841

Regions

Region

45 – 46

2

Alpha-ketoisovalerate binding HAMAP MF_00156

Sites

Active site

181

1

Proton acceptor HAMAP MF_00156

Metal binding

45

1

Magnesium HAMAP MF_00156

Metal binding

84

1

Magnesium HAMAP MF_00156

Metal binding

114

1

Magnesium By similarity

Binding site

84

1

Alpha-ketoisovalerate HAMAP MF_00156

Binding site

112

1

Alpha-ketoisovalerate HAMAP MF_00156

Experimental info

Sequence conflict

7 – 8

2

SL → AS in CAA46505. Ref.2

Sequence conflict

12

1

Y → C in CAA46505. Ref.2

Sequence conflict

15

1

E → D in CAA46505. Ref.2

Sequence conflict

63

1

A → E in CAA46505. Ref.2

Sequence conflict

124

1

Q → K in CAA46505. Ref.2

Secondary structure

1

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264

Helix Strand Turn

Details...

Helix

6 – 15

10

Beta strand

19 – 23

5

Helix

27 – 36

10

Beta strand

40 – 43

4

Helix

47 – 50

4

Beta strand

55 – 57

3

Helix

62 – 75

14

Beta strand

79 – 84

6

Beta strand

89 – 92

4

Helix

93 – 105

13

Beta strand

109 – 112

4

Helix

117 – 119

3

Helix

120 – 128

9

Beta strand

133 – 139

7

Helix

141 – 143

3

Helix

144 – 147

4

Helix

157 – 173

17

Beta strand

177 – 182

6

Helix

185 – 194

10

Beta strand

199 – 204

6

Beta strand

208 – 213

6

Helix

215 – 218

4

Turn

235 – 237

3

Helix

240 – 252

13

Helix

259 – 261

3

Sequences

	Sequence		Length	Mass (Da)
	P31057-1 [UniParc]. Last modified July 1, 1993. Version 1. Checksum: 0437D6BB9EBF817B	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

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: 8096212] [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: 8202364] [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: 9278503] [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: 16738553] [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: 9298646] [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: 776976] [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: 6463] [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: 12906829] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH ITS PRODUCT AND MAGNESIUM IONS, REACTION MECHANISM, MASS SPECTROMETRY, SUBUNIT.

Cross-references

Sequence databases

EMBLGenBankDDBJ

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

AP_000795.1.
NP_414676.1.

3D structure databases

PDBPDBe

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

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:10436N.

STRING

P31057.

Genome annotation databases

GeneID

944839.

GenomeReviews

Gene locus JW0130 in contig AP009048_GR.
Gene locus b0134 in contig U00096_GR.

KEGG

ecj:JW0130.
eco:b0134.

Organism-specific databases

EchoBASE

EB1626.

EcoGene

EG11675. panB.

CMR

Search...

Phylogenomic databases

HOGENOM

P31057.

OMA

YATPEQT.

Enzyme and pathway databases

BioCyc

EcoCyc:3-CH3-2-OXOBUTANOATE-OH-CH3-XFER-MON.
MetaCyc:3-CH3-2-OXOBUTANOATE-OH-CH3-XFER-MON.

Gene expression databases

Genevestigator

P31057.

Family and domain databases

HAMAP

MF_00156.
[Tree]

InterPro

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

Gene3D

G3DSA:3.20.20.60. Pyrv/PenolPyrv_Kinase_cat. 1 hit.

PANTHER

PTHR20881. Pantoate_transf. 1 hit.

Pfam

PF02548. Pantoate_transf. 1 hit.
[Graphical view]

PIRSF

PIRSF000388. Pantoate_hydroxy_MeTrfase. 1 hit.

TIGRFAMs

TIGR00222. panB. 1 hit.

ProtoNet

Search...

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:	November 3, 2009
This is version 92 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)