MetaCyc Enzyme: 3-methyl-2-oxobutanoate hydroxymethyltransferase

Gene: panB Accession Numbers: EG11675 (MetaCyc), b0134, ECK0133

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of 3-methyl-2-oxobutanoate hydroxymethyltransferase = [PanB]10
         3-methyl-2-oxobutanoate hydroxymethyltransferase monomer = PanB

3-methyl-2-oxobutanoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step of the pantothenate biosynthesis pathway, transferring the C11 carbon of 5,10-methylene-tetrahydrofolate onto 2-keto-isovalerate to form 2-dehydropantoate [Teller76]. 2-Dehydropantoate is an essential precursor of pantothenate [Powers76].

A crystal structure of the enzyme has been solved at 1.9 Å resolution; the quarternary structure can best be described as a pentamer of dimers [vonDelft03]. Structure-based sequence alignments show that it belongs to a family within the phosphoenolpyruvate/pyruvate superfamily [Schmitzberger03].

panB mutants are auxotrophic for pantothenate [Cronan82].

Locations: cytosol, membrane

Map Position: [148,807 <- 149,601]

Molecular Weight of Polypeptide: 28.237 kD (from nucleotide sequence), 27.0 kD (experimental) [Powers76 ]

Molecular Weight of Multimer: 285.0 kD (experimental) [Powers76]

pI: 5.37

Unification Links: ASAP:ABE-0000467 , CGSC:427 , DIP:DIP-10436N , EchoBASE:EB1626 , EcoGene:EG11675 , EcoliWiki:b0134 , Mint:MINT-1249247 , ModBase:P31057 , OU-Microarray:b0134 , PortEco:panB , PR:PRO_000023488 , Pride:P31057 , Protein Model Portal:P31057 , RefSeq:NP_414676 , RegulonDB:EG11675 , SMR:P31057 , String:511145.b0134 , UniProt:P31057

Relationship Links: InterPro:IN-FAMILY:IPR003700 , InterPro:IN-FAMILY:IPR015813 , Panther:IN-FAMILY:PTHR20881 , PDB:Structure:1M3U , Pfam:IN-FAMILY:PF02548

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0033317 - pantothenate biosynthetic process from valine Inferred from experiment [Teller76]
GO:0015940 - pantothenate biosynthetic process Inferred by computational analysis [UniProtGOA12, UniProtGOA11, GOA06, GOA01]
Molecular Function: GO:0000287 - magnesium ion binding Inferred from experiment [Powers76]
GO:0003864 - 3-methyl-2-oxobutanoate hydroxymethyltransferase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, GOA01, Teller76]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05, Lasserre06]
GO:0016020 - membrane Inferred from experiment [Lasserre06]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06]

MultiFun Terms: metabolism biosynthesis of building blocks cofactors, small molecule carriers Coenzyme A and its modification

Imported from EcoCyc 02-Jun-2015 by Paley S , SRI International

Enzymatic reaction of: 3-methyl-2-oxobutanoate hydroxymethyltransferase

Synonyms: α-ketoisovalerate hydroxymethyltransferase, dehydropantoate hydroxymethyltransferase, ketopantoate hydroxymethyltransferase, KPHMT, 5,10-methylenetetrahydrofolate:3-methyl-2-oxobutanoate hydroxymethyltransferase

EC Number:

a 5,10-methylene-tetrahydrofolate + 3-methyl-2-oxobutanoate + H2O <=> 2-dehydropantoate + a tetrahydrofolate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

This reaction is reversible. [Teller76]

In Pathways: pantothenate and coenzyme A biosynthesis I , phosphopantothenate biosynthesis I

Imported from EcoCyc 02-Jun-2015 by Paley S , SRI International

The forward and reverse reactions occur at similar Vmax [Powers76].

The enzyme requires the l-isomer of THF, but it can utilize conjugates containing 1-6 additional glutamate residues, such as tetrahydropteroylpentaglutamate, tetrahydropteroyltetraglutamate and tetrahydropteroyltriglutamate. The specificity for the ketoacid substrate is not as strict; α-ketobutyrate, α-ketovalerate and α-keto-β-methylvalerate could all replace 2-oxo-isovalerate as substrates [Powers76].

Cofactors or Prosthetic Groups: Mg2+ [Comment 1, Powers76]

Inhibitors (Unknown Mechanism): 3-methyl-2-butanone [Powers76] , formaldehyde [Powers76, Comment 2] , tetrahydropteroyl mono-L-glutamate [Powers76, Comment 2] , coenzyme A [Powers76, Comment 2] , (R)-pantothenate [Powers76, Comment 3] , (R)-pantoate [Powers76, Comment 4] , isovalerate [Comment 5] , pyruvate [Powers76, Comment 5] , L-valine [Powers76, Comment 6] , D-valine [Powers76, Comment 7]

Primary Physiological Regulators of Enzyme Activity: coenzyme A , (R)-pantothenate , (R)-pantoate

Kinetic Parameters:

Km (μM)
[Jones93a, BRENDA14]
[Powers76, BRENDA14]
a tetrahydrofolate
[Powers79, BRENDA14]
a tetrahydrofolate
[Powers76, BRENDA14]
a 5,10-methylene-tetrahydrofolate
[Powers79, BRENDA14]
a 5,10-methylene-tetrahydrofolate
[Powers76, BRENDA14]
[Powers76, BRENDA14]

T(opt): 70 °C [BRENDA14, Powers76]

pH(opt): 7 [BRENDA14, Powers76], 8 [BRENDA14, Teller76], 7-7.6 [Powers76]

Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 7 -> 8
[Jones93a, UniProt10]
UniProt: (in Ref. 2; CAA46505);
Sequence-Conflict 12
[Jones93a, UniProt10]
UniProt: (in Ref. 2; CAA46505);
Sequence-Conflict 15
[Jones93a, UniProt10]
UniProt: (in Ref. 2; CAA46505);
Metal-Binding-Site 45
UniProt: Magnesium.
Protein-Segment 45 -> 46
UniProt: Alpha-ketoisovalerate binding; Sequence Annotation Type: region of interest;
Sequence-Conflict 63
[Jones93a, UniProt10]
UniProt: (in Ref. 2; CAA46505);
Metal-Binding-Site 84
UniProt: Magnesium.
Amino-Acid-Sites-That-Bind 112
UniProt: Alpha-ketoisovalerate.
Metal-Binding-Site 114
UniProt: Magnesium; Non-Experimental Qualifier: by similarity;
Sequence-Conflict 124
[Jones93a, UniProt10]
UniProt: (in Ref. 2; CAA46505);
Active-Site 181
UniProt: Proton acceptor.

10/20/97 Gene b0134 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11675; confirmed by SwissProt match.


BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014."

Cronan82: Cronan JE, Littel KJ, Jackowski S (1982). "Genetic and biochemical analyses of pantothenate biosynthesis in Escherichia coli and Salmonella typhimurium." J Bacteriol 149(3);916-22. PMID: 7037743

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Jones93a: Jones CE, Brook JM, Buck D, Abell C, Smith AG (1993). "Cloning and sequencing of the Escherichia coli panB gene, which encodes ketopantoate hydroxymethyltransferase, and overexpression of the enzyme." J Bacteriol 1993;175(7);2125-30. PMID: 8096212

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Powers76: Powers SG, Snell EE (1976). "Ketopantoate hydroxymethyltransferase. II. Physical, catalytic, and regulatory properties." J Biol Chem 1976;251(12);3786-93. PMID: 6463

Powers79: Powers SG, Snell EE (1979). "Purification and properties of ketopantoate hydroxymethyltransferase." Methods Enzymol 62;204-9. PMID: 374973

Schmitzberger03: Schmitzberger F, Smith AG, Abell C, Blundell TL (2003). "Comparative analysis of the Escherichia coli ketopantoate hydroxymethyltransferase crystal structure confirms that it is a member of the (betaalpha)8 phosphoenolpyruvate/pyruvate superfamily." J Bacteriol 185(14);4163-71. PMID: 12837791

Teller76: Teller JH, Powers SG, Snell EE (1976). "Ketopantoate hydroxymethyltransferase. I. Purification and role in pantothenate biosynthesis." J Biol Chem 251(12);3780-5. PMID: 776976

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

vonDelft03: von Delft F, Inoue T, Saldanha SA, Ottenhof HH, Schmitzberger F, Birch LM, Dhanaraj V, Witty M, Smith AG, Blundell TL, Abell C (2003). "Structure of E. coli ketopantoate hydroxymethyl transferase complexed with ketopantoate and Mg2+, solved by locating 160 selenomethionine sites." Structure 11(8);985-96. PMID: 12906829

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 19.0 on Thu Oct 8, 2015, biocyc13.