Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
twitter

Escherichia coli K-12 substr. MG1655 Enzyme: 3-methyl-2-oxobutanoate hydroxymethyltransferase



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

Regulation Summary Diagram: ?

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

Summary:
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].

Gene Citations: [Vallari85, Merkel96]

Locations: cytosol, membrane

Map Position: [148,807 <- 149,601] (3.21 centisomes)
Length: 795 bp / 264 aa

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: ?

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

Essentiality data for panB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 0.4% glucose No 37 Aerobic 7.2 0.27 No [Patrick07, Comment 3]
M9 medium with 1% glycerol No 37 Aerobic 7.2 0.35 No [Joyce06]
MOPS medium with 0.4% glucose Indeterminate 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
No [Feist07, Comment 4]

Credits:
Last-Curated ? 24-Mar-2008 by Keseler I , 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: 2.1.2.11

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

Summary:
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 5, Powers76]

Inhibitors (Unknown Mechanism): 3-methyl-2-butanone [Powers76] , formaldehyde [Powers76, Comment 6] , tetrahydropteroyl mono-L-glutamate [Powers76, Comment 6] , coenzyme A [Powers76, Comment 6] , (R)-pantothenate [Powers76, Comment 7] , (R)-pantoate [Powers76, Comment 8] , isovalerate [Comment 9] , pyruvate [Powers76, Comment 9] , L-valine [Powers76, Comment 10] , D-valine [Powers76, Comment 11]

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

Kinetic Parameters:

Substrate
Km (μM)
Citations
2-dehydropantoate
150.0
[Jones93, BRENDA14]
2-dehydropantoate
160.0
[Powers76, BRENDA14]
a tetrahydrofolate
180.0, 180.0
[Powers79, BRENDA14]
a tetrahydrofolate
180.0, 180.0
[Powers76, BRENDA14]
a 5,10-methylene-tetrahydrofolate
180.0, 180.0
[Powers79, BRENDA14]
a 5,10-methylene-tetrahydrofolate
180.0, 180.0
[Powers76, BRENDA14]
3-methyl-2-oxobutanoate
1100.0
[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
[Jones93, UniProt10a]
Alternate sequence: SL → AS; UniProt: (in Ref. 2; CAA46505);
Sequence-Conflict 12
[Jones93, UniProt10a]
Alternate sequence: Y → C; UniProt: (in Ref. 2; CAA46505);
Sequence-Conflict 15
[Jones93, UniProt10a]
Alternate sequence: E → D; UniProt: (in Ref. 2; CAA46505);
Metal-Binding-Site 45
[UniProt10a]
UniProt: Magnesium;
Protein-Segment 45 -> 46
[UniProt10]
UniProt: Alpha-ketoisovalerate binding; Sequence Annotation Type: region of interest;
Sequence-Conflict 63
[Jones93, UniProt10a]
Alternate sequence: A → E; UniProt: (in Ref. 2; CAA46505);
Metal-Binding-Site 84
[UniProt10a]
UniProt: Magnesium;
Amino-Acid-Sites-That-Bind 112
[UniProt10a]
UniProt: Alpha-ketoisovalerate;
Metal-Binding-Site 114
[UniProt10]
UniProt: Magnesium; Non-Experimental Qualifier: by similarity;
Sequence-Conflict 124
[Jones93, UniProt10a]
Alternate sequence: Q → K; UniProt: (in Ref. 2; CAA46505);
Active-Site 181
[UniProt10a]
UniProt: Proton acceptor;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

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


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

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

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

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

Jones93: 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

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

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

Merkel96: Merkel WK, Nichols BP (1996). "Characterization and sequence of the Escherichia coli panBCD gene cluster." FEMS Microbiol Lett 143(2-3);247-52. PMID: 8837478

Patrick07: Patrick WM, Quandt EM, Swartzlander DB, Matsumura I (2007). "Multicopy suppression underpins metabolic evolvability." Mol Biol Evol 24(12);2716-22. PMID: 17884825

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 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 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."

Vallari85: Vallari DS, Rock CO (1985). "Isolation and characterization of Escherichia coli pantothenate permease (panF) mutants." J Bacteriol 1985;164(1);136-42. PMID: 2995306

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

Other References Related to Gene Regulation

Harley87: Harley CB, Reynolds RP (1987). "Analysis of E. coli promoter sequences." Nucleic Acids Res 15(5);2343-61. PMID: 3550697


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Sun Dec 21, 2014, biocyc13.