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Escherichia coli K-12 substr. MG1655 Enzyme: pantothenate synthetase



Gene: panC Accession Numbers: EG11746 (EcoCyc), b0133, ECK0132

Regulation Summary Diagram: ?

Subunit composition of pantothenate synthetase = [PanC]2
         pantothenate synthetase monomer = PanC

Summary:
Pantothenate synthetase catalyzes the synthesis of pantothenate from β-alanine and pantoate, requiring hydrolysis of ATP [Cronan82]. Detailed biochemical studies of the pure enzyme from E. coli K-12 are not available. The enzyme from strains W or B requires both monovalent and divalent cations [MAAS52, Miyatake79].

A crystal structure of the enzyme has been solved at 1.7 Å resolution. Pantothenate synthetase is dimeric both in solution and the crystal structure. It is a member of the cytidylyltransferase superfamily, with an N-terminal Rossmann fold domain containing the active site and a C-terminal domain that forms a hinged lid [vonDelft01].

panC mutants are auxotrophic for pantothenate [Cronan82].

PanC: "pantothenate"

Gene Citations: [Vallari85, Merkel96, Jones93]

Locations: cytosol

Map Position: [147,944 <- 148,795] (3.19 centisomes)
Length: 852 bp / 283 aa

Molecular Weight of Polypeptide: 31.598 kD (from nucleotide sequence), 30.0 kD (experimental) [vonDelft01 ]

Molecular Weight of Multimer: 65.0 kD (experimental) [vonDelft01]

pI: 6.26

Unification Links: ASAP:ABE-0000465 , CGSC:426 , DIP:DIP-10437N , EchoBASE:EB1696 , EcoGene:EG11746 , EcoliWiki:b0133 , Mint:MINT-1249237 , ModBase:P31663 , OU-Microarray:b0133 , PortEco:panC , PR:PRO_000023489 , Pride:P31663 , Protein Model Portal:P31663 , RefSeq:NP_414675 , RegulonDB:EG11746 , SMR:P31663 , String:511145.b0133 , UniProt:P31663

Relationship Links: InterPro:IN-FAMILY:IPR003721 , InterPro:IN-FAMILY:IPR004821 , InterPro:IN-FAMILY:IPR014729 , Panther:IN-FAMILY:PTHR21299:SF1 , PDB:Structure:1IHO , PDB:Structure:3GUZ , Pfam:IN-FAMILY:PF02569

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0033317 - pantothenate biosynthetic process from valine Inferred from experiment [Cronan82]
GO:0009058 - biosynthetic process Inferred by computational analysis [GOA01]
GO:0015940 - pantothenate biosynthetic process Inferred by computational analysis [UniProtGOA12, UniProtGOA11, GOA06, GOA01]
Molecular Function: GO:0004592 - pantoate-beta-alanine ligase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, GOA01, Tuck06, Cronan82]
GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Butland05]
GO:0042802 - identical protein binding Inferred from experiment [Hauser14, Chakrabarti10, Lasserre06]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11]
GO:0016874 - ligase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05, 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 panC 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 ? 25-Mar-2008 by Keseler I , SRI International


Enzymatic reaction of: pantothenate synthetase

Synonyms: pantoate activating enzyme, (R)-pantoate:β-alanine ligase (AMP-forming), pantoate-β-alanine ligase

EC Number: 6.3.2.1

β-alanine + (R)-pantoate + ATP <=> (R)-pantothenate + AMP + diphosphate + H+

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

The reaction is physiologically favored in the direction shown.

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

Summary:
The enzyme was first purified from E. coli W [MAAS52, Maas53] and B [Miyatake76, Miyatake78, Miyatake79]. With the exception of inhibitor studies [Tuck06], no biochemical studies of the pure enzyme from E. coli K-12 have been done.

Cofactors or Prosthetic Groups [MAAS52, Comment 5]: K+ , Mg2+

Alternative Cofactors for Mg2+: Mn2+

Alternative Cofactors for K+: ammonium

Inhibitors (Competitive): 3,3-dimethyl-2-oxobutyric acid 5-(6-aminopurin-9-yl)-3,4-dihydroxytetrahydrofuran-2-ylmethyl ester [Tuck06]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
(R)-pantoate
63.0
[vonDelft01, BRENDA14]
(R)-pantoate
1450.0
[Tuck06, BRENDA14]
ATP
100.0
[vonDelft01, BRENDA14]
ATP
1750.0
[Tuck06, BRENDA14]
β-alanine
150.0
[vonDelft01, BRENDA14]
β-alanine
310.0
1.4
[Tuck06, BRENDA14]

T(opt): 30 °C [BRENDA14, Miyatake78]

pH(opt): 5.5 [BRENDA14, Jonczyk06], 9 [BRENDA14, Jonczyk06], 10 [BRENDA14, vonDelft01]


Sequence Features

Feature Class Location Citations Comment
Nucleotide-Phosphate-Binding-Region 30 -> 37
[UniProt10]
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Active-Site 37
[UniProt10]
UniProt: Proton donor; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 61
[UniProt10]
UniProt: Beta-alanine; Non-Experimental Qualifier: by similarity;
Nucleotide-Phosphate-Binding-Region 149 -> 152
[UniProt10]
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 155
[UniProt10]
UniProt: Pantoate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 178
[UniProt10]
UniProt: ATP; via amide nitrogen and carbonyl oxygen; Non-Experimental Qualifier: by similarity;
Nucleotide-Phosphate-Binding-Region 186 -> 189
[UniProt10]
UniProt: ATP; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b0133 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11746; 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.

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

Chakrabarti10: Chakrabarti KS, Thakur KG, Gopal B, Sarma SP (2010). "X-ray crystallographic and NMR studies of pantothenate synthetase provide insights into the mechanism of homotropic inhibition by pantoate." FEBS J 277(3);697-712. PMID: 20059543

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."

Hauser14: Hauser R, Ceol A, Rajagopala SV, Mosca R, Siszler G, Wermke N, Sikorski P, Schwarz F, Schick M, Wuchty S, Aloy P, Uetz P (2014). "A Second-generation Protein-Protein Interaction Network of Helicobacter pylori." Mol Cell Proteomics 13(5);1318-29. PMID: 24627523

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

Jonczyk06: Jonczyk R, Genschel U (2006). "Molecular adaptation and allostery in plant pantothenate synthetases." J Biol Chem 281(49);37435-46. PMID: 17040917

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

MAAS52: Maas WK (1952). "Pantothenate studies. III. Description of the extracted pantothenate-synthesizing enzyme of Escherichia coli." J Biol Chem 1952;198:23-32. PMID: 12999714

Maas53: Maas WK, Novelli GD (1953). "Synthesis of pantothenic acid by depyrophosphorylation of adenosine triphosphate." Arch Biochem Biophys 43(1);236-8. PMID: 13031681

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

Miyatake76: Miyatake K, Nakano Y, Kitaoka S (1976). "Pantothenate synthetase of Escherichia coli B. I. Physicochemical properties." J Biochem 79(3);673-8. PMID: 780351

Miyatake78: Miyatake K, Nakano Y, Kitaoka S (1978). "Enzymological properties of pantothenate synthetase from Escherichia coli B." J Nutr Sci Vitaminol (Tokyo) 24(3);243-53. PMID: 357689

Miyatake79: Miyatake K, Nakano Y, Kitaoka S (1979). "Pantothenate synthetase from Escherichia coli [D-pantoate: beta-alanine ligase (AMP-forming), EC 6.3.2.1]." Methods Enzymol 1979;62;215-9. PMID: 374975

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

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Tuck06: Tuck KL, Saldanha SA, Birch LM, Smith AG, Abell C (2006). "The design and synthesis of inhibitors of pantothenate synthetase." Org Biomol Chem 4(19);3598-610. PMID: 16990935

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 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

vonDelft01: von Delft F, Lewendon A, Dhanaraj V, Blundell TL, Abell C, Smith AG (2001). "The crystal structure of E. coli pantothenate synthetase confirms it as a member of the cytidylyltransferase superfamily." Structure 9(5);439-50. PMID: 11377204

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


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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