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Escherichia coli K-12 substr. MG1655 Enzyme: 2-dehydropantoate 2-reductase



Gene: panE Accession Numbers: G6239 (EcoCyc), b0425, ECK0419

Synonyms: apbA

Regulation Summary Diagram: ?

Summary:
2-Dehydropantoate 2-reductase catalyzes the NADPH-dependent reduction of ketopantoate to pantoate. The enzyme does not require added divalent metal ions [Zheng00].

Kinetic data is consistent with an ordered sequential reaction mechanism, with NADPH binding followed by ketopantoate binding [Zheng00]. Residues involved in catalysis and substrate binding were identified by site-directed mutagenesis [Zheng00a, Lobley05, Ciulli06, Ciulli07]. The enzyme has relatively high substrate specificity [Zheng03].

Crystal structures of the enzyme have been solved [MatakVinkovic01, Lobley05, Ciulli07, Ciulli07a]. The enzyme is a monomer in solution [Zheng00, MatakVinkovic01] and is comprised of an N-terminal Rossmann fold domain and a C-terminal α-helical domain [MatakVinkovic01].

The enzyme was used as a target for fragment-based drug discovery [Ciulli06, Landon07].

A panE mutant alone is not auxotrophic for pantothenate, because in both E. coli and S. typhimurium, the reaction can also be carried out by IlvC (acetohydroxy acid isomeroreductase) [Elischewski99, Primerano83, Frodyma98].

ApbA: "alternative pyrimidine biosynthetic pathway" [Downs94] (Salmonella typhimurium)

PanE: "pantothenate"

Locations: cytosol

Map Position: [442,828 <- 443,739] (9.54 centisomes)
Length: 912 bp / 303 aa

Molecular Weight of Polypeptide: 33.871 kD (from nucleotide sequence), 33.0 kD (experimental) [Zheng00 ]

Unification Links: ASAP:ABE-0001474 , EchoBASE:EB3056 , EcoGene:EG13271 , EcoliWiki:B0425 , ModBase:P0A9J4 , OU-Microarray:b0425 , PortEco:panE , PR:PRO_000023491 , Pride:P0A9J4 , Protein Model Portal:P0A9J4 , RefSeq:NP_414959 , RegulonDB:G6239 , SMR:P0A9J4 , String:511145.b0425 , UniProt:P0A9J4

Relationship Links: InterPro:IN-FAMILY:IPR003710 , InterPro:IN-FAMILY:IPR008927 , InterPro:IN-FAMILY:IPR013328 , InterPro:IN-FAMILY:IPR013332 , InterPro:IN-FAMILY:IPR013752 , InterPro:IN-FAMILY:IPR016040 , PDB:Structure:1KS9 , PDB:Structure:1YJQ , PDB:Structure:1YON , PDB:Structure:2OFP , Pfam:IN-FAMILY:PF02558 , Pfam:IN-FAMILY:PF08546

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0033317 - pantothenate biosynthetic process from valine Inferred from experiment [Elischewski99]
GO:0015940 - pantothenate biosynthetic process Inferred by computational analysis [UniProtGOA12, UniProtGOA11a, GOA01a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0008677 - 2-dehydropantoate 2-reductase activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Zheng00]
GO:0050661 - NADP binding Inferred from experiment Inferred by computational analysis [GOA01a, Zheng00]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor Inferred by computational analysis [GOA01a]
GO:0050662 - coenzyme binding Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA01a]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

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

Essentiality data for panE 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 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Credits:
Last-Curated ? 25-Mar-2008 by Keseler I , SRI International


Enzymatic reaction of: 2-dehydropantoate 2-reductase

Synonyms: ketopantoate reductase, 2-dehydropantoate reductase, (R)-pantoate:NADP+ 2-oxidoreductase, α-ketopantoate reductase, 2-oxopantoate reductase

EC Number: 1.1.1.169

2-dehydropantoate + NADPH + H+ <=> (R)-pantoate + NADP+

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. [Zheng00]

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

Summary:
The enzyme can be assayed in both reaction directions, but the apparent equilibrium constant of 676 indicates that physiologically the enzyme functions in the direction of pantoate formation [Zheng00].

Inhibitors (Competitive): NADP+ [Zheng00, Comment 5]

Inhibitors (Noncompetitive): (R)-pantoate [Zheng00, Comment 6]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
(R)-pantoate
260.0
[Zheng00, BRENDA14]
NADP+
7.0
[Ciulli07, BRENDA14]
NADP+
7.0
[Zheng00, BRENDA14]
2-dehydropantoate
30.0
[Ciulli07, BRENDA14]
2-dehydropantoate
120.0
[Zheng00, BRENDA14]
2-dehydropantoate
60.0, 120.0
8.0, 40.0
[MatakVinkovic01, BRENDA14]
NADPH
20.0, 4.0
[MatakVinkovic01, BRENDA14]
NADPH
4.0, 7.0
[Zheng00, BRENDA14]
NADPH
7.0
25.0
[Ciulli07, BRENDA14]


Sequence Features

Feature Class Location Citations Comment
Nucleotide-Phosphate-Binding-Region 7 -> 12
[UniProt10a]
UniProt: NADP;
Mutagenesis-Variant 31
[Ciulli06, UniProt11a]
Alternate sequence: R → A; UniProt: Increases KM for NADP 4-fold.
Amino-Acid-Sites-That-Bind 31
[UniProt10a]
UniProt: NADP; via amide nitrogen;
Mutagenesis-Variant 72
[Ciulli07, UniProt11a]
Alternate sequence: K → A; UniProt: Increases KM for NADP 10-fold.
Mutagenesis-Variant 98
[Ciulli07a, Ciulli06, UniProt11a]
Alternate sequence: N → A; UniProt: Increases KM for ketopantoate 140- fold. Strongly decreases catalytic activity.
Amino-Acid-Sites-That-Bind 98
[UniProt10a]
UniProt: NADP; via amide nitrogen;
Amino-Acid-Sites-That-Bind 122
[UniProt10a]
UniProt: NADP; via amide nitrogen and carbonyl oxygen;
Mutagenesis-Variant 176
[Ciulli07a, Zheng00a, UniProt11a]
Alternate sequence: K → A; UniProt: Increases KM for ketopantoate 1400- fold. Decreases Vmax 230-fold. Loss of activity; when associated with A-256.
Active-Site 176
[UniProt10a]
UniProt: Proton donor;
Amino-Acid-Sites-That-Bind 180
[UniProt10a]
UniProt: Substrate;
Amino-Acid-Sites-That-Bind 184
[UniProt10a]
UniProt: Substrate;
Amino-Acid-Sites-That-Bind 194
[UniProt10a]
UniProt: Substrate;
Amino-Acid-Sites-That-Bind 241
[UniProt10a]
UniProt: Substrate;
Mutagenesis-Variant 244
[Ciulli07, UniProt11a]
Alternate sequence: S → A; UniProt: Increases KM for ketopantoate 230- fold.
Amino-Acid-Sites-That-Bind 244
[UniProt10a]
UniProt: Substrate;
Mutagenesis-Variant 256
[Ciulli07a, Zheng00a, UniProt11a]
Alternate sequence: E → A; UniProt: Increases KM for ketopantoate 1100- fold. Decreases Vmax 40-fold. Loss of activity; when associated with A-176.
Amino-Acid-Sites-That-Bind 256
[UniProt10a]
UniProt: NADP;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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.

Ciulli06: Ciulli A, Williams G, Smith AG, Blundell TL, Abell C (2006). "Probing hot spots at protein-ligand binding sites: a fragment-based approach using biophysical methods." J Med Chem 49(16);4992-5000. PMID: 16884311

Ciulli07: Ciulli A, Chirgadze DY, Smith AG, Blundell TL, Abell C (2007). "Crystal structure of Escherichia coli ketopantoate reductase in a ternary complex with NADP+ and pantoate bound: substrate recognition, conformational change, and cooperativity." J Biol Chem 282(11);8487-97. PMID: 17229734

Ciulli07a: Ciulli A, Lobley CM, Tuck KL, Smith AG, Blundell TL, Abell C (2007). "pH-tuneable binding of 2'-phospho-ADP-ribose to ketopantoate reductase: a structural and calorimetric study." Acta Crystallogr D Biol Crystallogr 63(Pt 2);171-8. PMID: 17242510

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

Downs94: Downs DM, Petersen L (1994). "apbA, a new genetic locus involved in thiamine biosynthesis in Salmonella typhimurium." J Bacteriol 176(16);4858-64. PMID: 7519593

Elischewski99: Elischewski F, Puhler A, Kalinowski J (1999). "Pantothenate production in Escherichia coli K12 by enhanced expression of the panE gene encoding ketopantoate reductase." J Biotechnol 75(2-3);135-46. PMID: 10553653

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

Frodyma98: Frodyma ME, Downs D (1998). "The panE gene, encoding ketopantoate reductase, maps at 10 minutes and is allelic to apbA in Salmonella typhimurium." J Bacteriol 1998;180(17);4757-9. PMID: 9721324

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

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

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

Landon07: Landon MR, Lancia DR, Yu J, Thiel SC, Vajda S (2007). "Identification of hot spots within druggable binding regions by computational solvent mapping of proteins." J Med Chem 50(6);1231-40. PMID: 17305325

Lobley05: Lobley CM, Ciulli A, Whitney HM, Williams G, Smith AG, Abell C, Blundell TL (2005). "The crystal structure of Escherichia coli ketopantoate reductase with NADP+ bound." Biochemistry 44(25);8930-9. PMID: 15966718

MatakVinkovic01: Matak-Vinkovic D, Vinkovic M, Saldanha SA, Ashurst JL, von Delft F, Inoue T, Miguel RN, Smith AG, Blundell TL, Abell C (2001). "Crystal structure of Escherichia coli ketopantoate reductase at 1.7 A resolution and insight into the enzyme mechanism." Biochemistry 40(48);14493-500. PMID: 11724562

Primerano83: Primerano DA, Burns RO (1983). "Role of acetohydroxy acid isomeroreductase in biosynthesis of pantothenic acid in Salmonella typhimurium." J Bacteriol 1983;153(1);259-69. PMID: 6401279

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

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

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

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

Zheng00: Zheng R, Blanchard JS (2000). "Kinetic and mechanistic analysis of the E. coli panE-encoded ketopantoate reductase." Biochemistry 2000;39(13);3708-17. PMID: 10736170

Zheng00a: Zheng R, Blanchard JS (2000). "Identification of active site residues in E. coli ketopantoate reductase by mutagenesis and chemical rescue." Biochemistry 39(51);16244-51. PMID: 11123955

Zheng03: Zheng R, Blanchard JS (2003). "Substrate specificity and kinetic isotope effect analysis of the Eschericia coli ketopantoate reductase." Biochemistry 42(38);11289-96. PMID: 14503879


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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 Sat Dec 20, 2014, BIOCYC13B.