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Escherichia coli K-12 substr. MG1655 Enzyme: erythronate-4-phosphate dehydrogenase



Gene: pdxB Accession Numbers: G0-9461 (EcoCyc), b2320, ECK2314

Synonyms: usg-2

Regulation Summary Diagram: ?

Summary:
Erythronate 4-phosphate dehydrogenase encoded by the pdxB gene in E. coli catalyses the second reaction of NAD-dependent oxidation of 4-phosphoerythronate to 2-oxo-3-hydroxy-4-phosphobutanoate in the de novo pyridoxine 5'-phosphate (vitamin B6) and pyridoxal 5'-phosphate biosynthesis [Zhao95a]. pdxB mutants show pyridoxine auxotrophy [Lam92].

Gene Citations: [Arps87, Schoenlein89, Arps87a, Pease02]

Locations: cytosol

Map Position: [2,434,737 <- 2,435,873] (52.48 centisomes)
Length: 1137 bp / 378 aa

Molecular Weight of Polypeptide: 41.368 kD (from nucleotide sequence)

pI: 6.63

Unification Links: ASAP:ABE-0007663 , DIP:DIP-10449N , EchoBASE:EB0686 , EcoGene:EG10692 , EcoliWiki:b2320 , Entrez-gene:946785 , ModBase:P05459 , PortEco:pdxB , PR:PRO_000023503 , Pride:P05459 , Protein Model Portal:P05459 , RefSeq:NP_416823 , RegulonDB:G0-9461 , SMR:P05459 , String:511145.b2320 , UniProt:P05459

Relationship Links: InterPro:IN-FAMILY:IPR006139 , InterPro:IN-FAMILY:IPR006140 , InterPro:IN-FAMILY:IPR016040 , InterPro:IN-FAMILY:IPR020921 , InterPro:IN-FAMILY:IPR024531 , Panther:IN-FAMILY:PTHR10996:SF4 , Pfam:IN-FAMILY:PF00389 , Pfam:IN-FAMILY:PF02826 , Pfam:IN-FAMILY:PF11890 , Prosite:IN-FAMILY:PS00065 , Prosite:IN-FAMILY:PS00670 , Prosite:IN-FAMILY:PS00671

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0008615 - pyridoxine biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA06, GOA01, Zhao96a, Lam92, Zhao95a]
GO:0042823 - pyridoxal phosphate biosynthetic process Inferred from experiment [Zhao96a, Zhao95a]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0033711 - 4-phosphoerythronate dehydrogenase activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Zhao95a]
GO:0051287 - NAD binding Inferred from experiment Inferred by computational analysis [GOA01, Zhao95a]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11, GOA06]
GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor Inferred by computational analysis [GOA01]
GO:0046983 - protein dimerization activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06, GOA01]

MultiFun Terms: metabolism biosynthesis of building blocks cofactors, small molecule carriers pyridoxal 5'phosphate

Essentiality data for pdxB 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:
Reviewed 17-Mar-2010 by Sarker M


Enzymatic reaction of: erythronate-4-phosphate dehydrogenase

EC Number: 1.1.1.290

erythronate-4-phosphate + NAD+ <=> 2-oxo-3-hydroxy-4-phosphobutanoate + NADH + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

Alternative Substrates for erythronate-4-phosphate: 3-phospho-D-glycerate

In Pathways: superpathway of pyridoxal 5'-phosphate biosynthesis and salvage , pyridoxal 5'-phosphate biosynthesis I

Summary:

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
erythronate-4-phosphate
2.9
1.4
[Rudolph10, BRENDA14]


Sequence Features

Feature Class Location Citations Comment
Amino-Acid-Sites-That-Bind 45
[UniProt10]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 66
[UniProt10]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 146
[UniProt10]
UniProt: NAD; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 175
[UniProt10]
UniProt: NAD; via carbonyl oxygen; Non-Experimental Qualifier: by similarity;
Active-Site 208
[UniProt10]
UniProt: Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 232
[UniProt10]
UniProt: NAD; Non-Experimental Qualifier: by similarity;
Active-Site 237
[UniProt10]
UniProt: Non-Experimental Qualifier: by similarity;
Active-Site 254
[UniProt10]
UniProt: Proton donor; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 257
[UniProt10]
UniProt: NAD; via amide nitrogen; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 258
[UniProt10]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:


References

Arps87: Arps PJ, Winkler ME (1987). "Structural analysis of the Escherichia coli K-12 hisT operon by using a kanamycin resistance cassette." J Bacteriol 169(3);1061-70. PMID: 3029016

Arps87a: Arps PJ, Winkler ME (1987). "An unusual genetic link between vitamin B6 biosynthesis and tRNA pseudouridine modification in Escherichia coli K-12." J Bacteriol 1987;169(3);1071-9. PMID: 3029017

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.

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

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

Lam92: Lam HM, Tancula E, Dempsey WB, Winkler ME (1992). "Suppression of insertions in the complex pdxJ operon of Escherichia coli K-12 by lon and other mutations." J Bacteriol 1992;174(5);1554-67. PMID: 1537800

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

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

Pease02: Pease AJ, Roa BR, Luo W, Winkler ME (2002). "Positive growth rate-dependent regulation of the pdxA, ksgA, and pdxB genes of Escherichia coli K-12." J Bacteriol 184(5);1359-69. PMID: 11844765

Rudolph10: Rudolph J, Kim J, Copley SD (2010). "Multiple turnovers of the nicotino-enzyme PdxB require α-keto acids as cosubstrates." Biochemistry 49(43);9249-55. PMID: 20831184

Schoenlein89: Schoenlein PV, Roa BB, Winkler ME (1989). "Divergent transcription of pdxB and homology between the pdxB and serA gene products in Escherichia coli K-12." J Bacteriol 171(11);6084-92. PMID: 2681152

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."

Zhao95a: Zhao G, Pease AJ, Bharani N, Winkler ME (1995). "Biochemical characterization of gapB-encoded erythrose 4-phosphate dehydrogenase of Escherichia coli K-12 and its possible role in pyridoxal 5'-phosphate biosynthesis." J Bacteriol 1995;177(10);2804-12. PMID: 7751290

Zhao96a: Zhao G, Winkler ME (1996). "4-Phospho-hydroxy-L-threonine is an obligatory intermediate in pyridoxal 5'-phosphate coenzyme biosynthesis in Escherichia coli K-12." FEMS Microbiol Lett 1996;135(2-3);275-80. PMID: 8595869


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 Mon Dec 29, 2014, BIOCYC15B.