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Escherichia coli K-12 substr. MG1655 Enzyme: D-sedoheptulose 7-phosphate isomerase



Gene: lpcA Accession Numbers: G6106 (EcoCyc), b0222, ECK0223

Synonyms: isn(H.i.), yafI, gmhA, tfrA

Regulation Summary Diagram: ?

Subunit composition of D-sedoheptulose 7-phosphate isomerase = [LpcA]4
         D-sedoheptulose 7-phosphate isomerase = LpcA

Summary:
Sedoheptulose 7-phosphate isomerase catalyzes the first committed step in the biosynthesis of a core component of lipopolysaccharide, the isomerization of D-sedoheptulose 7-phosphate to D-glycero-D-manno-heptose 7-phosphate.

Crystal structures of LpcA alone and in complex with the substrate D-sedoheptulose 7-phosphate have been solved. The protein appears to be a tetramer in both the crystal structures and in solution. A reaction mechanism utilizing an enediol intermediate has been proposed [Taylor08a].

Mutations in lpcA confer novobiocin hypersensitivity [Tamaki71, Havekes76, Taylor08a] and F plasmid conjugation deficiency [Havekes76]; lpcA mutants were shown to contain lipopolysaccharides lacking heptose [Tamaki71, Havekes76, Brooke96]. Potential active site residues were mutagenized and their enzymatic activity was measured both in vivo and in vitro [Taylor08a].

LpcA = "LPS-core synthesis" [Tamaki71]

GmhA = "glycero-manno-heptose synthesis" [Kneidinger02]

Review: [Raetz02]

Locations: cytosol

Map Position: [243,543 -> 244,121] (5.25 centisomes)
Length: 579 bp / 192 aa

Molecular Weight of Polypeptide: 20.815 kD (from nucleotide sequence), 22.6 kD (experimental) [Brooke96 ]

Unification Links: ASAP:ABE-0000751 , DIP:DIP-48179N , EchoBASE:EB2940 , EcoGene:EG13146 , EcoliWiki:b0222 , ModBase:P63224 , OU-Microarray:b0222 , PortEco:lpcA , PR:PRO_000022820 , Pride:P63224 , Protein Model Portal:P63224 , RefSeq:NP_414757 , RegulonDB:G6106 , SMR:P63224 , String:511145.b0222 , Swiss-Model:P63224 , UniProt:P63224

Relationship Links: InterPro:IN-FAMILY:IPR001347 , InterPro:IN-FAMILY:IPR004515 , PDB:Structure:2I22 , PDB:Structure:2I2W , Pfam:IN-FAMILY:PF13580 , Prosite:IN-FAMILY:PS51464

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0009244 - lipopolysaccharide core region biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, GOA et al., 2001, Brooke96]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [UniProt-GOA, 2011, GOA06, GOA et al., 2001]
GO:0009103 - lipopolysaccharide biosynthetic process Inferred by computational analysis [UniProt-GOA, 2011]
GO:2001061 - D-glycero-D-manno-heptose 7-phosphate biosynthetic process Inferred by computational analysis [UniProtGOA12]
Molecular Function: GO:0008968 - D-sedoheptulose 7-phosphate isomerase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA et al., 2001, Taylor08a]
GO:0008270 - zinc ion binding Inferred by computational analysis [GOA06]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProt-GOA, 2011]
GO:0030246 - carbohydrate binding Inferred by computational analysis [GOA et al., 2001]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProt-GOA, 2011]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [Diaz-Mejia et al., 2009, Ishihama et al., 2008, LopezCampistrou05]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProt-GOA, 2011, GOA06, GOA et al., 2001, Brooke96]

MultiFun Terms: metabolism biosynthesis of macromolecules (cellular constituents) lipopolysaccharide core region

Essentiality data for lpcA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes et al., 2003, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba et al., 2006, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce et al., 2006, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba et al., 2006, Comment 2]
Yes [Feist07, Comment 4]

Credits:
Created 14-Jan-2008 by Keseler I , SRI International
Last-Curated ? 14-Jan-2008 by Keseler I , SRI International


Enzymatic reaction of: D-sedoheptulose 7-phosphate isomerase

Synonyms: phosphoheptose isomerase

EC Number: 5.3.1.28

D-sedoheptulose 7-phosphate <=> D-glycero-D-manno-heptose 7-phosphate

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.

In Pathways: ADP-L-glycero-β-D-manno-heptose biosynthesis

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
D-sedoheptulose 7-phosphate
900.0
0.44
[Taylor08a, BRENDA14]


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 37 -> 192
[UniProt10]
UniProt: SIS;
Protein-Segment 54 -> 55
[UniProt10a]
UniProt: Substrate binding; Sequence Annotation Type: region of interest;
Mutagenesis-Variant 61
[Taylor08a, UniProt11]
Alternate sequence: H → Q; UniProt: Almost no effect.
Metal-Binding-Site 61
[UniProt10a]
UniProt: Zinc; Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 65
[Taylor08a, UniProt11]
Alternate sequence: E → Q; UniProt: No activity.
Alternate sequence: E → N; UniProt: No activity.
Metal-Binding-Site 65
[UniProt10a]
UniProt: Zinc; Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 69
[Taylor08a, UniProt11]
Alternate sequence: R → Q; UniProt: Almost no effect.
Protein-Segment 93 -> 94
[UniProt10a]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 94
[Taylor08a, UniProt11]
Alternate sequence: D → N; UniProt: No activity.
Protein-Segment 119 -> 121
[UniProt10a]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 120
[Taylor08a, UniProt11]
Alternate sequence: T → A; UniProt: No activity.
Amino-Acid-Sites-That-Bind 120
[UniProt10a]
UniProt: Substrate;
Amino-Acid-Sites-That-Bind 124
[UniProt10a]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 169
[Taylor08a, UniProt11]
Alternate sequence: D → N; UniProt: No activity.
Amino-Acid-Sites-That-Bind 169
[UniProt10a]
UniProt: Substrate;
Mutagenesis-Variant 172
[Taylor08a, UniProt11]
Alternate sequence: Q → E; UniProt: No activity.
Metal-Binding-Site 172
[UniProt10a]
UniProt: Zinc; Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 180
[Taylor08a, UniProt11]
Alternate sequence: H → Q; UniProt: No activity.
Metal-Binding-Site 180
[UniProt10a]
UniProt: Zinc; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
3/2/1998 (pkarp) Merged genes G343/lpcA and G6106/lpcA
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

Baba et al., 2006: 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.

Brooke96: Brooke JS, Valvano MA (1996). "Biosynthesis of inner core lipopolysaccharide in enteric bacteria identification and characterization of a conserved phosphoheptose isomerase." J Biol Chem 271(7);3608-14. PMID: 8631969

Diaz-Mejia et al., 2009: 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

Gerdes et al., 2003: 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

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

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

Havekes76: Havekes LM, Lugtenberg BJ, Hoekstra WP (1976). "Conjugation deficient E. coli K12 F- mutants with heptose-less lipopolysaccharide." Mol Gen Genet 146(1);43-50. PMID: 785207

Ishihama et al., 2008: 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

Joyce et al., 2006: 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

Kneidinger02: Kneidinger B, Marolda C, Graninger M, Zamyatina A, McArthur F, Kosma P, Valvano MA, Messner P (2002). "Biosynthesis pathway of ADP-L-glycero-beta-D-manno-heptose in Escherichia coli." J Bacteriol 184(2);363-9. PMID: 11751812

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

Raetz02: Raetz CR, Whitfield C (2002). "Lipopolysaccharide endotoxins." Annu Rev Biochem 71;635-700. PMID: 12045108

Tamaki71: Tamaki S, Sato T, Matsuhashi M (1971). "Role of lipopolysaccharides in antibiotic resistance and bacteriophage adsorption of Escherichia coli K-12." J Bacteriol 105(3);968-75. PMID: 4926688

Taylor08a: Taylor PL, Blakely KM, de Leon GP, Walker JR, McArthur F, Evdokimova E, Zhang K, Valvano MA, Wright GD, Junop MS (2008). "Structure and function of GmhA (sedoheptulose 7-phosphate isomerase): A critical enzyme for lipopolysaccharide biosynthesis and a target for antibiotic adjuvants." J Biol Chem 283(5):2835-45. PMID: 18056714

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-12 released on 2010-12-01 00:00:00." Database.

UniProt11: 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."

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


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 Thu Dec 18, 2014, biocyc11.