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Escherichia coli K-12 substr. MG1655 Enzyme: D-arabinose 5-phosphate isomerase



Gene: gutQ Accession Numbers: EG10973 (EcoCyc), b2708, ECK2703

Synonyms: srlQ

Regulation Summary Diagram: ?

Subunit composition of D-arabinose 5-phosphate isomerase = [GutQ]4
         D-arabinose 5-phosphate isomerase = GutQ

Summary:
gutQ encodes the second of two D-arabinose 5-phosphate isomerases (API) in E. coli. Its biochemical properties are very similar to those of KdsD, the first identified D-arabinose 5-phosphate isomerase. Strains containing single mutations in either the kdsD or gutQ genes are viable and have a functional LPS. A kdsD gutQ double mutant strain required the addition of exogenous arabinose 5-phosphate for viability [Meredith05].

GutQ has previously been shown to have a sugar isomerase (SIS) domain [Bateman99] and a predicted ATP binding site [Yamada90a]. GutQ also has similarity to of E. coli K1 KpsF, which plays a role in polysialic acid capsule expression [Cieslewicz97].

gutQ is the last gene in the gut operon, and its expression is induced by glucitol [Yamada90a, Meredith05]. GutQ appears to be involved in biofilm formation. A mutant with a deletion of gutQ shows a significant decrease in biofilm formation. Expression of gutQ increases 9-fold upon deletion of tqsA, which increases biofilm formation [Herzberg06].

Gene Citations: [Yamada87, McEntee77, Yamada88]

Locations: cytosol, membrane

Map Position: [2,827,835 -> 2,828,800] (60.95 centisomes)
Length: 966 bp / 321 aa

Molecular Weight of Polypeptide: 34.031 kD (from nucleotide sequence), 33 kD (experimental) [Meredith05 ]

Molecular Weight of Multimer: 133 kD (experimental) [Meredith05]

Unification Links: ASAP:ABE-0008902 , CGSC:33206 , EchoBASE:EB0966 , EcoGene:EG10973 , EcoliWiki:b2708 , ModBase:P17115 , OU-Microarray:b2708 , PortEco:gutQ , Pride:P17115 , Protein Model Portal:P17115 , RefSeq:NP_417188 , RegulonDB:EG10973 , SMR:P17115 , String:511145.b2708 , UniProt:P17115

Relationship Links: InterPro:IN-FAMILY:IPR000644 , InterPro:IN-FAMILY:IPR001347 , InterPro:IN-FAMILY:IPR004800 , Pfam:IN-FAMILY:PF00571 , Pfam:IN-FAMILY:PF01380 , Prosite:IN-FAMILY:PS51371 , Prosite:IN-FAMILY:PS51464 , Smart:IN-FAMILY:SM00116

In Paralogous Gene Group: 446 (2 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009244 - lipopolysaccharide core region biosynthetic process Inferred from experiment
GO:0019294 - keto-3-deoxy-D-manno-octulosonic acid biosynthetic process Inferred from experiment [Meredith05]
GO:0042710 - biofilm formation Inferred from experiment [Herzberg06]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [GOA01]
GO:0009103 - lipopolysaccharide biosynthetic process Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0019146 - arabinose-5-phosphate isomerase activity Inferred from experiment Inferred by computational analysis [GOA01a, Meredith05]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030246 - carbohydrate binding Inferred by computational analysis [GOA01]
GO:0030554 - adenyl nucleotide binding Inferred by computational analysis [GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:0016020 - membrane

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

Essentiality data for gutQ 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:
Created 06-Dec-2005 by Keseler I , SRI International
Last-Curated ? 13-Apr-2007 by Keseler I , SRI International


Enzymatic reaction of: D-arabinose 5-phosphate isomerase

EC Number: 5.3.1.13

D-arabinose 5-phosphate <=> D-ribulose 5-phosphate

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.

In Pathways: superpathway of (KDO)2-lipid A biosynthesis , superpathway of lipopolysaccharide biosynthesis , CMP-KDO biosynthesis I

Inhibitors (Unknown Mechanism): Zn2+ [Meredith05]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
D-ribulose 5-phosphate
300.0, 350.0, 640.0
[Meredith06, BRENDA14]
D-ribulose 5-phosphate
700.0
10.5
[Mosberg11, BRENDA14]
D-ribulose 5-phosphate
19.0
[DAniello05a, BRENDA14]
D-ribulose 5-phosphate
640.0
242.0
[Meredith05, BRENDA14]
D-ribulose 5-phosphate
255.0
[Meredith03, BRENDA14]
D-arabinose 5-phosphate
100.0
[Bigham84, BRENDA14]
D-arabinose 5-phosphate
570.0, 610.0, 1200.0
[Meredith06, BRENDA14]
D-arabinose 5-phosphate
15.0
[DAniello05a, BRENDA14]
D-arabinose 5-phosphate
1920.0
16.8
[Mosberg11, BRENDA14]
D-arabinose 5-phosphate
157.0
[Meredith03, BRENDA14]
D-arabinose 5-phosphate
1200.0
218.0
[Meredith05, BRENDA14]

pH(opt): 6.6 [BRENDA14, Mosberg11], 7.75 [BRENDA14, Meredith06], 7.8 [BRENDA14, DAniello05a], 8.3 [BRENDA14, Meredith05], 8.4 [BRENDA14, Meredith06], 8.25 [Meredith05]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Maillet07, UniProt11]
UniProt: Removed.
Chain 2 -> 321
[UniProt11]
UniProt: Arabinose 5-phosphate isomerase GutQ.
Conserved-Region 34 -> 177
[UniProt10a]
UniProt: SIS;
Nucleotide-Phosphate-Binding-Region 49 -> 54
[UniProt10a]
UniProt: ATP; Non-Experimental Qualifier: potential;
Amino-Acid-Site 52
[UniProt11]
UniProt: Catalytically relevant; Sequence Annotation Type: site; Non-Experimental Qualifier: by similarity.
Protein-Segment 68 -> 69
[UniProt11]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 75
[UniProt11]
UniProt: Zinc; Non-Experimental Qualifier: by similarity.
Amino-Acid-Sites-That-Bind 81
[UniProt12]
UniProt: Substrate; Non-Experimental Qualifier: by similarity.
Amino-Acid-Site 104
[UniProt11]
UniProt: Catalytically relevant; Sequence Annotation Type: site; Non-Experimental Qualifier: by similarity.
Protein-Segment 107 -> 116
[UniProt11]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Protein-Segment 141 -> 143
[UniProt11]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Amino-Acid-Site 145
[UniProt11]
UniProt: Catalytically relevant; Sequence Annotation Type: site; Non-Experimental Qualifier: by similarity.
Amino-Acid-Site 186
[UniProt11]
UniProt: Catalytically relevant; Sequence Annotation Type: site; Non-Experimental Qualifier: by similarity.
Conserved-Region 203 -> 261
[UniProt09]
UniProt: CBS 1;
Amino-Acid-Sites-That-Bind 215
[UniProt11]
UniProt: Substrate; Non-Experimental Qualifier: by similarity.
Amino-Acid-Sites-That-Bind 267
[UniProt11]
UniProt: Substrate; Non-Experimental Qualifier: by similarity.
Conserved-Region 269 -> 321
[UniProt09]
UniProt: CBS 2;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene left-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
10/20/97 Gene b2708 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10973; 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

Bateman99: Bateman A (1999). "The SIS domain: a phosphosugar-binding domain." Trends Biochem Sci 24(3);94-5. PMID: 10203754

Bigham84: Bigham EC, Gragg CE, Hall WR, Kelsey JE, Mallory WR, Richardson DC, Benedict C, Ray PH (1984). "Inhibition of arabinose 5-phosphate isomerase. An approach to the inhibition of bacterial lipopolysaccharide biosynthesis." J Med Chem 27(6);717-26. PMID: 6429331

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

Cieslewicz97: Cieslewicz M, Vimr E (1997). "Reduced polysialic acid capsule expression in Escherichia coli K1 mutants with chromosomal defects in kpsF." Mol Microbiol 26(2);237-49. PMID: 9383150

DAniello05a: D'Aniello S, Spinelli P, Ferrandino G, Peterson K, Tsesarskia M, Fisher G, D'Aniello A (2005). "Cephalopod vision involves dicarboxylic amino acids: D-aspartate, L-aspartate and L-glutamate." Biochem J 386(Pt 2);331-40. PMID: 15491279

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.

Herzberg06: Herzberg M, Kaye IK, Peti W, Wood TK (2006). "YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport." J Bacteriol 188(2);587-98. PMID: 16385049

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

Maillet07: Maillet I, Berndt P, Malo C, Rodriguez S, Brunisholz RA, Pragai Z, Arnold S, Langen H, Wyss M (2007). "From the genome sequence to the proteome and back: evaluation of E. coli genome annotation with a 2-D gel-based proteomics approach." Proteomics 7(7);1097-106. PMID: 17366475

McEntee77: McEntee K (1977). "Genetic analysis of the Escherichia coli K-12 srl region." J Bacteriol 1977;132(3);904-11. PMID: 336611

Meredith03: Meredith TC, Woodard RW (2003). "Escherichia coli YrbH is a D-arabinose 5-phosphate isomerase." J Biol Chem 278(35);32771-7. PMID: 12805358

Meredith05: Meredith TC, Woodard RW (2005). "Identification of GutQ from Escherichia coli as a D-arabinose 5-phosphate isomerase." J Bacteriol 187(20);6936-42. PMID: 16199563

Meredith06: Meredith TC, Woodard RW (2006). "Characterization of Escherichia coli D-arabinose 5-phosphate isomerase encoded by kpsF: implications for group 2 capsule biosynthesis." Biochem J 395(2);427-32. PMID: 16390329

Mosberg11: Mosberg JA, Yep A, Meredith TC, Smith S, Wang PF, Holler TP, Mobley HL, Woodard RW (2011). "A unique arabinose 5-phosphate isomerase found within a genomic island associated with the uropathogenicity of Escherichia coli CFT073." J Bacteriol 193(12);2981-8. PMID: 21498648

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

UniProt12: UniProt Consortium (2012). "UniProt version 2012-09 released on 2012-09-12 00:00:00." Database.

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

Yamada87: Yamada M, Saier MH (1987). "Glucitol-specific enzymes of the phosphotransferase system in Escherichia coli. Nucleotide sequence of the gut operon." J Biol Chem 1987;262(12);5455-63. PMID: 3553176

Yamada88: Yamada M, Saier MH (1988). "Positive and negative regulators for glucitol (gut) operon expression in Escherichia coli." J Mol Biol 1988;203(3);569-83. PMID: 3062173

Yamada90a: Yamada M, Yamada Y, Saier MH (1990). "Nucleotide sequence and expression of the gutQ gene within the glucitol operon of Escherichia coli." DNA Seq 1(2);141-5. PMID: 2134185

Other References Related to Gene Regulation

Beisel11: Beisel CL, Storz G (2011). "The base-pairing RNA spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli." Mol Cell 41(3);286-97. PMID: 21292161

WhiteZiegler07: White-Ziegler CA, Malhowski AJ, Young S (2007). "Human body temperature (37degrees C) increases the expression of iron, carbohydrate, and amino acid utilization genes in Escherichia coli K-12." J Bacteriol 189(15);5429-40. PMID: 17526711

Zheng04: Zheng D, Constantinidou C, Hobman JL, Minchin SD (2004). "Identification of the CRP regulon using in vitro and in vivo transcriptional profiling." Nucleic Acids Res 32(19);5874-93. PMID: 15520470


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 Nov 20, 2014, BIOCYC14A.