Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

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



Gene: kdsD Accession Numbers: G7662 (EcoCyc), b3197, ECK3186

Synonyms: yrbH

Regulation Summary Diagram: ?

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

Summary:
D-arabinose-5-phosphate is a precursor for KDO (2-keto-3-deoxy-octulosonate), a constituent of the cell wall lipopolysaccharide. Arabinose-5-phosphate isomerase is responsible for the interconversion of D-ribulose-5-phosphate and D-arabinose-5-phosphate, the first committed step in the biosynthesis of KDO. The enzyme was originally isolated and partially characterized from E. coli strain B. As E. coli K-12 has limited D-arabinose metabolism, there was some uncertainty whether or not this enzyme is present in K-12 [Lim66].

KdsD is a tetramer in solution. The reaction kinetics, specificity, and optimal conditions have been characterized, and the physical characteristics of the active site are discussed [Meredith03]. Substrate specificity was investigated by saturation transfer difference NMR spectroscopy [Airoldi10]. The structure of the sugar isomerase domain of KdsD was predicted using homology modeling, and residues important for catalysis or substrate recognition were identified by site-directed mutagenesis [Sommaruga09]. A crystal structure of the sugar isomerase domain of a catalytic mutant has been solved at 2.6 Å resolution, and the highly conserved H88 residue was shown to be involved in catalysis [Gourlay10].

An isozyme, GutQ, is present in E. coli; therefore, deletion of kdsD does not lead to a defect in LPS synthesis [Meredith05]. A gutQ kdsD double mutant is not viable [Sperandeo06].

Gene Citations: [Martorana11]

Locations: cytosol

Map Position: [3,339,288 -> 3,340,274] (71.97 centisomes)
Length: 987 bp / 328 aa

Molecular Weight of Polypeptide: 35.196 kD (from nucleotide sequence), 35 kD (experimental) [Meredith03 ]

Molecular Weight of Multimer: 122 kD (experimental) [Meredith03]

Unification Links: ASAP:ABE-0010504 , DIP:DIP-12910N , EchoBASE:EB2655 , EcoGene:EG12803 , EcoliWiki:b3197 , ModBase:P45395 , OU-Microarray:b3197 , PortEco:kdsD , PR:PRO_000023057 , Pride:P45395 , Protein Model Portal:P45395 , RefSeq:NP_417664 , RegulonDB:G7662 , SMR:P45395 , String:511145.b3197 , UniProt:P45395

Relationship Links: InterPro:IN-FAMILY:IPR000644 , InterPro:IN-FAMILY:IPR001347 , InterPro:IN-FAMILY:IPR004800 , PDB:Structure:2XHZ , Pfam:IN-FAMILY:PF00571 , Pfam:IN-FAMILY:PF01380 , Prosite:IN-FAMILY:PS51371 , Prosite:IN-FAMILY:PS51464 , Smart:IN-FAMILY:SM00116

In Paralogous Gene Group: 505 (2 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0019294 - keto-3-deoxy-D-manno-octulosonic acid biosynthetic process Inferred from experiment [Sperandeo06, Meredith03]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0009103 - lipopolysaccharide biosynthetic process Inferred by computational analysis [UniProtGOA12, UniProtGOA11a]
Molecular Function: GO:0019146 - arabinose-5-phosphate isomerase activity Inferred from experiment Inferred by computational analysis [GOA01, Meredith03]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0030246 - carbohydrate binding Inferred by computational analysis [GOA01a]
GO:0030554 - adenyl nucleotide binding Inferred by computational analysis [GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

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

Essentiality data for kdsD 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 ? 27-Oct-2010 by Keseler I , SRI International


Enzymatic reaction of: D-arabinose 5-phosphate isomerase

Synonyms: D-phosphoarabinoisomerase, D-arabinose-5-phosphate ketol-isomerase, API

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. [Meredith03]

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

Summary:
The Keq, as determined by the endpoint assay, is 0.50 [Meredith03]. The thermodynamic equilibrium was measured at A5P/Ru5P, 7:3 [Airoldi10].

Inhibitors (Other): Zn2+ [Lim66, Meredith03, Airoldi10]

Inhibitors (Unknown Mechanism): Cd2+ [Meredith03, Lim66] , p-chloromercuribenzoate [Lim66] , phosphate [Lim66] , Hg2+ [Meredith03]

Kinetic Parameters:

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

pH(opt): 7.75 [BRENDA14, Meredith06], 8.25 [BRENDA14, Meredith06], 6.6 [BRENDA14, Mosberg11], 7.8 [BRENDA14, DAniello05a], 8.3 [BRENDA14, Meredith05], 8.4 [BRENDA14, Meredith03], 8.4 [Meredith03]


Sequence Features

Feature Class Location Common Name Citations Comment
Conserved-Region 42 -> 184  
[UniProt10a]
UniProt: SIS;
Mutagenesis-Variant 59  
[Sommaruga09, UniProt11a]
Alternate sequence: K → A; UniProt: Inactive.
Amino-Acid-Site 59  
[UniProt11a]
UniProt: Catalytically relevant; Sequence Annotation Type: site.
Protein-Segment 75 -> 76  
[UniProt11a]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 82  
[UniProt11a]
UniProt: Zinc; Non-Experimental Qualifier: by similarity.
Amino-Acid-Sites-That-Bind 88  
[UniProt12a]
UniProt: Substrate; Non-Experimental Qualifier: by similarity.
Mutagenesis-Variant 88  
[Gourlay10, UniProt11a]
Alternate sequence: H → A; UniProt: Shows 9.5% of residual activity compared to the wild-type.
Mutagenesis-Variant 88 H88A mutant
[Gourlay10]
The H88A mutant has 9.5% of wild type activity [Gourlay10].
Mutagenesis-Variant 111  
[Sommaruga09, UniProt11a]
Alternate sequence: E → A; UniProt: Shows 62% of residual activity compared to the wild-type.
Amino-Acid-Site 111  
[UniProt11a]
UniProt: Catalytically relevant; Sequence Annotation Type: site.
Protein-Segment 114 -> 123  
[UniProt11a]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Protein-Segment 148 -> 150  
[UniProt11a]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Mutagenesis-Variant 152  
[Sommaruga09, UniProt11a]
Alternate sequence: E → A; UniProt: Shows 19% of residual activity compared to the wild-type. It is able to support growth.
Amino-Acid-Site 152  
[UniProt11a]
UniProt: Catalytically relevant; Sequence Annotation Type: site.
Mutagenesis-Variant 193  
[Sommaruga09, UniProt11a]
Alternate sequence: H → A; UniProt: Inactive.
Amino-Acid-Site 193  
[UniProt11a]
UniProt: Catalytically relevant; Sequence Annotation Type: site.
Conserved-Region 210 -> 268  
[UniProt09]
UniProt: CBS 1;
Amino-Acid-Sites-That-Bind 222  
[UniProt11a]
UniProt: Substrate; Non-Experimental Qualifier: by similarity.
Amino-Acid-Sites-That-Bind 275  
[UniProt11a]
UniProt: Substrate; Non-Experimental Qualifier: by similarity.
Conserved-Region 277 -> 328  
[UniProt09]
UniProt: CBS 2;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

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


References

Airoldi10: Airoldi C, Sommaruga S, Merlo S, Sperandeo P, Cipolla L, Polissi A, Nicotra F (2010). "Targeting bacterial membranes: NMR spectroscopy characterization of substrate recognition and binding requirements of D-arabinose-5-phosphate isomerase." Chemistry 16(6);1897-902. PMID: 20039350

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

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.

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, 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."

Gourlay10: Gourlay LJ, Sommaruga S, Nardini M, Sperandeo P, Deho G, Polissi A, Bolognesi M (2010). "Probing the active site of the sugar isomerase domain from E. coli arabinose-5-phosphate isomerase via X-ray crystallography." Protein Sci 19(12);2430-9. PMID: 20954237

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

Lim66: Lim R, Cohen SS (1966). "D-phosphoarabinoisomerase and D-ribulokinase in Escherichia coli." J Biol Chem 1966;241(19);4304-15. PMID: 5332197

Martorana11: Martorana AM, Sperandeo P, Polissi A, Deho G (2011). "Complex transcriptional organization regulates an Escherichia coli locus implicated in lipopolysaccharide biogenesis." Res Microbiol 162(5);470-82. PMID: 21402154

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

Sommaruga09: Sommaruga S, Gioia LD, Tortora P, Polissi A (2009). "Structure prediction and functional analysis of KdsD, an enzyme involved in lipopolysaccharide biosynthesis." Biochem Biophys Res Commun 388(2);222-7. PMID: 19664604

Sperandeo06: Sperandeo P, Pozzi C, Deho G, Polissi A (2006). "Non-essential KDO biosynthesis and new essential cell envelope biogenesis genes in the Escherichia coli yrbG-yhbG locus." Res Microbiol 157(6);547-58. PMID: 16765569

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.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

UniProt12a: UniProt Consortium (2012). "UniProt version 2012-09 released on 2012-09-12 00:00:00." Database.

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."


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 Fri Nov 28, 2014, BIOCYC13B.