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BioCyc websites down
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MetaCyc Enzyme: D-arabinose 5-phosphate isomerase

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

Synonyms: yrbH

Species: Escherichia coli K-12 substr. MG1655

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].

Locations: cytosol

Map Position: [3,339,288 -> 3,340,274]

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

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

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , 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 lipopolysaccharide biosynthesis , superpathway of (KDO)2-lipid A biosynthesis , CMP-KDO biosynthesis I

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

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: 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  
[UniProt12]
UniProt: Substrate; Non-Experimental Qualifier: by similarity.
Mutagenesis-Variant 88  
[Gourlay10, UniProt11a]
Alternate sequence: 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: 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: 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: 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;

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

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

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

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

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.

UniProt12: 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 MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Fri Dec 19, 2014, BIOCYC14A.