GENTAUR Molecular Products.

 KDSD_ECOLI              Reviewed;         328 AA.
 P45395; Q2M915;
 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
 01-NOV-1995, sequence version 1.
 13-FEB-2019, entry version 127.
 RecName: Full=Arabinose 5-phosphate isomerase KdsD;
          Short=API;
          Short=L-API;
          EC=5.3.1.13;
 Name=kdsD; Synonyms=yrbH; OrderedLocusNames=b3197, JW3164;
 Escherichia coli (strain K12).
 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
 Enterobacteriaceae; Escherichia.
 NCBI_TaxID=83333;
 [1]
 NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
 STRAIN=K12 / MG1655 / ATCC 47076;
 PubMed=9278503; DOI=10.1126/science.277.5331.1453;
 Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
 Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
 Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
 Mau B., Shao Y.;
 "The complete genome sequence of Escherichia coli K-12.";
 Science 277:1453-1462(1997).
 [2]
 NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
 STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
 PubMed=16738553; DOI=10.1038/msb4100049;
 Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
 Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
 "Highly accurate genome sequences of Escherichia coli K-12 strains
 MG1655 and W3110.";
 Mol. Syst. Biol. 2:E1-E5(2006).
 [3]
 FUNCTION AS A ARABINOSE 5-PHOSPHATE ISOMERASE AND IN
 LIPOPOLYSACCHARIDE BIOSYNTHESIS, BIOPHYSICOCHEMICAL PROPERTIES,
 ACTIVITY REGULATION, AND SUBUNIT.
 STRAIN=K12;
 PubMed=12805358; DOI=10.1074/jbc.M303661200;
 Meredith T.C., Woodard R.W.;
 "Escherichia coli YrbH is a D-arabinose 5-phosphate isomerase.";
 J. Biol. Chem. 278:32771-32777(2003).
 [4]
 FUNCTION AS A ARABINOSE 5-PHOSPHATE ISOMERASE, AND NOMENCLATURE.
 STRAIN=K12 / MG1655 / ATCC 47076;
 PubMed=16199563; DOI=10.1128/JB.187.20.6936-6942.2005;
 Meredith T.C., Woodard R.W.;
 "Identification of GutQ from Escherichia coli as a D-arabinose 5-
 phosphate isomerase.";
 J. Bacteriol. 187:6936-6942(2005).
 [5]
 FUNCTION IN KDO BIOSYNTHESIS.
 STRAIN=K12 / MG1655 / ATCC 47076;
 PubMed=16765569; DOI=10.1016/j.resmic.2005.11.014;
 Sperandeo P., Pozzi C., Deho G., Polissi A.;
 "Non-essential KDO biosynthesis and new essential cell envelope
 biogenesis genes in the Escherichia coli yrbG-yhbG locus.";
 Res. Microbiol. 157:547-558(2006).
 [6]
 MUTAGENESIS OF LYS-59; GLU-111; GLU-152 AND HIS-193.
 STRAIN=K12;
 PubMed=19664604; DOI=10.1016/j.bbrc.2009.07.154;
 Sommaruga S., Gioia L.D., Tortora P., Polissi A.;
 "Structure prediction and functional analysis of KdsD, an enzyme
 involved in lipopolysaccharide biosynthesis.";
 Biochem. Biophys. Res. Commun. 388:222-227(2009).
 [7]
 REACTION MECHANISM, AND ACTIVITY REGULATION.
 STRAIN=K12;
 PubMed=20039350; DOI=10.1002/chem.200902619;
 Airoldi C., Sommaruga S., Merlo S., Sperandeo P., Cipolla L.,
 Polissi A., Nicotra F.;
 "Targeting bacterial membranes: NMR spectroscopy characterization of
 substrate recognition and binding requirements of D-arabinose-5-
 phosphate isomerase.";
 Chemistry 16:1897-1902(2010).
 [8]
 X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 1-183 OF MUTANT ALA-59,
 MUTAGENESIS OF HIS-88, AND SUBUNIT.
 STRAIN=K12;
 PubMed=20954237; DOI=10.1002/pro.525;
 Gourlay L.J., Sommaruga S., Nardini M., Sperandeo P., Deho G.,
 Polissi A., Bolognesi M.;
 "Probing the active site of the sugar isomerase domain from E. coli
 arabinose-5-phosphate isomerase via X-ray crystallography.";
 Protein Sci. 19:2430-2439(2010).
 -!- FUNCTION: Involved in the biosynthesis of 3-deoxy-D-manno-
     octulosonate (KDO), a unique 8-carbon sugar component of
     lipopolysaccharides (LPSs). KdsD is not essential in the KDO
     biosynthesis and can be substituted by GutQ. Catalyzes the
     reversible aldol-ketol isomerization between D-ribulose 5-
     phosphate (Ru5P) and D-arabinose 5-phosphate (A5P).
     {ECO:0000269|PubMed:12805358, ECO:0000269|PubMed:16199563,
     ECO:0000269|PubMed:16765569}.
 -!- CATALYTIC ACTIVITY:
     Reaction=D-arabinose 5-phosphate = D-ribulose 5-phosphate;
       Xref=Rhea:RHEA:23104, ChEBI:CHEBI:57693, ChEBI:CHEBI:58121;
       EC=5.3.1.13;
 -!- ACTIVITY REGULATION: Completely inhibited by 10 uM of nickel,
     copper, cadmium and mercury ions. Inhibited by zinc with an IC(50)
     of 1-3 uM. Metal ion inhibition may be a mechanism to control
     activity in vivo. {ECO:0000269|PubMed:12805358,
     ECO:0000269|PubMed:20039350}.
 -!- BIOPHYSICOCHEMICAL PROPERTIES:
     Kinetic parameters:
       KM=0.35 mM for Ru5P (at pH 8.5 and at 37 degrees Celsius)
       {ECO:0000269|PubMed:12805358};
       KM=0.61 mM for A5P (at pH 8.5 and at 37 degrees Celsius)
       {ECO:0000269|PubMed:12805358};
     pH dependence:
       Optimum pH is 8.4. {ECO:0000269|PubMed:12805358};
 -!- PATHWAY: Carbohydrate biosynthesis; 3-deoxy-D-manno-octulosonate
     biosynthesis; 3-deoxy-D-manno-octulosonate from D-ribulose 5-
     phosphate: step 1/3.
 -!- PATHWAY: Bacterial outer membrane biogenesis; lipopolysaccharide
     biosynthesis.
 -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:12805358,
     ECO:0000269|PubMed:20954237}.
 -!- SIMILARITY: Belongs to the SIS family. GutQ/KpsF subfamily.
     {ECO:0000305}.
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 EMBL; U18997; AAA57998.1; -; Genomic_DNA.
 EMBL; U00096; AAC76229.1; -; Genomic_DNA.
 EMBL; AP009048; BAE77241.1; -; Genomic_DNA.
 PIR; G65110; G65110.
 RefSeq; NP_417664.1; NC_000913.3.
 RefSeq; WP_001295557.1; NZ_LN832404.1.
 PDB; 2XHZ; X-ray; 2.60 A; A/B/C/D=1-183.
 PDBsum; 2XHZ; -.
 ProteinModelPortal; P45395; -.
 SMR; P45395; -.
 BioGrid; 4259369; 339.
 DIP; DIP-12910N; -.
 IntAct; P45395; 9.
 STRING; 316385.ECDH10B_3371; -.
 jPOST; P45395; -.
 PaxDb; P45395; -.
 PRIDE; P45395; -.
 EnsemblBacteria; AAC76229; AAC76229; b3197.
 EnsemblBacteria; BAE77241; BAE77241; BAE77241.
 GeneID; 947734; -.
 KEGG; ecj:JW3164; -.
 KEGG; eco:b3197; -.
 PATRIC; fig|1411691.4.peg.3534; -.
 EchoBASE; EB2655; -.
 EcoGene; EG12803; kdsD.
 eggNOG; ENOG4105C2X; Bacteria.
 eggNOG; COG0517; LUCA.
 eggNOG; COG0794; LUCA.
 HOGENOM; HOG000264729; -.
 InParanoid; P45395; -.
 KO; K06041; -.
 PhylomeDB; P45395; -.
 BioCyc; EcoCyc:G7662-MONOMER; -.
 BioCyc; ECOL316407:JW3164-MONOMER; -.
 BioCyc; MetaCyc:G7662-MONOMER; -.
 BRENDA; 5.3.1.13; 2026.
 UniPathway; UPA00030; -.
 UniPathway; UPA00357; UER00473.
 EvolutionaryTrace; P45395; -.
 PRO; PR:P45395; -.
 Proteomes; UP000000318; Chromosome.
 Proteomes; UP000000625; Chromosome.
 GO; GO:0019146; F:arabinose-5-phosphate isomerase activity; IDA:EcoCyc.
 GO; GO:0097367; F:carbohydrate derivative binding; IEA:InterPro.
 GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
 GO; GO:0019294; P:keto-3-deoxy-D-manno-octulosonic acid biosynthetic process; IDA:EcoCyc.
 CDD; cd05014; SIS_Kpsf; 1.
 InterPro; IPR000644; CBS_dom.
 InterPro; IPR004800; KdsD/KpsF-type.
 InterPro; IPR001347; SIS.
 InterPro; IPR035474; SIS_Kpsf.
 Pfam; PF00571; CBS; 2.
 Pfam; PF01380; SIS; 1.
 PIRSF; PIRSF004692; KdsD_KpsF; 1.
 TIGRFAMs; TIGR00393; kpsF; 1.
 PROSITE; PS51371; CBS; 2.
 PROSITE; PS51464; SIS; 1.
 1: Evidence at protein level;
 3D-structure; Carbohydrate metabolism; CBS domain; Complete proteome;
 Isomerase; Lipopolysaccharide biosynthesis; Metal-binding;
 Reference proteome; Repeat; Zinc.
 CHAIN         1    328       Arabinose 5-phosphate isomerase KdsD.
                              /FTId=PRO_0000136575.
 DOMAIN       42    184       SIS. {ECO:0000255|PROSITE-
                              ProRule:PRU00797}.
 DOMAIN      210    268       CBS 1. {ECO:0000255|PROSITE-
                              ProRule:PRU00703}.
 DOMAIN      277    328       CBS 2. {ECO:0000255|PROSITE-
                              ProRule:PRU00703}.
 REGION       75     76       Substrate binding. {ECO:0000250}.
 REGION      114    123       Substrate binding. {ECO:0000250}.
 REGION      148    150       Substrate binding. {ECO:0000250}.
 METAL        82     82       Zinc. {ECO:0000250}.
 BINDING      82     82       Substrate. {ECO:0000250}.
 BINDING      88     88       Substrate. {ECO:0000250}.
 BINDING     222    222       Substrate. {ECO:0000250}.
 BINDING     275    275       Substrate. {ECO:0000250}.
 SITE         59     59       Catalytically relevant.
 SITE        111    111       Catalytically relevant.
 SITE        152    152       Catalytically relevant.
 SITE        193    193       Catalytically relevant.
 MUTAGEN      59     59       K->A: Inactive.
                              {ECO:0000269|PubMed:19664604}.
 MUTAGEN      88     88       H->A: Shows 9.5% of residual activity
                              compared to the wild-type.
                              {ECO:0000269|PubMed:20954237}.
 MUTAGEN     111    111       E->A: Shows 62% of residual activity
                              compared to the wild-type.
                              {ECO:0000269|PubMed:19664604}.
 MUTAGEN     152    152       E->A: Shows 19% of residual activity
                              compared to the wild-type. It is able to
                              support growth.
                              {ECO:0000269|PubMed:19664604}.
 MUTAGEN     193    193       H->A: Inactive.
                              {ECO:0000269|PubMed:19664604}.
 HELIX        12     27       {ECO:0000244|PDB:2XHZ}.
 HELIX        28     32       {ECO:0000244|PDB:2XHZ}.
 HELIX        36     46       {ECO:0000244|PDB:2XHZ}.
 STRAND       52     56       {ECO:0000244|PDB:2XHZ}.
 HELIX        58     72       {ECO:0000244|PDB:2XHZ}.
 TURN         73     75       {ECO:0000244|PDB:2XHZ}.
 STRAND       78     80       {ECO:0000244|PDB:2XHZ}.
 HELIX        85     89       {ECO:0000244|PDB:2XHZ}.
 STRAND       99    103       {ECO:0000244|PDB:2XHZ}.
 STRAND      105    107       {ECO:0000244|PDB:2XHZ}.
 HELIX       110    120       {ECO:0000244|PDB:2XHZ}.
 TURN        121    123       {ECO:0000244|PDB:2XHZ}.
 STRAND      126    131       {ECO:0000244|PDB:2XHZ}.
 HELIX       136    140       {ECO:0000244|PDB:2XHZ}.
 STRAND      141    146       {ECO:0000244|PDB:2XHZ}.
 HELIX       162    182       {ECO:0000244|PDB:2XHZ}.
 SEQUENCE   328 AA;  35196 MW;  B2BE546C8F56C1B4 CRC64;
 MSHVELQPGF DFQQAGKEVL AIERECLAEL DQYINQNFTL ACEKMFWCKG KVVVMGMGKS
 GHIGRKMAAT FASTGTPSFF VHPGEAAHGD LGMVTPQDVV IAISNSGESS EITALIPVLK
 RLHVPLICIT GRPESSMARA ADVHLCVKVA KEACPLGLAP TSSTTATLVM GDALAVALLK
 ARGFTAEDFA LSHPGGALGR KLLLRVNDIM HTGDEIPHVK KTASLRDALL EVTRKNLGMT
 VICDDNMMIE GIFTDGDLRR VFDMGVDVRQ LSIADVMTPG GIRVRPGILA VEALNLMQSR
 HITSVMVADG DHLLGVLHMH DLLRAGVV

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