KDSD_ECOLI
ID KDSD_ECOLI Reviewed; 328 AA.
AC P45395; Q2M915;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1995, sequence version 1.
DT 03-AUG-2022, entry version 145.
DE RecName: Full=Arabinose 5-phosphate isomerase KdsD;
DE Short=API;
DE Short=L-API;
DE EC=5.3.1.13 {ECO:0000269|PubMed:12805358, ECO:0000269|PubMed:20039350};
GN Name=kdsD; Synonyms=yrbH; OrderedLocusNames=b3197, JW3164;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [3]
RP FUNCTION AS A ARABINOSE 5-PHOSPHATE ISOMERASE AND IN LIPOPOLYSACCHARIDE
RP BIOSYNTHESIS, CATALYTIC ACTIVITY, PATHWAY, BIOPHYSICOCHEMICAL PROPERTIES,
RP ACTIVITY REGULATION, AND SUBUNIT.
RC STRAIN=K12;
RX PubMed=12805358; DOI=10.1074/jbc.m303661200;
RA Meredith T.C., Woodard R.W.;
RT "Escherichia coli YrbH is a D-arabinose 5-phosphate isomerase.";
RL J. Biol. Chem. 278:32771-32777(2003).
RN [4]
RP FUNCTION AS A ARABINOSE 5-PHOSPHATE ISOMERASE, AND NOMENCLATURE.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=16199563; DOI=10.1128/jb.187.20.6936-6942.2005;
RA Meredith T.C., Woodard R.W.;
RT "Identification of GutQ from Escherichia coli as a D-arabinose 5-phosphate
RT isomerase.";
RL J. Bacteriol. 187:6936-6942(2005).
RN [5]
RP FUNCTION IN KDO BIOSYNTHESIS.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=16765569; DOI=10.1016/j.resmic.2005.11.014;
RA Sperandeo P., Pozzi C., Deho G., Polissi A.;
RT "Non-essential KDO biosynthesis and new essential cell envelope biogenesis
RT genes in the Escherichia coli yrbG-yhbG locus.";
RL Res. Microbiol. 157:547-558(2006).
RN [6]
RP MUTAGENESIS OF LYS-59; GLU-111; GLU-152 AND HIS-193.
RC STRAIN=K12;
RX PubMed=19664604; DOI=10.1016/j.bbrc.2009.07.154;
RA Sommaruga S., Gioia L.D., Tortora P., Polissi A.;
RT "Structure prediction and functional analysis of KdsD, an enzyme involved
RT in lipopolysaccharide biosynthesis.";
RL Biochem. Biophys. Res. Commun. 388:222-227(2009).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, REACTION MECHANISM, AND ACTIVITY REGULATION.
RC STRAIN=K12;
RX PubMed=20039350; DOI=10.1002/chem.200902619;
RA Airoldi C., Sommaruga S., Merlo S., Sperandeo P., Cipolla L., Polissi A.,
RA Nicotra F.;
RT "Targeting bacterial membranes: NMR spectroscopy characterization of
RT substrate recognition and binding requirements of D-arabinose-5-phosphate
RT isomerase.";
RL Chemistry 16:1897-1902(2010).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 1-183 OF MUTANT ALA-59,
RP MUTAGENESIS OF HIS-88, AND SUBUNIT.
RC STRAIN=K12;
RX PubMed=20954237; DOI=10.1002/pro.525;
RA Gourlay L.J., Sommaruga S., Nardini M., Sperandeo P., Deho G., Polissi A.,
RA Bolognesi M.;
RT "Probing the active site of the sugar isomerase domain from E. coli
RT arabinose-5-phosphate isomerase via X-ray crystallography.";
RL Protein Sci. 19:2430-2439(2010).
CC -!- FUNCTION: Involved in the biosynthesis of 3-deoxy-D-manno-octulosonate
CC (KDO), a unique 8-carbon sugar component of lipopolysaccharides (LPSs).
CC KdsD is not essential in the KDO biosynthesis and can be substituted by
CC GutQ. Catalyzes the reversible aldol-ketol isomerization between D-
CC ribulose 5-phosphate (Ru5P) and D-arabinose 5-phosphate (A5P).
CC {ECO:0000269|PubMed:12805358, ECO:0000269|PubMed:16199563,
CC ECO:0000269|PubMed:16765569, ECO:0000269|PubMed:20039350}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-arabinose 5-phosphate = D-ribulose 5-phosphate;
CC Xref=Rhea:RHEA:23104, ChEBI:CHEBI:57693, ChEBI:CHEBI:58121;
CC EC=5.3.1.13; Evidence={ECO:0000269|PubMed:12805358,
CC ECO:0000269|PubMed:20039350};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:23105;
CC Evidence={ECO:0000305|PubMed:12805358, ECO:0000305|PubMed:20039350};
CC PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:23106;
CC Evidence={ECO:0000305|PubMed:12805358, ECO:0000305|PubMed:20039350};
CC -!- ACTIVITY REGULATION: Completely inhibited by 10 uM of nickel, copper,
CC cadmium and mercury ions. Inhibited by zinc with an IC(50) of 1-3 uM.
CC Metal ion inhibition may be a mechanism to control activity in vivo.
CC {ECO:0000269|PubMed:12805358, ECO:0000269|PubMed:20039350}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.35 mM for Ru5P (at pH 8.5 and at 37 degrees Celsius)
CC {ECO:0000269|PubMed:12805358};
CC KM=0.61 mM for A5P (at pH 8.5 and at 37 degrees Celsius)
CC {ECO:0000269|PubMed:12805358};
CC pH dependence:
CC Optimum pH is 8.4. {ECO:0000269|PubMed:12805358};
CC -!- PATHWAY: Carbohydrate biosynthesis; 3-deoxy-D-manno-octulosonate
CC biosynthesis; 3-deoxy-D-manno-octulosonate from D-ribulose 5-phosphate:
CC step 1/3. {ECO:0000305|PubMed:12805358}.
CC -!- PATHWAY: Bacterial outer membrane biogenesis; lipopolysaccharide
CC biosynthesis. {ECO:0000305|PubMed:12805358}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:12805358,
CC ECO:0000269|PubMed:20954237}.
CC -!- SIMILARITY: Belongs to the SIS family. GutQ/KpsF subfamily.
CC {ECO:0000305}.
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DR EMBL; U18997; AAA57998.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76229.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77241.1; -; Genomic_DNA.
DR PIR; G65110; G65110.
DR RefSeq; NP_417664.1; NC_000913.3.
DR RefSeq; WP_001295557.1; NZ_STEB01000012.1.
DR PDB; 2XHZ; X-ray; 2.60 A; A/B/C/D=1-183.
DR PDBsum; 2XHZ; -.
DR AlphaFoldDB; P45395; -.
DR SMR; P45395; -.
DR BioGRID; 4259369; 339.
DR BioGRID; 852047; 2.
DR DIP; DIP-12910N; -.
DR IntAct; P45395; 9.
DR STRING; 511145.b3197; -.
DR jPOST; P45395; -.
DR PaxDb; P45395; -.
DR PRIDE; P45395; -.
DR EnsemblBacteria; AAC76229; AAC76229; b3197.
DR EnsemblBacteria; BAE77241; BAE77241; BAE77241.
DR GeneID; 66672901; -.
DR GeneID; 947734; -.
DR KEGG; ecj:JW3164; -.
DR KEGG; eco:b3197; -.
DR PATRIC; fig|1411691.4.peg.3534; -.
DR EchoBASE; EB2655; -.
DR eggNOG; COG0517; Bacteria.
DR eggNOG; COG0794; Bacteria.
DR HOGENOM; CLU_040681_13_1_6; -.
DR InParanoid; P45395; -.
DR OMA; LMACLMR; -.
DR PhylomeDB; P45395; -.
DR BioCyc; EcoCyc:G7662-MON; -.
DR BioCyc; MetaCyc:G7662-MON; -.
DR BRENDA; 5.3.1.13; 2026.
DR UniPathway; UPA00030; -.
DR UniPathway; UPA00357; UER00473.
DR EvolutionaryTrace; P45395; -.
DR PRO; PR:P45395; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0019146; F:arabinose-5-phosphate isomerase activity; IDA:EcoCyc.
DR GO; GO:0097367; F:carbohydrate derivative binding; IEA:InterPro.
DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0019294; P:keto-3-deoxy-D-manno-octulosonic acid biosynthetic process; IDA:EcoCyc.
DR GO; GO:0051289; P:protein homotetramerization; IDA:EcoCyc.
DR CDD; cd05014; SIS_Kpsf; 1.
DR Gene3D; 3.10.580.10; -; 1.
DR InterPro; IPR000644; CBS_dom.
DR InterPro; IPR046342; CBS_dom_sf.
DR InterPro; IPR004800; KdsD/KpsF-type.
DR InterPro; IPR001347; SIS_dom.
DR InterPro; IPR046348; SIS_dom_sf.
DR InterPro; IPR035474; SIS_Kpsf.
DR Pfam; PF00571; CBS; 2.
DR Pfam; PF01380; SIS; 1.
DR PIRSF; PIRSF004692; KdsD_KpsF; 1.
DR SUPFAM; SSF53697; SSF53697; 1.
DR TIGRFAMs; TIGR00393; kpsF; 1.
DR PROSITE; PS51371; CBS; 2.
DR PROSITE; PS51464; SIS; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Carbohydrate metabolism; CBS domain; Isomerase;
KW Lipopolysaccharide biosynthesis; Metal-binding; Reference proteome; Repeat;
KW Zinc.
FT CHAIN 1..328
FT /note="Arabinose 5-phosphate isomerase KdsD"
FT /id="PRO_0000136575"
FT DOMAIN 42..184
FT /note="SIS"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00797"
FT DOMAIN 210..268
FT /note="CBS 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00703"
FT DOMAIN 277..328
FT /note="CBS 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00703"
FT BINDING 75..76
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 82
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 82
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 88
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 114..123
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 148..150
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 222
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 275
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT SITE 59
FT /note="Catalytically relevant"
FT SITE 111
FT /note="Catalytically relevant"
FT SITE 152
FT /note="Catalytically relevant"
FT SITE 193
FT /note="Catalytically relevant"
FT MUTAGEN 59
FT /note="K->A: Inactive."
FT /evidence="ECO:0000269|PubMed:19664604"
FT MUTAGEN 88
FT /note="H->A: Shows 9.5% of residual activity compared to
FT the wild-type."
FT /evidence="ECO:0000269|PubMed:20954237"
FT MUTAGEN 111
FT /note="E->A: Shows 62% of residual activity compared to the
FT wild-type."
FT /evidence="ECO:0000269|PubMed:19664604"
FT MUTAGEN 152
FT /note="E->A: Shows 19% of residual activity compared to the
FT wild-type. It is able to support growth."
FT /evidence="ECO:0000269|PubMed:19664604"
FT MUTAGEN 193
FT /note="H->A: Inactive."
FT /evidence="ECO:0000269|PubMed:19664604"
FT HELIX 12..27
FT /evidence="ECO:0007829|PDB:2XHZ"
FT HELIX 28..32
FT /evidence="ECO:0007829|PDB:2XHZ"
FT HELIX 36..46
FT /evidence="ECO:0007829|PDB:2XHZ"
FT STRAND 52..56
FT /evidence="ECO:0007829|PDB:2XHZ"
FT HELIX 58..72
FT /evidence="ECO:0007829|PDB:2XHZ"
FT TURN 73..75
FT /evidence="ECO:0007829|PDB:2XHZ"
FT STRAND 78..80
FT /evidence="ECO:0007829|PDB:2XHZ"
FT HELIX 85..89
FT /evidence="ECO:0007829|PDB:2XHZ"
FT STRAND 99..103
FT /evidence="ECO:0007829|PDB:2XHZ"
FT STRAND 105..107
FT /evidence="ECO:0007829|PDB:2XHZ"
FT HELIX 110..120
FT /evidence="ECO:0007829|PDB:2XHZ"
FT TURN 121..123
FT /evidence="ECO:0007829|PDB:2XHZ"
FT STRAND 126..131
FT /evidence="ECO:0007829|PDB:2XHZ"
FT HELIX 136..140
FT /evidence="ECO:0007829|PDB:2XHZ"
FT STRAND 141..146
FT /evidence="ECO:0007829|PDB:2XHZ"
FT HELIX 162..182
FT /evidence="ECO:0007829|PDB:2XHZ"
SQ 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
