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Arabinose 5-phosphate isomerase KdsD (API) (L-API) (EC 5.3.1.13)

 KDSD_ECOLI              Reviewed;         328 AA.
P45395; Q2M915;
01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
01-NOV-1995, sequence version 1.
28-MAR-2018, entry version 122.
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, ENZYME
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 ENZYME 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: D-arabinose 5-phosphate = D-ribulose 5-
phosphate.
-!- ENZYME 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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Distributed under the Creative Commons Attribution (CC BY 4.0) License
-----------------------------------------------------------------------
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; -.
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; -.
OMA; FMHAADA; -.
PhylomeDB; P45395; -.
BioCyc; EcoCyc:G7662-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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