KDUI_ECOLI
ID KDUI_ECOLI Reviewed; 278 AA.
AC Q46938; Q2M9Z4;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 154.
DE RecName: Full=4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase;
DE EC=5.3.1.17;
DE AltName: Full=5-keto-4-deoxyuronate isomerase;
DE AltName: Full=DKI isomerase;
GN Name=kduI; Synonyms=yqeE; OrderedLocusNames=b2843, JW2811;
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 PROTEIN SEQUENCE OF 1-20 AND 227-247, CRYSTALLIZATION, AND SUBUNIT.
RX PubMed=9761873; DOI=10.1107/s090744499701785x;
RA Dunten P., Jaffe H., Aksamit R.R.;
RT "Crystallization of 5-keto-4-deoxyuronate isomerase from Escherichia
RT coli.";
RL Acta Crystallogr. D 54:678-680(1998).
RN [4]
RP INDUCTION.
RC STRAIN=K12;
RX PubMed=22427493; DOI=10.1128/aem.00244-12;
RA Rothe M., Alpert C., Engst W., Musiol S., Loh G., Blaut M.;
RT "Impact of nutritional factors on the proteome of intestinal Escherichia
RT coli: induction of OxyR-dependent proteins AhpF and Dps by a lactose-rich
RT diet.";
RL Appl. Environ. Microbiol. 78:3580-3591(2012).
RN [5]
RP FUNCTION, AND INDUCTION.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=23437267; DOI=10.1371/journal.pone.0056906;
RA Rothe M., Alpert C., Loh G., Blaut M.;
RT "Novel insights into E. coli's hexuronate metabolism: KduI facilitates the
RT conversion of galacturonate and glucuronate under osmotic stress
RT conditions.";
RL PLoS ONE 8:E56906-E56906(2013).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS).
RA Fedorov A.A., Fedorov E.V., Almo S.C.;
RT "The crystal structure of pectin degrading enzyme 5-keto 4-deoxyuronate
RT isomerase from Escherichia coli.";
RL Submitted (AUG-2004) to the PDB data bank.
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.94 ANGSTROMS) IN COMPLEX WITH ZINC, COFACTOR, AND
RP SUBUNIT.
RC STRAIN=K12 / DH5-alpha;
RX PubMed=16152643; DOI=10.1002/prot.20598;
RA Crowther R.L., Georgiadis M.M.;
RT "The crystal structure of 5-keto-4-deoxyuronate isomerase from Escherichia
RT coli.";
RL Proteins 61:680-684(2005).
CC -!- FUNCTION: Catalyzes the isomerization of 5-dehydro-4-deoxy-D-
CC glucuronate to 3-deoxy-D-glycero-2,5-hexodiulosonate (By similarity).
CC Plays a role in the catabolism of hexuronates under osmotic stress
CC conditions, likely substituting for the regular hexuronate degrading
CC enzyme UxaC whose expression is repressed in these conditions
CC (PubMed:23437267). {ECO:0000250|UniProtKB:Q05529,
CC ECO:0000269|PubMed:23437267}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-dehydro-4-deoxy-D-glucuronate = 3-deoxy-D-glycero-2,5-
CC hexodiulosonate; Xref=Rhea:RHEA:23896, ChEBI:CHEBI:17117,
CC ChEBI:CHEBI:29071; EC=5.3.1.17;
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:16152643, ECO:0000305};
CC Note=Binds 1 zinc ion per subunit. The bound metal seen in the crystal
CC structure was tentatively identified as zinc, and its requirement for
CC activity has not been shown. {ECO:0000269|PubMed:16152643,
CC ECO:0000305};
CC -!- PATHWAY: Glycan metabolism; pectin degradation; 2-dehydro-3-deoxy-D-
CC gluconate from pectin: step 4/5.
CC -!- SUBUNIT: Homohexamer. {ECO:0000269|PubMed:16152643,
CC ECO:0000269|PubMed:9761873}.
CC -!- INDUCTION: Its expression is up-regulated in the presence of
CC galacturonate and glucuronate (PubMed:23437267). Is also down-regulated
CC in E.coli of mice fed a casein-rich diet (PubMed:22427493).
CC {ECO:0000269|PubMed:22427493, ECO:0000269|PubMed:23437267}.
CC -!- SIMILARITY: Belongs to the KduI family. {ECO:0000305}.
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DR EMBL; U29581; AAB40490.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75882.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76912.1; -; Genomic_DNA.
DR PIR; D65067; D65067.
DR RefSeq; NP_417320.1; NC_000913.3.
DR RefSeq; WP_000383237.1; NZ_SSUV01000026.1.
DR PDB; 1X8M; X-ray; 2.60 A; A/B/C/D/E/F=2-278.
DR PDB; 1XRU; X-ray; 1.94 A; A/B=1-278.
DR PDBsum; 1X8M; -.
DR PDBsum; 1XRU; -.
DR AlphaFoldDB; Q46938; -.
DR SASBDB; Q46938; -.
DR SMR; Q46938; -.
DR BioGRID; 4261944; 15.
DR DIP; DIP-10069N; -.
DR IntAct; Q46938; 2.
DR STRING; 511145.b2843; -.
DR jPOST; Q46938; -.
DR PaxDb; Q46938; -.
DR PRIDE; Q46938; -.
DR DNASU; 947319; -.
DR EnsemblBacteria; AAC75882; AAC75882; b2843.
DR EnsemblBacteria; BAE76912; BAE76912; BAE76912.
DR GeneID; 947319; -.
DR KEGG; ecj:JW2811; -.
DR KEGG; eco:b2843; -.
DR PATRIC; fig|1411691.4.peg.3891; -.
DR EchoBASE; EB2899; -.
DR eggNOG; COG3717; Bacteria.
DR HOGENOM; CLU_062609_0_0_6; -.
DR InParanoid; Q46938; -.
DR OMA; TFIWAMA; -.
DR PhylomeDB; Q46938; -.
DR BioCyc; EcoCyc:G7463-MON; -.
DR BioCyc; MetaCyc:G7463-MON; -.
DR BRENDA; 5.3.1.17; 2026.
DR UniPathway; UPA00545; UER00826.
DR EvolutionaryTrace; Q46938; -.
DR PRO; PR:Q46938; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; HDA:UniProtKB.
DR GO; GO:0008697; F:4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase activity; IDA:EcoCyc.
DR GO; GO:0004347; F:glucose-6-phosphate isomerase activity; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0046872; F:metal ion binding; IDA:EcoCyc.
DR GO; GO:0008270; F:zinc ion binding; IDA:EcoCyc.
DR GO; GO:0019698; P:D-galacturonate catabolic process; IDA:EcoCyc.
DR GO; GO:0042840; P:D-glucuronate catabolic process; IDA:EcoCyc.
DR GO; GO:0045490; P:pectin catabolic process; IEA:UniProtKB-UniRule.
DR Gene3D; 2.60.120.10; -; 1.
DR Gene3D; 2.60.120.520; -; 1.
DR HAMAP; MF_00687; KduI; 1.
DR InterPro; IPR007045; KduI.
DR InterPro; IPR021120; KduI/IolB_isomerase.
DR InterPro; IPR027449; KduI_N.
DR InterPro; IPR014710; RmlC-like_jellyroll.
DR InterPro; IPR011051; RmlC_Cupin_sf.
DR PANTHER; PTHR38461; PTHR38461; 1.
DR Pfam; PF04962; KduI; 1.
DR PIRSF; PIRSF006625; KduI; 1.
DR SUPFAM; SSF51182; SSF51182; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Isomerase; Metal-binding;
KW Reference proteome; Zinc.
FT CHAIN 1..278
FT /note="4-deoxy-L-threo-5-hexosulose-uronate ketol-
FT isomerase"
FT /id="PRO_0000215485"
FT BINDING 196
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:16152643"
FT BINDING 198
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:16152643"
FT BINDING 203
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:16152643"
FT BINDING 245
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:16152643"
FT STRAND 2..4
FT /evidence="ECO:0007829|PDB:1XRU"
FT HELIX 9..12
FT /evidence="ECO:0007829|PDB:1XRU"
FT HELIX 17..24
FT /evidence="ECO:0007829|PDB:1XRU"
FT STRAND 38..40
FT /evidence="ECO:0007829|PDB:1XRU"
FT TURN 41..44
FT /evidence="ECO:0007829|PDB:1XRU"
FT STRAND 45..51
FT /evidence="ECO:0007829|PDB:1XRU"
FT STRAND 53..55
FT /evidence="ECO:0007829|PDB:1XRU"
FT STRAND 57..60
FT /evidence="ECO:0007829|PDB:1XRU"
FT HELIX 61..66
FT /evidence="ECO:0007829|PDB:1XRU"
FT STRAND 69..71
FT /evidence="ECO:0007829|PDB:1XRU"
FT TURN 72..75
FT /evidence="ECO:0007829|PDB:1XRU"
FT STRAND 76..82
FT /evidence="ECO:0007829|PDB:1XRU"
FT STRAND 87..91
FT /evidence="ECO:0007829|PDB:1XRU"
FT STRAND 94..98
FT /evidence="ECO:0007829|PDB:1XRU"
FT STRAND 103..106
FT /evidence="ECO:0007829|PDB:1XRU"
FT STRAND 113..118
FT /evidence="ECO:0007829|PDB:1XRU"
FT STRAND 126..132
FT /evidence="ECO:0007829|PDB:1XRU"
FT STRAND 140..142
FT /evidence="ECO:0007829|PDB:1XRU"
FT HELIX 144..147
FT /evidence="ECO:0007829|PDB:1XRU"
FT STRAND 150..152
FT /evidence="ECO:0007829|PDB:1XRU"
FT HELIX 155..157
FT /evidence="ECO:0007829|PDB:1XRU"
FT STRAND 161..168
FT /evidence="ECO:0007829|PDB:1XRU"
FT TURN 169..171
FT /evidence="ECO:0007829|PDB:1XRU"
FT STRAND 178..184
FT /evidence="ECO:0007829|PDB:1XRU"
FT STRAND 190..192
FT /evidence="ECO:0007829|PDB:1XRU"
FT STRAND 194..197
FT /evidence="ECO:0007829|PDB:1XRU"
FT STRAND 201..209
FT /evidence="ECO:0007829|PDB:1XRU"
FT STRAND 216..222
FT /evidence="ECO:0007829|PDB:1XRU"
FT STRAND 225..231
FT /evidence="ECO:0007829|PDB:1XRU"
FT STRAND 233..239
FT /evidence="ECO:0007829|PDB:1XRU"
FT STRAND 244..251
FT /evidence="ECO:0007829|PDB:1XRU"
FT STRAND 254..262
FT /evidence="ECO:0007829|PDB:1XRU"
FT STRAND 269..272
FT /evidence="ECO:0007829|PDB:1XRU"
FT HELIX 274..277
FT /evidence="ECO:0007829|PDB:1XRU"
SQ SEQUENCE 278 AA; 31076 MW; F7CD5C259503CD1A CRC64;
MDVRQSIHSA HAKTLDTQGL RNEFLVEKVF VADEYTMVYS HIDRIIVGGI MPITKTVSVG
GEVGKQLGVS YFLERRELGV INIGGAGTIT VDGQCYEIGH RDALYVGKGA KEVVFASIDT
GTPAKFYYNC APAHTTYPTK KVTPDEVSPV TLGDNLTSNR RTINKYFVPD VLETCQLSMG
LTELAPGNLW NTMPCHTHER RMEVYFYFNM DDDACVFHMM GQPQETRHIV MHNEQAVISP
SWSIHSGVGT KAYTFIWGMV GENQVFDDMD HVAVKDLR
