AROD_CLOD6
ID AROD_CLOD6 Reviewed; 255 AA.
AC Q186A6;
DT 18-MAR-2008, integrated into UniProtKB/Swiss-Prot.
DT 18-MAR-2008, sequence version 2.
DT 03-AUG-2022, entry version 90.
DE RecName: Full=3-dehydroquinate dehydratase {ECO:0000255|HAMAP-Rule:MF_00214, ECO:0000303|PubMed:21087925};
DE Short=3-dehydroquinase {ECO:0000255|HAMAP-Rule:MF_00214, ECO:0000303|PubMed:21087925};
DE EC=4.2.1.10 {ECO:0000255|HAMAP-Rule:MF_00214, ECO:0000303|PubMed:21087925};
DE AltName: Full=Type I DHQase {ECO:0000255|HAMAP-Rule:MF_00214};
DE AltName: Full=Type I dehydroquinase {ECO:0000255|HAMAP-Rule:MF_00214};
DE Short=DHQ1 {ECO:0000255|HAMAP-Rule:MF_00214};
GN Name=aroD {ECO:0000255|HAMAP-Rule:MF_00214}; OrderedLocusNames=CD630_22170;
OS Clostridioides difficile (strain 630) (Peptoclostridium difficile).
OC Bacteria; Firmicutes; Clostridia; Eubacteriales; Peptostreptococcaceae;
OC Clostridioides.
OX NCBI_TaxID=272563;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=630;
RX PubMed=16804543; DOI=10.1038/ng1830;
RA Sebaihia M., Wren B.W., Mullany P., Fairweather N.F., Minton N.,
RA Stabler R., Thomson N.R., Roberts A.P., Cerdeno-Tarraga A.M., Wang H.,
RA Holden M.T.G., Wright A., Churcher C., Quail M.A., Baker S., Bason N.,
RA Brooks K., Chillingworth T., Cronin A., Davis P., Dowd L., Fraser A.,
RA Feltwell T., Hance Z., Holroyd S., Jagels K., Moule S., Mungall K.,
RA Price C., Rabbinowitsch E., Sharp S., Simmonds M., Stevens K., Unwin L.,
RA Whithead S., Dupuy B., Dougan G., Barrell B., Parkhill J.;
RT "The multidrug-resistant human pathogen Clostridium difficile has a highly
RT mobile, mosaic genome.";
RL Nat. Genet. 38:779-786(2006).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) IN COMPLEX WITH 3-DEHYDROSHIKIMATE,
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVE SITE,
RP SUBUNIT, AND REACTION MECHANISM.
RC STRAIN=630;
RX PubMed=21087925; DOI=10.1074/jbc.m110.192831;
RA Light S.H., Minasov G., Shuvalova L., Duban M.E., Caffrey M.,
RA Anderson W.F., Lavie A.;
RT "Insights into the mechanism of type I dehydroquinate dehydratases from
RT structures of reaction intermediates.";
RL J. Biol. Chem. 286:3531-3539(2011).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS,
RP ACTIVE SITE, AND SUBUNIT.
RG Center for Structural Genomics of Infectious Diseases (CSGID);
RA Minasov G., Light S.H., Shuvalova L., Duban M.E., Dubrovska I., Winsor J.,
RA Papazisi L., Anderson W.F.;
RT "1.95 Angstrom crystal structure of type I 3-dehydroquinate dehydratase
RT (aroD) from Clostridium difficile with covalent modified comenic acid.";
RL Submitted (SEP-2012) to the PDB data bank.
CC -!- FUNCTION: Involved in the third step of the chorismate pathway, which
CC leads to the biosynthesis of aromatic amino acids. Catalyzes the cis-
CC dehydration of 3-dehydroquinate (DHQ) and introduces the first double
CC bond of the aromatic ring to yield 3-dehydroshikimate. The reaction
CC involves the formation of an imine intermediate between the keto group
CC of 3-dehydroquinate and the epsilon-amino group of Lys-170 at the
CC active site. {ECO:0000255|HAMAP-Rule:MF_00214,
CC ECO:0000269|PubMed:21087925}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3-dehydroquinate = 3-dehydroshikimate + H2O;
CC Xref=Rhea:RHEA:21096, ChEBI:CHEBI:15377, ChEBI:CHEBI:16630,
CC ChEBI:CHEBI:32364; EC=4.2.1.10; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00214, ECO:0000269|PubMed:21087925};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=36 uM for 3-dehydroquinate (at pH 7.5 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:21087925};
CC Note=kcat is 125 sec(-1) for dehydratase activity with 3-
CC dehydroquinate (at pH 7.5 and 37 degrees Celsius).
CC {ECO:0000269|PubMed:21087925};
CC -!- PATHWAY: Metabolic intermediate biosynthesis; chorismate biosynthesis;
CC chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step
CC 3/7. {ECO:0000255|HAMAP-Rule:MF_00214}.
CC -!- SUBUNIT: Homodimer or homotetramer. {ECO:0000255|HAMAP-Rule:MF_00214,
CC ECO:0000269|PubMed:21087925, ECO:0000269|Ref.3}.
CC -!- SIMILARITY: Belongs to the type-I 3-dehydroquinase family.
CC {ECO:0000255|HAMAP-Rule:MF_00214}.
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DR EMBL; AM180355; CAJ69102.2; -; Genomic_DNA.
DR RefSeq; WP_009897376.1; NZ_CP010905.2.
DR RefSeq; YP_001088731.2; NC_009089.1.
DR PDB; 3JS3; X-ray; 2.20 A; A/B/C/D=1-255.
DR PDB; 4H3D; X-ray; 1.95 A; A/B/C/D=1-255.
DR PDBsum; 3JS3; -.
DR PDBsum; 4H3D; -.
DR AlphaFoldDB; Q186A6; -.
DR SMR; Q186A6; -.
DR STRING; 272563.CD630_22170; -.
DR EnsemblBacteria; CAJ69102; CAJ69102; CD630_22170.
DR GeneID; 66354608; -.
DR KEGG; cdf:CD630_22170; -.
DR KEGG; pdc:CDIF630_02450; -.
DR PATRIC; fig|272563.120.peg.2341; -.
DR eggNOG; COG0710; Bacteria.
DR OMA; ATMAMGE; -.
DR PhylomeDB; Q186A6; -.
DR BioCyc; PDIF272563:G12WB-2373-MON; -.
DR UniPathway; UPA00053; UER00086.
DR EvolutionaryTrace; Q186A6; -.
DR Proteomes; UP000001978; Chromosome.
DR GO; GO:0003855; F:3-dehydroquinate dehydratase activity; IDA:UniProtKB.
DR GO; GO:0046279; P:3,4-dihydroxybenzoate biosynthetic process; IDA:UniProtKB.
DR GO; GO:0009073; P:aromatic amino acid family biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0008652; P:cellular amino acid biosynthetic process; IEA:UniProtKB-KW.
DR GO; GO:0009423; P:chorismate biosynthetic process; IEA:UniProtKB-UniPathway.
DR CDD; cd00502; DHQase_I; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_00214; AroD; 1.
DR InterPro; IPR018508; 3-dehydroquinate_DH_AS.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR001381; DHquinase_I.
DR Pfam; PF01487; DHquinase_I; 1.
DR TIGRFAMs; TIGR01093; aroD; 1.
DR PROSITE; PS01028; DEHYDROQUINASE_I; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Amino-acid biosynthesis; Aromatic amino acid biosynthesis;
KW Lyase; Reference proteome; Schiff base.
FT CHAIN 1..255
FT /note="3-dehydroquinate dehydratase"
FT /id="PRO_0000325520"
FT ACT_SITE 144
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00214,
FT ECO:0000269|Ref.3"
FT ACT_SITE 171
FT /note="Schiff-base intermediate with substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00214,
FT ECO:0000269|PubMed:21087925, ECO:0000269|Ref.3"
FT BINDING 47..49
FT /ligand="3-dehydroquinate"
FT /ligand_id="ChEBI:CHEBI:32364"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00214,
FT ECO:0000269|PubMed:21087925"
FT BINDING 83
FT /ligand="3-dehydroquinate"
FT /ligand_id="ChEBI:CHEBI:32364"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00214,
FT ECO:0000269|PubMed:21087925, ECO:0000269|Ref.3"
FT BINDING 214
FT /ligand="3-dehydroquinate"
FT /ligand_id="ChEBI:CHEBI:32364"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00214,
FT ECO:0000269|PubMed:21087925, ECO:0000269|Ref.3"
FT BINDING 233
FT /ligand="3-dehydroquinate"
FT /ligand_id="ChEBI:CHEBI:32364"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00214,
FT ECO:0000269|PubMed:21087925"
FT BINDING 237
FT /ligand="3-dehydroquinate"
FT /ligand_id="ChEBI:CHEBI:32364"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00214,
FT ECO:0000269|PubMed:21087925, ECO:0000269|Ref.3"
FT STRAND 5..7
FT /evidence="ECO:0007829|PDB:4H3D"
FT STRAND 10..12
FT /evidence="ECO:0007829|PDB:4H3D"
FT STRAND 14..16
FT /evidence="ECO:0007829|PDB:4H3D"
FT STRAND 18..23
FT /evidence="ECO:0007829|PDB:4H3D"
FT HELIX 28..38
FT /evidence="ECO:0007829|PDB:4H3D"
FT STRAND 44..49
FT /evidence="ECO:0007829|PDB:4H3D"
FT HELIX 50..52
FT /evidence="ECO:0007829|PDB:4H3D"
FT TURN 54..57
FT /evidence="ECO:0007829|PDB:4H3D"
FT HELIX 59..72
FT /evidence="ECO:0007829|PDB:4H3D"
FT STRAND 78..81
FT /evidence="ECO:0007829|PDB:4H3D"
FT HELIX 85..87
FT /evidence="ECO:0007829|PDB:4H3D"
FT HELIX 95..107
FT /evidence="ECO:0007829|PDB:4H3D"
FT STRAND 112..117
FT /evidence="ECO:0007829|PDB:4H3D"
FT HELIX 118..120
FT /evidence="ECO:0007829|PDB:4H3D"
FT HELIX 122..134
FT /evidence="ECO:0007829|PDB:4H3D"
FT STRAND 138..147
FT /evidence="ECO:0007829|PDB:4H3D"
FT HELIX 152..164
FT /evidence="ECO:0007829|PDB:4H3D"
FT STRAND 168..174
FT /evidence="ECO:0007829|PDB:4H3D"
FT HELIX 179..195
FT /evidence="ECO:0007829|PDB:4H3D"
FT STRAND 201..205
FT /evidence="ECO:0007829|PDB:4H3D"
FT HELIX 208..214
FT /evidence="ECO:0007829|PDB:4H3D"
FT HELIX 217..220
FT /evidence="ECO:0007829|PDB:4H3D"
FT STRAND 224..226
FT /evidence="ECO:0007829|PDB:4H3D"
FT STRAND 228..231
FT /evidence="ECO:0007829|PDB:3JS3"
FT HELIX 240..252
FT /evidence="ECO:0007829|PDB:4H3D"
SQ SEQUENCE 255 AA; 28876 MW; 60B9943466E5C9AD CRC64;
MKRKVQVKNI TIGEGRPKIC VPIIGKNKKD IIKEAKELKD ACLDIIEWRV DFFENVENIK
EVKEVLYELR SYIHDIPLLF TFRSVVEGGE KLISRDYYTT LNKEISNTGL VDLIDVELFM
GDEVIDEVVN FAHKKEVKVI ISNHDFNKTP KKEEIVSRLC RMQELGADLP KIAVMPQNEK
DVLVLLEATN EMFKIYADRP IITMSMSGMG VISRLCGEIF GSALTFGAAK SVSAPGQISF
KELNSVLNLL HKSIN
