AROD_SALTY
ID AROD_SALTY Reviewed; 252 AA.
AC P58687;
DT 31-JAN-2002, integrated into UniProtKB/Swiss-Prot.
DT 31-JAN-2002, sequence version 1.
DT 03-AUG-2022, entry version 124.
DE RecName: Full=3-dehydroquinate dehydratase {ECO:0000255|HAMAP-Rule:MF_00214};
DE Short=3-dehydroquinase {ECO:0000255|HAMAP-Rule:MF_00214};
DE Short=DHQD {ECO:0000303|PubMed:21291284};
DE EC=4.2.1.10 {ECO:0000255|HAMAP-Rule:MF_00214, ECO:0000269|PubMed:21087925, ECO:0000269|PubMed:21291284, ECO:0000269|PubMed:23341204, ECO:0000269|PubMed:24957267};
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=STM1358;
OS Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=99287;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=11677609; DOI=10.1038/35101614;
RA McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P.,
RA Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D.,
RA Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E.,
RA Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R.,
RA Wilson R.K.;
RT "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.";
RL Nature 413:852-856(2001).
RN [2]
RP ACTIVE SITE.
RX PubMed=22847490; DOI=10.1039/c2ob25605c;
RA Yao Y., Li Z.S.;
RT "New insights into the mechanism of the Schiff base hydrolysis catalyzed by
RT type I dehydroquinate dehydratase from S. enterica: a theoretical study.";
RL Org. Biomol. Chem. 10:7037-7044(2012).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND ACTIVITY
RP REGULATION.
RX PubMed=24957267; DOI=10.1042/bj20140614;
RA Maneiro M., Peon A., Lence E., Otero J.M., Van Raaij M.J., Thompson P.,
RA Hawkins A.R., Gonzalez-Bello C.;
RT "Insights into substrate binding and catalysis in bacterial type I
RT dehydroquinase.";
RL Biochem. J. 462:415-424(2014).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS,
RP AND SUBUNIT.
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RA Minasov G., Light S.H., Shuvalova L., Papazisi L., Anderson W.F.;
RT "Crystal structure of the 3-dehydroquinate dehydratase (aroD) from
RT Salmonella typhimurium LT2 with citrate bound to the active Site.";
RL Submitted (JAN-2010) to the PDB data bank.
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.03 ANGSTROMS) OF WILD-TYPE AND MUTANT ALA-236,
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVE SITE,
RP SUBUNIT, MUTAGENESIS OF SER-232 AND GLN-236, AND REACTION MECHANISM.
RX PubMed=21291284; DOI=10.1021/bi102020s;
RA Light S.H., Minasov G., Shuvalova L., Peterson S.N., Caffrey M.,
RA Anderson W.F., Lavie A.;
RT "A conserved surface loop in type I dehydroquinate dehydratases positions
RT an active site arginine and functions in substrate binding.";
RL Biochemistry 50:2357-2363(2011).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF WILD-TYPE AND MUTANT MET-170 IN
RP COMPLEX WITH 3-DEHYDROQUINIC ACID, FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, ACTIVE SITE, SUBUNIT, MUTAGENESIS OF
RP LYS-170, AND REACTION MECHANISM.
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
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 [7]
RP X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS,
RP AND SUBUNIT.
RA Light S.H., Minasov G., Duban M.-E., Halavaty A.S., Krishna S.N.,
RA Shuvalova L., Kwon K., Anderson W.F.;
RT "Crystal structure of the 3-dehydroquinate dehydratase (aroD) from
RT Salmonella enterica typhimurium LT2 with malonate and boric acid at the
RT active site.";
RL Submitted (MAY-2011) to the PDB data bank.
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG,
RP AND SUBUNIT.
RA Light S.H., Minasov G., Krishna S.N., Shuvalova L., Kwon K., Lavie A.,
RA Anderson W.F.;
RT "1.8 angstrom crystal structure of the 3-dehydroquinate dehydratase (aroD)
RT from Salmonella typhimurium LT2 with nickel bound at active site.";
RL Submitted (AUG-2012) to the PDB data bank.
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) OF MUTANT ALA-86 IN COMPLEX WITH
RP SUBSTRATE ANALOGS, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, MUTAGENESIS OF GLU-86, ACTIVE SITE, SUBUNIT, AND REACTION
RP MECHANISM.
RX PubMed=23341204; DOI=10.1002/pro.2218;
RA Light S.H., Anderson W.F., Lavie A.;
RT "Reassessing the type I dehydroquinate dehydratase catalytic triad: kinetic
RT and structural studies of Glu86 mutants.";
RL Protein Sci. 22:418-424(2013).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) WILD-TYPE AND MUTANT MET-170 IN
RP COMPLEX WITH SUBSTRATE ANALOGS, MUTAGENESIS OF LYS-170, AND SUBUNIT.
RX PubMed=24437575; DOI=10.1021/bi4015506;
RA Light S.H., Antanasijevic A., Krishna S.N., Caffrey M., Anderson W.F.,
RA Lavie A.;
RT "Crystal structures of type I dehydroquinate dehydratase in complex with
RT quinate and shikimate suggest a novel mechanism of Schiff base formation.";
RL Biochemistry 53:872-880(2014).
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 a Lys-170 at the
CC active site. {ECO:0000255|HAMAP-Rule:MF_00214,
CC ECO:0000269|PubMed:21087925, ECO:0000269|PubMed:21291284,
CC ECO:0000269|PubMed:23341204, ECO:0000269|PubMed:24957267}.
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 ECO:0000269|PubMed:21291284, ECO:0000269|PubMed:23341204,
CC ECO:0000269|PubMed:24957267};
CC -!- ACTIVITY REGULATION: Inhibited by (2R)-2-methyl-3-dehydroquinic acid.
CC {ECO:0000269|PubMed:24957267}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=18 uM for 3-dehydroquinate (at pH 7.2 and 25 degrees Celsius)
CC {ECO:0000269|PubMed:24957267};
CC KM=21 uM for 3-dehydroquinate (at pH 7.5 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:21087925};
CC KM=53 uM for 3-dehydroquinate (at pH 7.5 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:23341204};
CC Note=kcat is 210 sec(-1) for dehydratase activity with 3-
CC dehydroquinate (at pH 7.5 and 37 degrees Celsius). kcat is 255 sec(-
CC 1) for dehydratase activity with 3-dehydroquinate (at pH 7.2 and 25
CC degrees Celsius). kcat is 310 sec(-1) for dehydratase activity with
CC 3-dehydroquinate (at pH 7.5 and 37 degrees Celsius).
CC {ECO:0000269|PubMed:21087925, ECO:0000269|PubMed:21291284,
CC ECO:0000269|PubMed:23341204, ECO:0000269|PubMed:24957267};
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. {ECO:0000255|HAMAP-Rule:MF_00214,
CC ECO:0000269|PubMed:21087925, ECO:0000269|PubMed:21291284,
CC ECO:0000269|PubMed:23341204, ECO:0000269|PubMed:24437575,
CC ECO:0000269|Ref.4, ECO:0000269|Ref.7, ECO:0000269|Ref.8}.
CC -!- SIMILARITY: Belongs to the type-I 3-dehydroquinase family.
CC {ECO:0000255|HAMAP-Rule:MF_00214}.
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DR EMBL; AE006468; AAL20283.1; -; Genomic_DNA.
DR RefSeq; NP_460324.1; NC_003197.2.
DR RefSeq; WP_000860225.1; NC_003197.2.
DR PDB; 3L2I; X-ray; 1.85 A; A/B=1-252.
DR PDB; 3LB0; X-ray; 1.65 A; A/B=1-252.
DR PDB; 3M7W; X-ray; 1.95 A; A/B/C/D/E/F=1-252.
DR PDB; 3NNT; X-ray; 1.60 A; A/B=1-252.
DR PDB; 3O1N; X-ray; 1.03 A; A/B=1-252.
DR PDB; 3OEX; X-ray; 1.90 A; A/B/C/D=1-252.
DR PDB; 3S42; X-ray; 1.45 A; A/B=1-252.
DR PDB; 4GFS; X-ray; 1.80 A; A/B=1-252.
DR PDB; 4GUF; X-ray; 1.50 A; A/B=1-252.
DR PDB; 4GUG; X-ray; 1.62 A; A/B=1-252.
DR PDB; 4GUH; X-ray; 1.95 A; A/B=1-252.
DR PDB; 4GUI; X-ray; 1.78 A; A/B=1-252.
DR PDB; 4GUJ; X-ray; 1.50 A; A/B=1-252.
DR PDB; 4IUO; X-ray; 1.80 A; A/B=1-252.
DR PDBsum; 3L2I; -.
DR PDBsum; 3LB0; -.
DR PDBsum; 3M7W; -.
DR PDBsum; 3NNT; -.
DR PDBsum; 3O1N; -.
DR PDBsum; 3OEX; -.
DR PDBsum; 3S42; -.
DR PDBsum; 4GFS; -.
DR PDBsum; 4GUF; -.
DR PDBsum; 4GUG; -.
DR PDBsum; 4GUH; -.
DR PDBsum; 4GUI; -.
DR PDBsum; 4GUJ; -.
DR PDBsum; 4IUO; -.
DR AlphaFoldDB; P58687; -.
DR SMR; P58687; -.
DR STRING; 99287.STM1358; -.
DR PaxDb; P58687; -.
DR EnsemblBacteria; AAL20283; AAL20283; STM1358.
DR GeneID; 1252876; -.
DR KEGG; stm:STM1358; -.
DR PATRIC; fig|99287.12.peg.1442; -.
DR HOGENOM; CLU_064444_0_0_6; -.
DR OMA; ATMAMGE; -.
DR PhylomeDB; P58687; -.
DR BioCyc; SENT99287:STM1358-MON; -.
DR BRENDA; 4.2.1.10; 2169.
DR UniPathway; UPA00053; UER00086.
DR EvolutionaryTrace; P58687; -.
DR Proteomes; UP000001014; 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..252
FT /note="3-dehydroquinate dehydratase"
FT /id="PRO_0000138806"
FT ACT_SITE 143
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00214,
FT ECO:0000269|PubMed:21087925, ECO:0000269|PubMed:23341204,
FT ECO:0000269|PubMed:24437575, ECO:0000269|Ref.4,
FT ECO:0000269|Ref.8"
FT ACT_SITE 170
FT /note="Schiff-base intermediate with substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00214,
FT ECO:0000269|PubMed:21087925, ECO:0000269|PubMed:23341204,
FT ECO:0000269|Ref.4, ECO:0000269|Ref.7, ECO:0000269|Ref.8"
FT BINDING 21
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|PubMed:24437575,
FT ECO:0000269|Ref.4, ECO:0000269|Ref.7"
FT BINDING 46..48
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|PubMed:23341204,
FT ECO:0000269|PubMed:24437575, ECO:0000269|Ref.4,
FT ECO:0000269|Ref.7"
FT BINDING 82
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|PubMed:23341204,
FT ECO:0000269|PubMed:24437575, ECO:0000269|Ref.4,
FT ECO:0000269|Ref.7, ECO:0000269|Ref.8"
FT BINDING 213
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|PubMed:23341204,
FT ECO:0000269|PubMed:24437575, ECO:0000269|Ref.4,
FT ECO:0000269|Ref.7"
FT BINDING 232
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|PubMed:24437575,
FT ECO:0000269|Ref.4"
FT BINDING 236
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|PubMed:23341204,
FT ECO:0000269|PubMed:24437575, ECO:0000269|Ref.4,
FT ECO:0000269|Ref.7"
FT MUTAGEN 86
FT /note="E->A: Very strong reduction of the catalytic
FT efficiency and almost the same affinity for 3-
FT dehydroquinate."
FT /evidence="ECO:0000269|PubMed:23341204"
FT MUTAGEN 86
FT /note="E->Q: Strong reduction of the catalytic efficiency
FT and slight increase of the affinity for 3-dehydroquinate."
FT /evidence="ECO:0000269|PubMed:23341204"
FT MUTAGEN 170
FT /note="K->M: Abolishes enzyme activity and 1.5-fold
FT reduction of the affinity for 3-dehydroquinate."
FT /evidence="ECO:0000269|PubMed:21087925,
FT ECO:0000269|PubMed:24437575"
FT MUTAGEN 232
FT /note="S->A: Reduces enzyme activity 50-fold."
FT /evidence="ECO:0000269|PubMed:21291284"
FT MUTAGEN 236
FT /note="Q->A: Nearly abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:21291284"
FT STRAND 4..6
FT /evidence="ECO:0007829|PDB:3O1N"
FT STRAND 9..11
FT /evidence="ECO:0007829|PDB:3O1N"
FT STRAND 13..15
FT /evidence="ECO:0007829|PDB:3O1N"
FT STRAND 17..22
FT /evidence="ECO:0007829|PDB:3O1N"
FT HELIX 27..37
FT /evidence="ECO:0007829|PDB:3O1N"
FT STRAND 43..48
FT /evidence="ECO:0007829|PDB:3O1N"
FT HELIX 49..51
FT /evidence="ECO:0007829|PDB:3O1N"
FT TURN 53..56
FT /evidence="ECO:0007829|PDB:3O1N"
FT HELIX 58..71
FT /evidence="ECO:0007829|PDB:3O1N"
FT STRAND 77..80
FT /evidence="ECO:0007829|PDB:3O1N"
FT HELIX 84..86
FT /evidence="ECO:0007829|PDB:3O1N"
FT HELIX 94..107
FT /evidence="ECO:0007829|PDB:3O1N"
FT STRAND 111..116
FT /evidence="ECO:0007829|PDB:3O1N"
FT HELIX 117..119
FT /evidence="ECO:0007829|PDB:3O1N"
FT HELIX 121..133
FT /evidence="ECO:0007829|PDB:3O1N"
FT STRAND 137..146
FT /evidence="ECO:0007829|PDB:3O1N"
FT HELIX 151..163
FT /evidence="ECO:0007829|PDB:3O1N"
FT STRAND 167..173
FT /evidence="ECO:0007829|PDB:3O1N"
FT HELIX 178..194
FT /evidence="ECO:0007829|PDB:3O1N"
FT STRAND 201..204
FT /evidence="ECO:0007829|PDB:3O1N"
FT HELIX 207..210
FT /evidence="ECO:0007829|PDB:3O1N"
FT HELIX 211..214
FT /evidence="ECO:0007829|PDB:3O1N"
FT HELIX 216..219
FT /evidence="ECO:0007829|PDB:3O1N"
FT STRAND 223..225
FT /evidence="ECO:0007829|PDB:3O1N"
FT STRAND 227..229
FT /evidence="ECO:0007829|PDB:3O1N"
FT HELIX 239..251
FT /evidence="ECO:0007829|PDB:3O1N"
SQ SEQUENCE 252 AA; 27325 MW; 10BB561E38EA0A75 CRC64;
MKTVTVRDLV VGEGAPKIIV SLMGKTITDV KSEALAYREA DFDILEWRVD HFANVTTAES
VLEAAGAIRE IITDKPLLFT FRSAKEGGEQ ALTTGQYIDL NRAAVDSGLV DMIDLELFTG
DDEVKATVGY AHQHNVAVIM SNHDFHKTPA AEEIVQRLRK MQELGADIPK IAVMPQTKAD
VLTLLTATVE MQERYADRPI ITMSMSKTGV ISRLAGEVFG SAATFGAVKK ASAPGQISVA
DLRTVLTILH QA
