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Protein

3-dehydroquinate dehydratase

Gene

aroD

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the third step of the chorismate pathway, which leads to the biosynthesis of aromatic amino acids. Catalyzes the cis-dehydration of 3-dehydroquinate (DHQ) and introduces the first double bond of the aromatic ring to yield 3-dehydroshikimate. The reaction involves the formation of an imine intermediate between the keto group of 3-dehydroquinate and the epsylon-amino group of a lys-170 at the active site.4 PublicationsUniRule annotation

Catalytic activityi

3-dehydroquinate = 3-dehydroshikimate + H2O.4 PublicationsUniRule annotation

Enzyme regulationi

Inhibited by (2R)-2-methyl-3-dehydroquinic acid.1 Publication

Kineticsi

Kcat is 210 sec(-1) for dehydratase activity with 3-dehydroquinate (at pH 7.5 and 37 degrees Celsius). Kcat is 255 sec(-1) for dehydratase activity with 3-dehydroquinate (at pH 7.2 and 25 degrees Celsius). Kcat is 310 sec(-1) for dehydratase activity with 3-dehydroquinate (at pH 7.5 and 37 degrees Celsius).4 Publications

  1. KM=18 µM for 3-dehydroquinate (at pH 7.2 and 25 degrees Celsius).1 Publication
  2. KM=21 µM for 3-dehydroquinate (at pH 7.5 and 37 degrees Celsius).1 Publication
  3. KM=53 µM for 3-dehydroquinate (at pH 7.5 and 37 degrees Celsius).1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei21 – 2113-dehydroquinate4 PublicationsUniRule annotation
Binding sitei82 – 8213-dehydroquinate6 PublicationsUniRule annotation
Active sitei143 – 1431Proton donor/acceptor5 PublicationsUniRule annotation
Active sitei170 – 1701Schiff-base intermediate with substrate5 PublicationsUniRule annotation
Binding sitei213 – 21313-dehydroquinate5 PublicationsUniRule annotation
Binding sitei232 – 23213-dehydroquinate3 PublicationsUniRule annotation
Binding sitei236 – 23613-dehydroquinate5 PublicationsUniRule annotation

GO - Molecular functioni

  1. 3-dehydroquinate dehydratase activity Source: UniProtKB

GO - Biological processi

  1. aromatic amino acid family biosynthetic process Source: UniProtKB-HAMAP
  2. chorismate biosynthetic process Source: UniProtKB-UniPathway
  3. protocatechuate biosynthetic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Amino-acid biosynthesis, Aromatic amino acid biosynthesis

Keywords - Ligandi

Schiff base

Enzyme and pathway databases

BioCyciSENT99287:GCTI-1368-MONOMER.
UniPathwayiUPA00053; UER00086.

Names & Taxonomyi

Protein namesi
Recommended name:
3-dehydroquinate dehydrataseUniRule annotation (EC:4.2.1.104 PublicationsUniRule annotation)
Short name:
3-dehydroquinaseUniRule annotation
Short name:
DHQD1 Publication
Alternative name(s):
Type I DHQaseUniRule annotation
Type I dehydroquinaseUniRule annotation
Short name:
DHQ1UniRule annotation
Gene namesi
Name:aroDUniRule annotation
Ordered Locus Names:STM1358
OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Taxonomic identifieri99287 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
ProteomesiUP000001014: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi86 – 861E → A: Very strong reduction of the catalytic efficiency and almost the same affinity for 3-dehydroquinate. 1 Publication
Mutagenesisi86 – 861E → Q: Strong reduction of the catalytic efficiency and slight increase of the affinity for 3-dehydroquinate. 1 Publication
Mutagenesisi170 – 1701K → M: Abolishes enzyme activity and 1.5-fold reduction of the affinity for 3-dehydroquinate. 2 Publications
Mutagenesisi232 – 2321S → A: Reduces enzyme activity 50-fold. 1 Publication
Mutagenesisi236 – 2361Q → A: Nearly abolishes enzyme activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 2522523-dehydroquinate dehydratasePRO_0000138806Add
BLAST

Proteomic databases

PRIDEiP58687.

Interactioni

Subunit structurei

Homodimer.7 PublicationsUniRule annotation

Protein-protein interaction databases

STRINGi99287.STM1358.

Structurei

Secondary structure

1
252
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 63Combined sources
Beta strandi9 – 113Combined sources
Beta strandi13 – 153Combined sources
Beta strandi17 – 226Combined sources
Helixi27 – 3711Combined sources
Beta strandi43 – 486Combined sources
Helixi49 – 513Combined sources
Turni53 – 564Combined sources
Helixi58 – 7114Combined sources
Beta strandi77 – 804Combined sources
Helixi84 – 863Combined sources
Helixi94 – 10714Combined sources
Beta strandi111 – 1166Combined sources
Helixi117 – 1193Combined sources
Helixi121 – 13313Combined sources
Beta strandi137 – 14610Combined sources
Helixi151 – 16313Combined sources
Beta strandi167 – 1737Combined sources
Helixi178 – 19417Combined sources
Beta strandi201 – 2044Combined sources
Helixi207 – 2104Combined sources
Helixi211 – 2144Combined sources
Helixi216 – 2194Combined sources
Beta strandi223 – 2253Combined sources
Beta strandi227 – 2293Combined sources
Helixi239 – 25113Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3L2IX-ray1.85A/B1-252[»]
3LB0X-ray1.65A/B1-252[»]
3M7WX-ray1.95A/B/C/D/E/F1-252[»]
3NNTX-ray1.60A/B1-252[»]
3O1NX-ray1.03A/B1-252[»]
3OEXX-ray1.90A/B/C/D1-252[»]
3S42X-ray1.45A/B1-252[»]
4GFSX-ray1.80A/B1-252[»]
4GUFX-ray1.50A/B1-252[»]
4GUGX-ray1.62A/B1-252[»]
4GUHX-ray1.95A/B1-252[»]
4GUIX-ray1.78A/B1-252[»]
4GUJX-ray1.50A/B1-252[»]
4IUOX-ray1.80A/B1-252[»]
ProteinModelPortaliP58687.
SMRiP58687. Positions 1-252.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP58687.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni46 – 4833-dehydroquinate binding5 PublicationsUniRule annotation

Sequence similaritiesi

Belongs to the type-I 3-dehydroquinase family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000105514.
KOiK03785.
OMAiLFTFRSK.
OrthoDBiEOG6P33BK.
PhylomeDBiP58687.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00214. AroD.
InterProiIPR018508. 3-dehydroquinate_DH_AS.
IPR013785. Aldolase_TIM.
IPR001381. DHquinase_I.
[Graphical view]
PfamiPF01487. DHquinase_I. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01093. aroD. 1 hit.
PROSITEiPS01028. DEHYDROQUINASE_I. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P58687-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MKTVTVRDLV VGEGAPKIIV SLMGKTITDV KSEALAYREA DFDILEWRVD
60 70 80 90 100
HFANVTTAES VLEAAGAIRE IITDKPLLFT FRSAKEGGEQ ALTTGQYIDL
110 120 130 140 150
NRAAVDSGLV DMIDLELFTG DDEVKATVGY AHQHNVAVIM SNHDFHKTPA
160 170 180 190 200
AEEIVQRLRK MQELGADIPK IAVMPQTKAD VLTLLTATVE MQERYADRPI
210 220 230 240 250
ITMSMSKTGV ISRLAGEVFG SAATFGAVKK ASAPGQISVA DLRTVLTILH

QA
Length:252
Mass (Da):27,325
Last modified:January 31, 2002 - v1
Checksum:i10BB561E38EA0A75
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE006468 Genomic DNA. Translation: AAL20283.1.
RefSeqiNP_460324.1. NC_003197.1.

Genome annotation databases

EnsemblBacteriaiAAL20283; AAL20283; STM1358.
GeneIDi1252876.
KEGGistm:STM1358.
PATRICi32381199. VBISalEnt20916_1442.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE006468 Genomic DNA. Translation: AAL20283.1.
RefSeqiNP_460324.1. NC_003197.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3L2IX-ray1.85A/B1-252[»]
3LB0X-ray1.65A/B1-252[»]
3M7WX-ray1.95A/B/C/D/E/F1-252[»]
3NNTX-ray1.60A/B1-252[»]
3O1NX-ray1.03A/B1-252[»]
3OEXX-ray1.90A/B/C/D1-252[»]
3S42X-ray1.45A/B1-252[»]
4GFSX-ray1.80A/B1-252[»]
4GUFX-ray1.50A/B1-252[»]
4GUGX-ray1.62A/B1-252[»]
4GUHX-ray1.95A/B1-252[»]
4GUIX-ray1.78A/B1-252[»]
4GUJX-ray1.50A/B1-252[»]
4IUOX-ray1.80A/B1-252[»]
ProteinModelPortaliP58687.
SMRiP58687. Positions 1-252.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi99287.STM1358.

Proteomic databases

PRIDEiP58687.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL20283; AAL20283; STM1358.
GeneIDi1252876.
KEGGistm:STM1358.
PATRICi32381199. VBISalEnt20916_1442.

Phylogenomic databases

HOGENOMiHOG000105514.
KOiK03785.
OMAiLFTFRSK.
OrthoDBiEOG6P33BK.
PhylomeDBiP58687.

Enzyme and pathway databases

UniPathwayiUPA00053; UER00086.
BioCyciSENT99287:GCTI-1368-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP58687.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00214. AroD.
InterProiIPR018508. 3-dehydroquinate_DH_AS.
IPR013785. Aldolase_TIM.
IPR001381. DHquinase_I.
[Graphical view]
PfamiPF01487. DHquinase_I. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01093. aroD. 1 hit.
PROSITEiPS01028. DEHYDROQUINASE_I. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: LT2 / SGSC1412 / ATCC 700720.
  2. "New insights into the mechanism of the Schiff base hydrolysis catalyzed by type I dehydroquinate dehydratase from S. enterica: a theoretical study."
    Yao Y., Li Z.S.
    Org. Biomol. Chem. 10:7037-7044(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACTIVE SITE.
  3. "Insights into substrate binding and catalysis in bacterial type I dehydroquinase."
    Maneiro M., Peon A., Lence E., Otero J.M., Van Raaij M.J., Thompson P., Hawkins A.R., Gonzalez-Bello C.
    Biochem. J. 462:415-424(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION.
  4. "Crystal structure of the 3-dehydroquinate dehydratase (aroD) from Salmonella typhimurium LT2 with citrate bound to the active Site."
    Minasov G., Light S.H., Shuvalova L., Papazisi L., Anderson W.F.
    Submitted (JAN-2010) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS, SUBUNIT.
    Strain: LT2 / SGSC1412 / ATCC 700720.
  5. "A conserved surface loop in type I dehydroquinate dehydratases positions an active site arginine and functions in substrate binding."
    Light S.H., Minasov G., Shuvalova L., Peterson S.N., Caffrey M., Anderson W.F., Lavie A.
    Biochemistry 50:2357-2363(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.03 ANGSTROMS) OF WILD-TYPE AND MUTANT ALA-236, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVE SITE, SUBUNIT, MUTAGENESIS OF SER-232 AND GLN-236, REACTION MECHANISM.
  6. "Insights into the mechanism of type I dehydroquinate dehydratases from structures of reaction intermediates."
    Light S.H., Minasov G., Shuvalova L., Duban M.E., Caffrey M., Anderson W.F., Lavie A.
    J. Biol. Chem. 286:3531-3539(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF WILD-TYPE AND MUTANT MET-170 IN COMPLEX WITH 3-DEHYDROQUINIC ACID, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVE SITE, SUBUNIT, MUTAGENESIS OF LYS-170, REACTION MECHANISM.
    Strain: LT2 / SGSC1412 / ATCC 700720.
  7. "Crystal structure of the 3-dehydroquinate dehydratase (aroD) from Salmonella enterica typhimurium LT2 with malonate and boric acid at the active site."
    Light S.H., Minasov G., Duban M.-E., Halavaty A.S., Krishna S.N., Shuvalova L., Kwon K., Anderson W.F.
    Submitted (MAY-2011) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS, SUBUNIT.
  8. "1.8 angstrom crystal structure of the 3-dehydroquinate dehydratase (aroD) from Salmonella typhimurium LT2 with nickel bound at active site."
    Light S.H., Minasov G., Krishna S.N., Shuvalova L., Kwon K., Lavie A., Anderson W.F.
    Submitted (AUG-2012) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG, SUBUNIT.
  9. "Reassessing the type I dehydroquinate dehydratase catalytic triad: kinetic and structural studies of Glu86 mutants."
    Light S.H., Anderson W.F., Lavie A.
    Protein Sci. 22:418-424(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) OF MUTANT ALA-86 IN COMPLEX WITH SUBSTRATE ANALOGS, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF GLU-86, ACTIVE SITE, SUBUNIT, REACTION MECHANISM.
  10. "Crystal structures of type I dehydroquinate dehydratase in complex with quinate and shikimate suggest a novel mechanism of Schiff base formation."
    Light S.H., Antanasijevic A., Krishna S.N., Caffrey M., Anderson W.F., Lavie A.
    Biochemistry 53:872-880(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) WILD-TYPE AND MUTANT MET-170 IN COMPLEX WITH SUBSTRATE ANALOGS, MUTAGENESIS OF LYS-170, SUBUNIT.

Entry informationi

Entry nameiAROD_SALTY
AccessioniPrimary (citable) accession number: P58687
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 31, 2002
Last sequence update: January 31, 2002
Last modified: February 4, 2015
This is version 93 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.