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Protein

3-dehydroquinate dehydratase

Gene

aroD

Organism
Salmonella typhi
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 Lys-170 at the active site.UniRule annotation1 Publication

Catalytic activityi

3-dehydroquinate = 3-dehydroshikimate + H2O.UniRule annotation1 Publication

Enzyme regulationi

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

Kineticsi

Kcat is 1.1 sec(-1) for dehydratase activity with 3-dehydroquinate (at pH 7.2 and 25 degrees Celsius).1 Publication

  1. KM=24 µM for 3-dehydroquinate (at pH 7.2 and 25 degrees Celsius).1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei21 – 2113-dehydroquinateUniRule annotation2 Publications
Binding sitei82 – 8213-dehydroquinateUniRule annotation1 Publication
Active sitei143 – 1431Proton donor/acceptorUniRule annotation1 Publication
Active sitei170 – 1701Schiff-base intermediate with substrateUniRule annotation2 Publications
Binding sitei213 – 21313-dehydroquinateUniRule annotation3 Publications
Binding sitei232 – 23213-dehydroquinateUniRule annotation2 Publications
Binding sitei236 – 23613-dehydroquinateUniRule annotation3 Publications

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

SABIO-RKP24670.
UniPathwayiUPA00053; UER00086.

Names & Taxonomyi

Protein namesi
Recommended name:
3-dehydroquinate dehydratase1 PublicationUniRule annotation (EC:4.2.1.10UniRule annotation1 Publication)
Short name:
3-dehydroquinase1 PublicationUniRule annotation
Alternative name(s):
Type I DHQaseUniRule annotation
Type I dehydroquinase1 PublicationUniRule annotation
Short name:
DHQ11 PublicationUniRule annotation
Gene namesi
Name:aroD1 PublicationUniRule annotation
Ordered Locus Names:STY1760, t1231
OrganismiSalmonella typhi
Taxonomic identifieri90370 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
ProteomesiUP000002670 Componenti: Chromosome UP000000541 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 2522523-dehydroquinate dehydratasePRO_0000138805Add
BLAST

Interactioni

Subunit structurei

Dimer of dimers.UniRule annotation3 Publications

Protein-protein interaction databases

STRINGi220341.STY1760.

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 – 10613Combined 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
Helixi206 – 2149Combined sources
Helixi216 – 2194Combined sources
Beta strandi223 – 2253Combined sources
Beta strandi227 – 2304Combined sources
Helixi239 – 25113Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1GQNX-ray1.78A1-252[»]
1L9WX-ray2.10A/B/C/D1-252[»]
1QFEX-ray2.10A/B1-252[»]
4CLMX-ray1.40A/B1-252[»]
4CNOX-ray1.50A/B/C/D1-252[»]
ProteinModelPortaliP24670.
SMRiP24670. Positions 1-252.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP24670.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni46 – 4833-dehydroquinate bindingUniRule annotation3 Publications

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0710.
HOGENOMiHOG000105514.
KOiK03785.
OMAiLFTFRSK.
OrthoDBiEOG6P33BK.

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.

P24670-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKTVTVKNLI IGEGMPKIIV SLMGRDINSV KAEALAYREA TFDILEWRVD
60 70 80 90 100
HFMDIASTQS VLTAARVIRD AMPDIPLLFT FRSAKEGGEQ TITTQHYLTL
110 120 130 140 150
NRAAIDSGLV DMIDLELFTG DADVKATVDY AHAHNVYVVM SNHDFHQTPS
160 170 180 190 200
AEEMVLRLRK MQALGADIPK IAVMPQSKHD VLTLLTATLE MQQHYADRPV
210 220 230 240 250
ITMSMAKEGV ISRLAGEVFG SAATFGAVKQ ASAPGQIAVN DLRSVLMILH

NA
Length:252
Mass (Da):27,649
Last modified:December 5, 2001 - v2
Checksum:iF9D4D4C86D18F17B
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti156 – 1561L → S in CAA38418 (PubMed:2045778).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X54546 Genomic DNA. Translation: CAA38418.1.
AL513382 Genomic DNA. Translation: CAD02002.1.
AE014613 Genomic DNA. Translation: AAO68886.1.
PIRiS15652.
RefSeqiNP_456161.1. NC_003198.1.
NP_805037.1. NC_004631.1.

Genome annotation databases

EnsemblBacteriaiAAO68886; AAO68886; t1231.
CAD02002; CAD02002; CAD02002.
GeneIDi1248131.
KEGGisty:STY1760.
PATRICi18541418. VBISalEnt120419_1771.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X54546 Genomic DNA. Translation: CAA38418.1.
AL513382 Genomic DNA. Translation: CAD02002.1.
AE014613 Genomic DNA. Translation: AAO68886.1.
PIRiS15652.
RefSeqiNP_456161.1. NC_003198.1.
NP_805037.1. NC_004631.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1GQNX-ray1.78A1-252[»]
1L9WX-ray2.10A/B/C/D1-252[»]
1QFEX-ray2.10A/B1-252[»]
4CLMX-ray1.40A/B1-252[»]
4CNOX-ray1.50A/B/C/D1-252[»]
ProteinModelPortaliP24670.
SMRiP24670. Positions 1-252.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi220341.STY1760.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAO68886; AAO68886; t1231.
CAD02002; CAD02002; CAD02002.
GeneIDi1248131.
KEGGisty:STY1760.
PATRICi18541418. VBISalEnt120419_1771.

Phylogenomic databases

eggNOGiCOG0710.
HOGENOMiHOG000105514.
KOiK03785.
OMAiLFTFRSK.
OrthoDBiEOG6P33BK.

Enzyme and pathway databases

UniPathwayiUPA00053; UER00086.
SABIO-RKP24670.

Miscellaneous databases

EvolutionaryTraceiP24670.

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. "Molecular cloning and characterization of the aroD gene encoding 3-dehydroquinase from Salmonella typhi."
    Servos S., Chatfield S., Hone D., Levine M., Dimitriadis G., Pickard D., Dougan G., Fairweather N., Charles I.G.
    J. Gen. Microbiol. 137:147-152(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 700931 / Ty2.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: CT18.
  3. "Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18."
    Deng W., Liou S.-R., Plunkett G. III, Mayhew G.F., Rose D.J., Burland V., Kodoyianni V., Schwartz D.C., Blattner F.R.
    J. Bacteriol. 185:2330-2337(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700931 / Ty2.
  4. "The two types of 3-dehydroquinase have distinct structures but catalyze the same overall reaction."
    Gourley D.G., Shrive A.K., Polikarpov I., Krell T., Coggins J.R., Hawkins A.R., Isaacs N.W., Sawyer L.
    Nat. Struct. Biol. 6:521-525(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEX WITH 3-DEHYDROQUINATE, SUBUNIT, ACTIVE SITE.
  5. "Comparison of different crystal forms of 3-dehydroquinase from Salmonella typhi and its implication for the enzyme activity."
    Lee W.H., Perles L.A., Nagem R.A., Shrive A.K., Hawkins A., Sawyer L., Polikarpov I.
    Acta Crystallogr. D 58:798-804(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.78 ANGSTROMS) IN COMPLEX WITH 3-DEHYDROSHIKIMATE, ACTIVE SITE, SUBUNIT.
  6. "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: X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, SUBUNIT.

Entry informationi

Entry nameiAROD_SALTI
AccessioniPrimary (citable) accession number: P24670
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 1, 1992
Last sequence update: December 5, 2001
Last modified: February 4, 2015
This is version 117 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete 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.