1DQS Lyase date Apr 09, 1998
title Crystal Structure Of Dehydroquinate Synthase (Dhqs) Complexed With Carbaphosphonate, Nad+ And Zn2+
authors E.P.Carpenter, A.R.Hawkins, J.W.Frost, K.A.Brown
compound source
Molecule: 3-Dehydroquinate Synthase
Chain: A, B
Fragment: N-Terminal Domain Of The Pentafunctional Arom Protein;
Synonym: Dhqs, 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Phosphate-Lyase (Cyclizing);
Ec: 4.6.1.3
Engineered: Yes
Biological_unit: Dimer
Other_details: Dhqs Is A Dimer, With One Nad+, One Zn2+ And One Substrate Analogue Inhibitor ( Carbaphosphonate, Crb) Bound Per Monomer
Organism_scientific: Emericella Nidulans (Aspergillus Nidulans);
Organism_common: Aspergillus
Strain: R153
Cellular_location: Cytoplasm
Gene: Part Of Aroma
Expression_system: Escherichia Coli
Expression_system_strain: Glw38 (Arob-) From The Glasgow Culture Collection;
Expression_system_cellular_location: Cytoplasm
Expression_system_vector_type: Plasmid
Expression_system_vector: Ptrc99a
Expression_system_plasmid: Ptr51
Expression_system_gene: Part Of Aroma
symmetry Space Group: P 21 21 21
R_factor 0.174
crystal
cell
length a length b length c angle alpha angle beta angle gamma
67.677 80.810 143.513 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand CL, CRB, NAD, ZN enzyme Lyase E.C.4.2.3.4 BRENDA
similarity In the n-terminal section; belongs to the dehydroquinate synthase family. In the 3rd section; belongs to the shikimate kinase family. In the 2nd section; belongs to the epsp synthase family. In the c-terminal section; belongs to the shikimate dehydrogenase family.[DHQ_synthase]
catalytic activ. Phosphoenolpyruvate + 3-phosphoshikimate = phosphate + 5-o-(1-carboxyvinyl)-3-phosphoshikimate. 3-deoxy-arabino-heptulonate 7-phosphate = 3- dehydroquinate + phosphate. Atp + shikimate = adp + shikimate 3-phosphate. 3-dehydroquinate = 3-dehydroshikimate + h(2)o. Shikimate + nadp(+) = 3-dehydroshikimate + nadph.
pathway Context. Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from d-erythrose 4-phosphate and pep: step 2. Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from d-erythrose 4-phosphate and pep: step 3. Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from d-erythrose 4-phosphate and pep: step 4. Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from d-erythrose 4-phosphate and pep: step 5. Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from d-erythrose 4-phosphate and pep: step 6.
subcellular loc. Cytoplasm.
gene aroMA (E. nidulans)
function The arom polypeptide catalyzes 5 consecutive enzymatic reactions in prechorismate polyaromatic amino acid biosynthesis.
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • nucleotide binding
  • catalytic activity
  • 3-dehydroquinate dehydratase...
  • 3-dehydroquinate synthase ac...
  • 3-phosphoshikimate 1-carboxy...
  • shikimate 5-dehydrogenase ac...
  • shikimate kinase activity
  • ATP binding
  • kinase activity
  • oxidoreductase activity
  • transferase activity
  • lyase activity
  • amino acid biosynthetic proc...
  • aromatic amino acid family b...
  • aromatic amino acid family b...
  • cytoplasm
  • Primary referenceStructure of dehydroquinate synthase reveals an active site capable of multistep catalysis., Carpenter EP, Hawkins AR, Frost JW, Brown KA, Nature 1998 Jul 16;394(6690):299-302. PMID:9685163
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (150 Kb) [Save to disk]
  • Biological Unit Coordinates (1dqs.pdb1.gz) 132 Kb
  • CSU: Contacts of Structural Units for 1DQS
  • Likely Quarternary Molecular Structure file(s) for 1DQS
  • Retrieve 1DQS in mmCIF format [Save to disk]
  • View 1DQS in 3D
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • On AstexViewer, from MSD-EBI (viewer documentation).
  • On RasMol (Install RasMol freeware) Here's help on how to use RasMol.
  • Visual 3D analysis of 1DQS
  • Protein Explorer, Easier to use and more powerful than RasMol. (Win and Mac only)
  • Noncovalent Bond Finder displays the closest contacts to ligand or interface, reports distances, walks over water bridges.
  • STING, shows the sequence and maps the locations of sequence residues or residue ranges onto the 3D structure.
  • GRASS (Graphical Representation and Analysis of Structure Server)
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1DQS, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dqsa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1dqsb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1dqs from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1dqs_A] [1dqs_B]
  • Other resources with information on 1DQS
  • InterPro: IPR006151 , IPR010110 , IPR002658 , IPR000623 , IPR001986 , IPR006264 , IPR008289 , IPR001381
  • PDBREPORT (protein verification by WHAT_CHECK procedures)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2006
    Bioinformatics and Biological Computing
    Weizmann Institute of Science