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- PDB-1dqs: CRYSTAL STRUCTURE OF DEHYDROQUINATE SYNTHASE (DHQS) COMPLEXED WIT... -

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Basic information

Entry
Database: PDB / ID: 1dqs
TitleCRYSTAL STRUCTURE OF DEHYDROQUINATE SYNTHASE (DHQS) COMPLEXED WITH CARBAPHOSPHONATE, NAD+ AND ZN2+
ComponentsPROTEIN (3-DEHYDROQUINATE SYNTHASE)
KeywordsLYASE / SHIKIMATE PATHWAY ENZYME / MULTI-STEP ENZYME / OXIDOREDUCTASE / PHOSPHATE ELIMINATION / INTRA MOLECULAR ALDOL CONDENSATION / NAD+ BINDING / ZN2+ BINDING / CYCLASE / AROMATIC AMINO ACID BIOSYNTHESIS
Function / homology
Function and homology information


3-dehydroquinate synthase / 3-dehydroquinate synthase activity / shikimate kinase / shikimate kinase activity / shikimate dehydrogenase (NADP+) / shikimate 3-dehydrogenase (NADP+) activity / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity ...3-dehydroquinate synthase / 3-dehydroquinate synthase activity / shikimate kinase / shikimate kinase activity / shikimate dehydrogenase (NADP+) / shikimate 3-dehydrogenase (NADP+) activity / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Pentafunctional AroM protein / Shikimate dehydrogenase, AroM-type / : / 3-dehydroquinate synthase C-terminal / 3-dehydroquinate synthase AroB / 3-dehydroquinate synthase domain / 3-dehydroquinate synthase N-terminal / 3-dehydroquinate dehydratase, active site / Dehydroquinase class I active site. / Shikimate kinase, conserved site ...Pentafunctional AroM protein / Shikimate dehydrogenase, AroM-type / : / 3-dehydroquinate synthase C-terminal / 3-dehydroquinate synthase AroB / 3-dehydroquinate synthase domain / 3-dehydroquinate synthase N-terminal / 3-dehydroquinate dehydratase, active site / Dehydroquinase class I active site. / Shikimate kinase, conserved site / Shikimate kinase signature. / SDH, C-terminal / Shikimate 5'-dehydrogenase C-terminal domain / Shikimate kinase/Threonine synthase-like 1 / Shikimate kinase/gluconokinase / Shikimate kinase / 3-dehydroquinate dehydratase type I / Type I 3-dehydroquinase / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Shikimate dehydrogenase substrate binding, N-terminal / Shikimate dehydrogenase substrate binding domain / EPSP synthase signature 1. / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase, conserved site / EPSP synthase signature 2. / Rossmann fold - #1970 / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Aminoacid dehydrogenase-like, N-terminal domain superfamily / Aldolase-type TIM barrel / NAD(P)-binding domain superfamily / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-CRB / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Pentafunctional AROM polypeptide
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å
AuthorsCarpenter, E.P. / Hawkins, A.R. / Frost, J.W. / Brown, K.A.
Citation
Journal: Nature / Year: 1998
Title: Structure of dehydroquinate synthase reveals an active site capable of multistep catalysis.
Authors: Carpenter, E.P. / Hawkins, A.R. / Frost, J.W. / Brown, K.A.
#1: Journal: J.Am.Chem.Soc. / Year: 1998
Title: Reactivation of 3-Dehydroquinate Synthase by Lanthanide Cations
Authors: Moore, J.D. / Skinner, M.A. / Swatman, D.R. / Hawkins, A.R. / Brown, K.A.
#2: Journal: J.Am.Chem.Soc. / Year: 1997
Title: Cyclohexenyl and Cyclohexylidene Inhibitors of 3-Dehydroquinate Synthase: Active Site Interactions Relevant to Enzyme Mechanism and Inhibitor Design
Authors: Montchamp, J.L. / Frost, J.W.
#3: Journal: Biochem.J. / Year: 1994
Title: Efficient Independent Activity of a Monomeric, Monofunctional Dehydroquinate Synthase Derived from the N-Terminus of the Pentafunctional Arom Protein of Aspergillus Nidulans
Authors: Moore, J.D. / Coggins, J.R. / Virden, R. / Hawkins, A.R.
#4: Journal: J.Gen.Microbiol. / Year: 1993
Title: The Pre-Chorismate (Shikimate) and Quinate Pathways in Filamentous Fungi: Theoretical and Practical Aspects
Authors: Hawkins, A.R. / Lamb, H.K. / Moore, J.D. / Charles, I.G. / Roberts, C.F.
#5: Journal: Biochem.J. / Year: 1992
Title: Overproduction in Escherichia Coli of the Dehydroquinate Synthase Domain of the Aspergillus Nidulans Pentafunctional Arom Protein
Authors: Van Den Hombergh, J.P. / Moore, J.D. / Charles, I.G. / Hawkins, A.R.
#6: Journal: Biochemistry / Year: 1989
Title: Dehydroquinate Synthase: The Use of Substrate Analogues to Probe the Early Steps of the Catalyzed Reaction
Authors: Bender, S.L. / Widlanski, T. / Knowles, J.R.
#7: Journal: J.Biol.Chem. / Year: 1963
Title: The Enzymatic Conversion of 3-Deoxy-D-Arabino-Heptulosinic Acid 7-Phosphate to 5-Dehydroquinate
Authors: Srinivasen, P.R. / Rothchild, J. / Sprinson, D.B.
History
DepositionApr 9, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 26, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (3-DEHYDROQUINATE SYNTHASE)
B: PROTEIN (3-DEHYDROQUINATE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9679
Polymers85,9332
Non-polymers2,0337
Water12,935718
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-109 kcal/mol
Surface area26140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.677, 80.810, 143.513
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PROTEIN (3-DEHYDROQUINATE SYNTHASE) / DHQS / 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE PHOSPHATE-LYASE (CYCLIZING)


Mass: 42966.535 Da / Num. of mol.: 2
Fragment: N-TERMINAL DOMAIN OF THE PENTAFUNCTIONAL AROM PROTEIN
Source method: isolated from a genetically manipulated source
Details: DHQS IS A DIMER, WITH ONE NAD+, ONE ZN2+ AND ONE SUBSTRATE ANALOGUE INHIBITOR (CARBAPHOSPHONATE, CRB) BOUND PER MONOMER
Source: (gene. exp.) Emericella nidulans (mold) / Strain: R153 / Cellular location: CYTOPLASM / Gene: PART OF AROMA / Plasmid: PTR51 / Cellular location (production host): CYTOPLASM / Gene (production host): PART OF AROMA / Production host: Escherichia coli (E. coli)
Strain (production host): GLW38 (AROB-) FROM THE GLASGOW CULTURE COLLECTION
References: UniProt: P07547, EC: 4.6.1.3

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Non-polymers , 5 types, 725 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical ChemComp-CRB / [1R-(1ALPHA,3BETA,4ALPHA,5BETA)]-5-(PHOSPHONOMETHYL)-1,3,4-TRIHYDROXYCYCLOHEXANE-1-CARBOXYLIC ACID / CARBAPHOSPHONATE


Mass: 270.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15O8P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 718 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 32 %
Crystal growpH: 6.8 / Details: pH 6.8
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. obs: 79632 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 19.22 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 15.1
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 3.3 / % possible all: 84.8
Reflection
*PLUS
Num. measured all: 297189
Reflection shell
*PLUS
% possible obs: 84.8 %

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Processing

Software
NameClassification
HASSPmodel building
MLPHAREphasing
DMMultimodel building
ENVATmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
HASSPphasing
DMMultiphasing
ENVATphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→25 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.224 3385 5 %RANDOM
Rwork0.1735 ---
obs-64534 91.2 %-
Displacement parametersBiso mean: 20.58 Å2
Refine analyzeLuzzati coordinate error obs: 0.249 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5696 0 125 718 6539
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0290.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0320.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.3012
X-RAY DIFFRACTIONp_mcangle_it1.7633
X-RAY DIFFRACTIONp_scbond_it1.6172
X-RAY DIFFRACTIONp_scangle_it2.283
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1190.15
X-RAY DIFFRACTIONp_singtor_nbd0.1750.3
X-RAY DIFFRACTIONp_multtor_nbd0.180.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor47
X-RAY DIFFRACTIONp_staggered_tor15.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor24.720
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS

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