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- PDB-3jyp: Quinate dehydrogenase from Corynebacterium glutamicum in complex ... -

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Basic information

Entry
Database: PDB / ID: 3jyp
TitleQuinate dehydrogenase from Corynebacterium glutamicum in complex with quinate and NADH
ComponentsQuinate/shikimate dehydrogenase
KeywordsOXIDOREDUCTASE / quinate dehyrogenase / ternary complex / quinate / NADH / Amino-acid biosynthesis / Aromatic amino acid biosynthesis / NAD
Function / homology
Function and homology information


quinate/shikimate dehydrogenase (NAD+) / quinate 3-dehydrogenase (NAD+) activity / shikimate 3-dehydrogenase (NAD+) activity / shikimate 3-dehydrogenase (NADP+) activity / shikimate metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / NAD+ binding ...quinate/shikimate dehydrogenase (NAD+) / quinate 3-dehydrogenase (NAD+) activity / shikimate 3-dehydrogenase (NAD+) activity / shikimate 3-dehydrogenase (NADP+) activity / shikimate metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / NAD+ binding / NADP binding / cytosol
Similarity search - Function
Shikimate dehydrogenase family / SDH, C-terminal / Shikimate 5'-dehydrogenase C-terminal domain / Shikimate dehydrogenase substrate binding, N-terminal / Shikimate dehydrogenase substrate binding domain / Leucine Dehydrogenase, chain A, domain 1 / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...Shikimate dehydrogenase family / SDH, C-terminal / Shikimate 5'-dehydrogenase C-terminal domain / Shikimate dehydrogenase substrate binding, N-terminal / Shikimate dehydrogenase substrate binding domain / Leucine Dehydrogenase, chain A, domain 1 / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-QIC / Quinate/shikimate dehydrogenase (NAD(+))
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsHoeppner, A. / Schomburg, D. / Niefind, K.
CitationJournal: Biol.Chem. / Year: 2013
Title: Enzyme-substrate complexes of the quinate/shikimate dehydrogenase from Corynebacterium glutamicum enable new insights in substrate and cofactor binding, specificity, and discrimination.
Authors: Hoppner, A. / Schomburg, D. / Niefind, K.
History
DepositionSep 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 4, 2013Group: Database references
Revision 1.3Oct 23, 2013Group: Database references
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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: Quinate/shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5803
Polymers29,7251
Non-polymers8562
Water6,648369
1
A: Quinate/shikimate dehydrogenase
hetero molecules

A: Quinate/shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1606
Polymers59,4492
Non-polymers1,7114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4720 Å2
ΔGint-23 kcal/mol
Surface area22120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.82, 63.25, 35.73
Angle α, β, γ (deg.)90.00, 94.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Quinate/shikimate dehydrogenase / NAD(+)-dependent quinate dehydrogenase / QDH / CglQDH


Mass: 29724.580 Da / Num. of mol.: 1 / Fragment: QDH
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Strain: ATCC13032 / Gene: aroE, cg0504, Cgl0424 / Plasmid: pNHis / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q9X5C9, quinate/shikimate dehydrogenase (NAD+), Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-QIC / (1S,3R,4S,5R)-1,3,4,5-tetrahydroxycyclohexanecarboxylic acid / Quinic acid


Mass: 192.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H12O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 24 % PEG 6000, 400 mM calcium chloride, 100 mM Tris/HCl, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.16→30 Å / Num. all: 92402 / Num. obs: 88244 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 17.48 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 26.87
Reflection shellResolution: 1.16→1.2 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.19 / Num. unique all: 8491 / Rsym value: 0.4 / % possible all: 92.5

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3jyo

3jyo


Resolution: 1.16→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.159 1758 -random
Rwork0.13796 ---
all0.13838 92402 --
obs0.13838 88244 95.5 %-
Displacement parametersBiso mean: 17.48 Å2
Refinement stepCycle: LAST / Resolution: 1.16→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2075 0 57 369 2501
LS refinement shell
Resolution (Å)Rfactor RfreeRefine-IDNum. reflection obs% reflection obs (%)
1.16-1.20.4X-RAY DIFFRACTION849192.5
1.2-1.250.3X-RAY DIFFRACTION856593.2
1.25-1.310.236X-RAY DIFFRACTION866893.8
1.31-1.380.183X-RAY DIFFRACTION866194.2
1.38-1.460.163X-RAY DIFFRACTION876995.3
1.46-1.570.136X-RAY DIFFRACTION885996
1.57-1.730.102X-RAY DIFFRACTION893596.6
1.73-1.980.081X-RAY DIFFRACTION895796.8
1.98-2.50.071X-RAY DIFFRACTION909998.3
2.5-300.077X-RAY DIFFRACTION924098.5

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