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- PDB-1wzi: Structural basis for alteration of cofactor specificity of Malate... -

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Basic information

Entry
Database: PDB / ID: 1wzi
TitleStructural basis for alteration of cofactor specificity of Malate dehydrogenase from Thermus flavus
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / Seven amino acid residues mutant / protein-NADPH complex
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / oxaloacetate metabolic process / NADH metabolic process / tricarboxylic acid cycle
Similarity search - Function
Malate dehydrogenase, type 2 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain ...Malate dehydrogenase, type 2 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Malate dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTomita, T. / Fushinobu, S. / Kuzuyama, T. / Nishiyama, M.
Citation
Journal: to be published
Title: Structural basis for alteration of cofactor specificity of malate dehydrogenase from Thermus flavus
Authors: Tomita, T. / Fushinobu, S. / Kuzuyama, T. / Nishiyama, M.
#1: Journal: Biochemistry / Year: 1993
Title: Determinants of protein thermostability observed in the 1.9 Angstroms crystal structure of malate dehydrogenase from the thermophilic bacterium Thermus flavus
Authors: Kelly, C.A. / Nishiyama, M. / Ohnishi, Y. / Beppu, T. / Birktoft, J.J.
#2: Journal: J.Mol.Biol. / Year: 1991
Title: Preliminary X-ray diffraction analysis of a crystallizable mutant of malate dehydrogenase from the thermophile Thermus flavus
Authors: Kelly, C.A. / Sarfaty, S. / Nishiyama, M. / Beppu, T. / Birktoft, J.J.
#3: Journal: Biochemistry / Year: 1989
Title: Refined crystal structure of cytoplasmic malate dehydrogenase at 2.5-A resolution
Authors: Birktoft, J.J. / Rhodes, G. / Banaszak, L.J.
#4: Journal: J.Biol.Chem. / Year: 1986
Title: Nucleotide sequence of the malate dehydrogenase gene of Thermus flavus and its mutation directing an increase in enzyme activity
Authors: Nishiyama, M. / Matsubara, N. / Yamamoto, K. / Iijima, S. / Uozumi, T. / Beppu, T.
#5: Journal: J.Biol.Chem. / Year: 1983
Title: The presence of a histidine-aspartic acid pair in the active site of 2-hydroxyacid dehydrogenases. X-ray refinement of cytoplasmic malate dehydrogenase
Authors: Birktoft, J.J. / Banaszak, L.J.
#6: Journal: Enzyme / Year: 1975
Title: Malate Dehydrogenases
Authors: Banaszak, L.J. / Bradshaw, R.A.
History
DepositionMar 5, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Category: struct_conf / struct_conf_type
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Malate dehydrogenase
B: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4124
Polymers70,9212
Non-polymers1,4912
Water11,241624
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-23 kcal/mol
Surface area25260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.310, 85.390, 117.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe second part of the biological assembly is generated by the two fold axis: -x+1, y, -z.

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Components

#1: Protein Malate dehydrogenase


Mass: 35460.637 Da / Num. of mol.: 2 / Mutation: E41G, I42S, P43E, Q44R, A45S, M46F, K47Q
Source method: isolated from a genetically manipulated source
Details: Malate dehydrogenase mutant EX7 / Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: AT-62 / Gene: mdh / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P10584, malate dehydrogenase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 624 / 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: 2.5 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, dithiothreitol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 24, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→28.89 Å / Num. all: 48624 / Num. obs: 48624 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 8.6 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05
Reflection shellResolution: 2→2.13 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BMD

1bmd


Resolution: 2→28.89 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2286096.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2407 5 %RANDOM
Rwork0.196 ---
obs0.196 48460 99.6 %-
all-48624 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.7329 Å2 / ksol: 0.350692 e/Å3
Displacement parametersBiso mean: 18.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2--0.73 Å20 Å2
3----0.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 2→28.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4980 0 78 624 5682
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d1.06
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it3.242
X-RAY DIFFRACTIONc_scangle_it4.42.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.237 390 4.9 %
Rwork0.193 7615 -
obs-7615 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2NADPHMODIFIED.PARAM
X-RAY DIFFRACTION3WATER.PARAM
X-RAY DIFFRACTION4CIS_PEPTIDE16.PARAM

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