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- PDB-1dxy: STRUCTURE OF D-2-HYDROXYISOCAPROATE DEHYDROGENASE -

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Basic information

Entry
Database: PDB / ID: 1dxy
TitleSTRUCTURE OF D-2-HYDROXYISOCAPROATE DEHYDROGENASE
ComponentsD-2-HYDROXYISOCAPROATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / D-2-HYDROXYCARBOXYLATE DEHYDROGENASE / D-LACTATE DEHYDROGENASE
Function / homology
Function and homology information


D-2-hydroxyacid dehydrogenase (NAD+) / phenyllactate dehydrogenase (NAD+) activity / D-lactate dehydrogenase (NAD+) activity / NAD binding
Similarity search - Function
D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain ...D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-OXO-4-METHYLPENTANOIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / D-2-hydroxyacid dehydrogenase (NAD+)
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsDengler, U. / Niefind, K. / Kiess, M. / Schomburg, D.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Crystal structure of a ternary complex of D-2-hydroxyisocaproate dehydrogenase from Lactobacillus casei, NAD+ and 2-oxoisocaproate at 1.9 A resolution.
Authors: Dengler, U. / Niefind, K. / Kiess, M. / Schomburg, D.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary Characterization of Crystals of D-2-Hydroxyisocaproate Dehydrogenase from Lactobacillus Casei
Authors: Niefind, K. / Hecht, H.J. / Schomburg, D.
#2: Journal: Thesis / Year: 1993
Title: Roentgenkristallographische Untersuchungen an Drei Mikrobiellen Enzymen: D-2-Hydroxyisocaproat-Dehydrogenase Aus Lactobacillus Casei L-2-Hydroxyisocaproat-Dehydrogenase Aus Lactobacillus ...Title: Roentgenkristallographische Untersuchungen an Drei Mikrobiellen Enzymen: D-2-Hydroxyisocaproat-Dehydrogenase Aus Lactobacillus Casei L-2-Hydroxyisocaproat-Dehydrogenase Aus Lactobacillus Confusus Alkalische Protease Aus Bacillus Alcalophilus/Variante Q59R
Authors: Niefind, K.
#3: Journal: ENZYME.MICROB.TECHNOL. / Year: 1992
Title: Potential of R-2-Hydroxyisocaproate Dehydrogenase from Lactobacillus Casei for Stereospecific Reductions
Authors: Kallwass, H.K.W.
#4: Journal: Gene / Year: 1989
Title: Cloning, Sequencing and Expression in Escherichia Coli of the D-2-Hydroxyisocaproate Dehydrogenase Gene of Lactobacillus Casei
Authors: Lerch, H.P. / Blocker, H. / Kallwass, H. / Hoppe, J. / Tsai, H. / Collins, J.
#5: Journal: Fems Microbiol.Lett. / Year: 1987
Title: Crystallization and Molecular Properties of D-2-Hydroxyisocaproate Dehydrogenase from Lactobacillus Casei
Authors: Kallwass, H. / Tsai, H. / Schuette, H.
#6: Journal: Appl.Microbiol.Biotechnol. / Year: 1985
Title: D-2-Hydroxyisocaproate Dehydrogenase from Lactobacillus Casei. A New Enzyme Suitable for Stereospecific Reduction of 2-Ketocarboxylic Acids
Authors: Hummel, W. / Schuette, H. / Kula, M.R.
History
DepositionAug 13, 1996Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Mar 15, 2017Group: Derived calculations
Revision 1.5Aug 9, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name
Revision 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-2-HYDROXYISOCAPROATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9165
Polymers36,9301
Non-polymers9864
Water3,279182
1
A: D-2-HYDROXYISOCAPROATE DEHYDROGENASE
hetero molecules

A: D-2-HYDROXYISOCAPROATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,83110
Polymers73,8602
Non-polymers1,9718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/21
Buried area8770 Å2
ΔGint-103 kcal/mol
Surface area26670 Å2
MethodPISA
2
A: D-2-HYDROXYISOCAPROATE DEHYDROGENASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)227,49330
Polymers221,5796
Non-polymers5,91424
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/21
crystal symmetry operation11_654-x+y+1,y,-z-1/21
crystal symmetry operation12_554x,x-y,-z-1/21
Buried area34670 Å2
ΔGint-342 kcal/mol
Surface area71660 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)134.100, 134.100, 125.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-543-

HOH

21A-545-

HOH

DetailsD-HICDH IS A DIMER OF IDENTICAL SUBUNITS, WHICH OCCUPIES A SPECIAL POSITION IN THE INVESTIGATED CRYSTALS.

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Components

#1: Protein D-2-HYDROXYISOCAPROATE DEHYDROGENASE / D-HICDH / R-HICDH / R-2-HYDROXYISOCAPROATE DEHYDROGENASE


Mass: 36929.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Gene: POTENTIAL / Variant: SSP. PSEUDOPLANTARUM / Plasmid: PJLA601 / Production host: Escherichia coli (E. coli)
References: UniProt: P17584, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-COI / 2-OXO-4-METHYLPENTANOIC ACID / alpha-ketoisocaproic acid


Mass: 130.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details2-OXOISOCAPROATE (OIC 337) AND A SULFATE ION (SO4 338) ARE MUTUALLY EXCLUSIVELY BOUND IN THE ACTIVE ...2-OXOISOCAPROATE (OIC 337) AND A SULFATE ION (SO4 338) ARE MUTUALLY EXCLUSIVELY BOUND IN THE ACTIVE SITE. THE OCCUPANCY FACTORS OF BOTH LIGANDS WERE SET TO 0.5, WHILE DIFFERENCES IN OCCUPATION WERE SIMULATED BY TEMPERATURE FACTOR REFINEMENT.
Sequence detailsA CONTACT IS OBSERVED BETWEEN THE SIDE CHAINS OF ASP 266 AND ASP 278. CHEMICAL PROTEIN SEQUENCING ...A CONTACT IS OBSERVED BETWEEN THE SIDE CHAINS OF ASP 266 AND ASP 278. CHEMICAL PROTEIN SEQUENCING CONFIRMED THESE RESIDUES TO BE ASPARTATES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 4.4 Å3/Da / Density % sol: 72 %
Crystal growTemperature: 277 K / pH: 7
Details: 1.9 M AMMONIUM SULFATE, 50 MM CITRATE/PHOSPHATE BUFFER, 30 MM NAD+, 60 MM 4-METHYL-2-OXOPENTANOATE, PH 7.0, 277 K; ENZYME CONCENTRATION 10 MG/ML.
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Niefind, K., (1994) J.Mol.Biol., 240, 400.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.8 Mammonium salfate1reservoir
250 mMpotassium phosphate1reservoir
30.9 Mammonium salfate1drop
425 mMpotassium phosphate1drop
55 mg/mlprotain1drop
625 mMpotassium phosphate1drop
70.5 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.1
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 1, 1994 / Details: MIRROR OPTICS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.86→12.1 Å / Num. obs: 53838 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rsym value: 0.089 / Net I/σ(I): 22.2
Reflection shellResolution: 1.86→2 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.48 / % possible all: 86.9
Reflection
*PLUS
Num. measured all: 314570 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
% possible obs: 86.9 % / Rmerge(I) obs: 0.48

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BACKBONE AND C-BETA ATOMS OF D-GLYCERATE DEHYDROGENASE (PDB ENTRY 1GDH)

1gdh


Resolution: 1.86→12.1 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.217 -5 %
Rwork0.196 --
obs0.196 53838 96.5 %
Displacement parametersBiso mean: 31.02 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å / Luzzati sigma a obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 1.86→12.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 63 182 2825
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.73
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.12
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.25
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.12
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.25

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