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Basic information

Entry
Database: PDB / ID: 1j4a
TitleINSIGHTS INTO DOMAIN CLOSURE, SUBSTRATE SPECIFICITY AND CATALYSIS OF D-LACTATE DEHYDROGENASE FROM LACTOBACILLUS BULGARICUS
ComponentsD-LACTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / NAD-DEPENDENT DEHYDROGENASE / REVERSIBLE INTERCONVERSION OF PYRUVATE INTO D-LACTATE
Function / homology
Function and homology information


D-lactate dehydrogenase / D-lactate dehydrogenase (NAD+) activity / lactate metabolic process / 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
D-lactate dehydrogenase
Similarity search - Component
Biological speciesLactobacillus delbrueckii subsp. bulgaricus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRazeto, A. / Kochhar, S. / Hottinger, H. / Dauter, M. / Wilson, K.S. / Lamzin, V.S.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Domain closure, substrate specificity and catalysis of D-lactate dehydrogenase from Lactobacillus bulgaricus.
Authors: Razeto, A. / Kochhar, S. / Hottinger, H. / Dauter, M. / Wilson, K.S. / Lamzin, V.S.
#1: Journal: Thesis / Year: 1999
Title: Lysine Replacing Histidine in the Acid-Base Catalysis of D-Lactate Dehydrogenase: Structural Investigation on Enzymatic Stereoselectivity.
Authors: Razeto, A.
History
DepositionAug 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-LACTATE DEHYDROGENASE
B: D-LACTATE DEHYDROGENASE
C: D-LACTATE DEHYDROGENASE
D: D-LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,50515
Polymers148,4494
Non-polymers1,05711
Water16,214900
1
A: D-LACTATE DEHYDROGENASE
B: D-LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,99310
Polymers74,2242
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-150 kcal/mol
Surface area26940 Å2
MethodPISA
2
C: D-LACTATE DEHYDROGENASE
D: D-LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5135
Polymers74,2242
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-65 kcal/mol
Surface area27380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.300, 188.000, 193.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.894, -0.096, 0.437), (-0.082, -0.925, -0.372), (0.44, -0.368, 0.819)-21.43531, 168.97028, 39.45271
2given(0.676, -0.557, -0.482), (-0.553, -0.816, 0.167), (-0.487, 0.154, -0.86)100.49666, 226.2424, 88.51561

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Components

#1: Protein
D-LACTATE DEHYDROGENASE / D-LDH


Mass: 37112.160 Da / Num. of mol.: 4 / Mutation: H297K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus delbrueckii subsp. bulgaricus (bacteria)
Species: Lactobacillus delbrueckii / Strain: N42 / Cellular location: CYTOPLASM / Gene: LDHD / Plasmid: PMD19 / Cellular location (production host): CYTOPLASM / Gene (production host): LDHD / Production host: Escherichia coli (E. coli) / Strain (production host): SURE / References: UniProt: P26297, D-lactate dehydrogenase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 900 / 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: 2.91 Å3/Da / Density % sol: 57.4 %
Crystal growpH: 6.5
Details: Orthorhombic crystals were grown by vapour diffusion from solutions of 20 % PEG 6K, 0.2 M ammonium sulphate in 0.1 M cacodylate buffer pH 6.5.
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %PEG60001reservoir
20.2 Mammonium sulfate1reservoir
30.1 Msodium cacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.906
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1998 / Details: MIRRORS
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.906 Å / Relative weight: 1
ReflectionResolution: 1.9→19 Å / Num. obs: 132348 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 0.215 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 16.1
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 2.2 / % possible all: 92.4
Reflection
*PLUS
Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 92.4 % / Rmerge(I) obs: 0.327

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODEL OF NATIVE D-LDH WHICH IS CURRENTLY BEING DEPOSITED IN THE PDB

Resolution: 1.9→19 Å / SU B: 2.44 / Cross valid method: THROUGHOUT APART FROM THE LAST 3 CYCLES / σ(F): 0 / ESU R Free: 0.15
Details: THE DENSITY OF THE CATALYTIC DOMAIN OF SUBUNIT C IS VERY POOR: 49 RESIDUES WERE ASSIGNED ZERO OCCUPANCY. IN ALL SUBUNITS THERE IS NO DENSITY FOR THE METHIONINE AT THE N-TERMINUS AND IN ...Details: THE DENSITY OF THE CATALYTIC DOMAIN OF SUBUNIT C IS VERY POOR: 49 RESIDUES WERE ASSIGNED ZERO OCCUPANCY. IN ALL SUBUNITS THERE IS NO DENSITY FOR THE METHIONINE AT THE N-TERMINUS AND IN SUBUNITS A,B,C FOR GLY-333 AT THE C-TERMINUS.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 6647 5 %RANDOM
Rwork0.204 ---
obs0.204 132346 98.4 %-
Displacement parametersBiso mean: 0.327 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10473 0 55 900 11428
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0350.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.92
X-RAY DIFFRACTIONp_mcangle_it2.53
X-RAY DIFFRACTIONp_scbond_it2.52
X-RAY DIFFRACTIONp_scangle_it3.23
X-RAY DIFFRACTIONp_plane_restr0.0230.02
X-RAY DIFFRACTIONp_chiral_restr0.130.15
X-RAY DIFFRACTIONp_singtor_nbd0.190.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1970.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.1970.3
X-RAY DIFFRACTIONp_planar_tor3.97
X-RAY DIFFRACTIONp_staggered_tor1515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor36.120
X-RAY DIFFRACTIONp_special_tor015
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.204 / Rfactor Rfree: 0.259 / Rfactor Rwork: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS

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