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- PDB-1ldn: STRUCTURE OF A TERNARY COMPLEX OF AN ALLOSTERIC LACTATE DEHYDROGE... -

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Basic information

Entry
Database: PDB / ID: 1ldn
TitleSTRUCTURE OF A TERNARY COMPLEX OF AN ALLOSTERIC LACTATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILUS AT 2.5 ANGSTROMS RESOLUTION
ComponentsL-LACTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE(CHOH(D)-NAD(A))
Function / homology
Function and homology information


L-lactate dehydrogenase / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / glycolytic process / NAD binding / cytoplasm
Similarity search - Function
L-lactate dehydrogenase / L-lactate dehydrogenase active site. / L-lactate dehydrogenase, active site / 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 ...L-lactate dehydrogenase / L-lactate dehydrogenase active site. / L-lactate dehydrogenase, active site / 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
1,6-di-O-phosphono-beta-D-fructofuranose / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / OXAMIC ACID / L-lactate dehydrogenase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsWigley, D.B. / Gamblin, S.J. / Turkenburg, J.P. / Dodson, E.J. / Piontek, K. / Muirhead, H. / Holbrook, J.J.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Structure of a ternary complex of an allosteric lactate dehydrogenase from Bacillus stearothermophilus at 2.5 A resolution.
Authors: Wigley, D.B. / Gamblin, S.J. / Turkenburg, J.P. / Dodson, E.J. / Piontek, K. / Muirhead, H. / Holbrook, J.J.
#1: Journal: J.Mol.Biol. / Year: 1988
Title: Crystallization of a Ternary Complex of Lactate Dehydrogenase from Bacillus Stearothermophilus
Authors: Wigley, D.B. / Muirhead, H. / Gamblin, S.J. / Holbrook, J.J.
#2: Journal: Gene / Year: 1986
Title: Cloning, Expression and Complete Nucleotide Sequence of the Bacillus Stearothermophilus L-Lactate Dehydrogenase Gene
Authors: Barstow, D.A. / Clarke, A.R. / Chia, W.N. / Wigley, D.B. / Sharman, A.F. / Holbrook, J.J. / Atkinson, T. / Minton, N.P.
History
DepositionNov 19, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-LACTATE DEHYDROGENASE
B: L-LACTATE DEHYDROGENASE
C: L-LACTATE DEHYDROGENASE
D: L-LACTATE DEHYDROGENASE
E: L-LACTATE DEHYDROGENASE
F: L-LACTATE DEHYDROGENASE
G: L-LACTATE DEHYDROGENASE
H: L-LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,34428
Polymers277,9648
Non-polymers7,38020
Water10,305572
1
A: L-LACTATE DEHYDROGENASE
B: L-LACTATE DEHYDROGENASE
C: L-LACTATE DEHYDROGENASE
D: L-LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,67214
Polymers138,9824
Non-polymers3,69010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21460 Å2
ΔGint-120 kcal/mol
Surface area38700 Å2
MethodPISA
2
E: L-LACTATE DEHYDROGENASE
F: L-LACTATE DEHYDROGENASE
G: L-LACTATE DEHYDROGENASE
H: L-LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,67214
Polymers138,9824
Non-polymers3,69010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21270 Å2
ΔGint-127 kcal/mol
Surface area38540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.900, 118.200, 135.500
Angle α, β, γ (deg.)90.00, 96.07, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUE PRO 139 OF EACH CHAIN IS A CIS PROLINE.
DetailsTHE COORDINATES OF ALL EIGHT MOLECULES OF THE ASYMMETRIC UNIT ARE PROVIDED BELOW BECAUSE OF THE REAL DIFFERENCES BETWEEN THEM DUE TO CRYSTAL CONTACTS.

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Components

#1: Protein
L-LACTATE DEHYDROGENASE


Mass: 34745.527 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
References: UniProt: P00344, L-lactate dehydrogenase
#2: Sugar
ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3NO3
#4: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE ENZYME WAS COCRYSTALLIZED IN THE PRESENCE OF THE COENZYME NADH AND THE ACTIVATOR FBP. THE NADH ...THE ENZYME WAS COCRYSTALLIZED IN THE PRESENCE OF THE COENZYME NADH AND THE ACTIVATOR FBP. THE NADH MOLECULE IS SITUATED AT THE LDH COENZYME BINDING SITE. ONE FBP MOLECULE BINDS ACROSS THE P-AXIS. THE P-AXIS INTERSECTS THE ACTIVATOR MOLECULE GIVING RISE TO A STATISTICAL DISORDER (OCCUPANCY 0.5) AS FBP HAS ONLY PSEUDO-TWO-FOLD SYMMETRY.
Nonpolymer detailsBECAUSE OF THE STATISTICAL DISORDER, TWO FBP MOLECULES WITH OCCUPANCIES OF 0.5 MODELLED WITH TWO ...BECAUSE OF THE STATISTICAL DISORDER, TWO FBP MOLECULES WITH OCCUPANCIES OF 0.5 MODELLED WITH TWO ALTERNATE LOCATIONS ARE INCLUDED AT EACH SITE.
Sequence detailsTHE RESIDUES IN THIS ENTRY ARE NUMBERED SEQUENTIALLY FROM 15 - 331. SEE C.ABAD-ZAPATERO,J.P. ...THE RESIDUES IN THIS ENTRY ARE NUMBERED SEQUENTIALLY FROM 15 - 331. SEE C.ABAD-ZAPATERO,J.P.GRIFFITH,J.L.SUSSMAN, M.G.ROSSMANN, J.MOL.BIOL., V. 198, P. 445 (1987) FOR AN EXPLANATION OF THE NUMBERING SYSTEM USED IN EARLIER LDH ENTRIES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.42 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Details: taken from Wigley, B., et al. (1988). J. Mol. Biol., 204, 1041-1044.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
212 %PEG60001dropor PEG8000
310 mMtrisethanolamine1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / Num. obs: 62506 / Num. measured all: 99326 / Rmerge(I) obs: 0.097

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor obs: 0.157 / Highest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19584 0 560 572 20716
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0450.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0540.06
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.1150.12
X-RAY DIFFRACTIONp_singtor_nbd0.2330.5
X-RAY DIFFRACTIONp_multtor_nbd0.2960.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2640.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.85
X-RAY DIFFRACTIONp_staggered_tor23.515
X-RAY DIFFRACTIONp_orthonormal_tor3320
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / Rfactor obs: 0.157
Solvent computation
*PLUS
Displacement parameters
*PLUS

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