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- PDB-1lth: T AND R STATES IN THE CRYSTALS OF BACTERIAL L-LACTATE DEHYDROGENA... -

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Basic information

Entry
Database: PDB / ID: 1lth
TitleT AND R STATES IN THE CRYSTALS OF BACTERIAL L-LACTATE DEHYDROGENASE REVEAL THE MECHANISM FOR ALLOSTERIC CONTROL
ComponentsL-LACTATE DEHYDROGENASE (T- AND R- STATE TETRAMER COMPLEX)
KeywordsOXIDOREDUCTASE / CHOH(D)-NAD(A) / ALLOSTERIC ENZYME
Function / homology
Function and homology information


L-lactate dehydrogenase / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / glycolytic process / 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 2 / L-lactate dehydrogenase 2
Similarity search - Component
Biological speciesBifidobacterium longum subsp. longum (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsIwata, S. / Ohta, T.
Citation
Journal: Nat.Struct.Biol. / Year: 1994
Title: T and R states in the crystals of bacterial L-lactate dehydrogenase reveal the mechanism for allosteric control.
Authors: Iwata, S. / Kamata, K. / Yoshida, S. / Minowa, T. / Ohta, T.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: A Regular 1:1 Complex of Two Allosteric States in the Single Crystal of L-Lactate Dehydrogenase from Bifidobacterium Longum
Authors: Iwata, S. / Yoshida, S. / Ohta, T.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Molecular Basis of Allosteric Activation of Bacterial L-Lactate Dehydrogenase
Authors: Iwata, S. / Ohta, T.
#3: Journal: FARADAY DISC.CHEM.SOC / Year: 1992
Title: Mechanism of Allosteric Transition of Bacterial L-Lactate Dehydrogenase
Authors: Ohta, T. / Minowa, T. / Yokota, K. / Iwata, S.
#4: Journal: J.Biochem.(Tokyo) / Year: 1989
Title: Crystallization of and Preliminary Crystallographic Data for Allosteric L-Lactate Dehydrogenase from Bifidobacterium Longum
Authors: Iwata, S. / Minowa, T. / Mikani, B. / Morita, Y. / Ohta, T.
#5: Journal: Gene / Year: 1989
Title: Sequence and Characteristics of the Bifidobacterium Longum Gene Encoding L-Lactate Dehydrogenase and the Primary Structure of the Enzyme: A New Feature of the Allosteric Site
Authors: Minowa, T. / Iwata, S. / Sakai, H. / Masaki, H. / Ohta, T.
#6: Journal: Agric.Biol.Chem. / Year: 1989
Title: Amino Acid Residues in the Allosteric Site of L-Lactate Dehydrogenase from Bifidobacterium Longum
Authors: Iwata, S. / Minowa, T. / Sakai, H. / Ohta, T.
History
DepositionJan 4, 1995Processing site: BNL
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_ref_seq_dif / 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 / _struct_ref_seq_dif.details
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
T: L-LACTATE DEHYDROGENASE (T- AND R- STATE TETRAMER COMPLEX)
R: L-LACTATE DEHYDROGENASE (T- AND R- STATE TETRAMER COMPLEX)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3547
Polymers68,2582
Non-polymers2,0965
Water5,423301
1
T: L-LACTATE DEHYDROGENASE (T- AND R- STATE TETRAMER COMPLEX)
hetero molecules

T: L-LACTATE DEHYDROGENASE (T- AND R- STATE TETRAMER COMPLEX)
hetero molecules

T: L-LACTATE DEHYDROGENASE (T- AND R- STATE TETRAMER COMPLEX)
hetero molecules

T: L-LACTATE DEHYDROGENASE (T- AND R- STATE TETRAMER COMPLEX)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,52912
Polymers136,5154
Non-polymers4,0148
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area18930 Å2
ΔGint-124 kcal/mol
Surface area45060 Å2
MethodPISA, PQS
2
R: L-LACTATE DEHYDROGENASE (T- AND R- STATE TETRAMER COMPLEX)
hetero molecules

R: L-LACTATE DEHYDROGENASE (T- AND R- STATE TETRAMER COMPLEX)
hetero molecules

R: L-LACTATE DEHYDROGENASE (T- AND R- STATE TETRAMER COMPLEX)
hetero molecules

R: L-LACTATE DEHYDROGENASE (T- AND R- STATE TETRAMER COMPLEX)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,88516
Polymers136,5154
Non-polymers4,37012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y+1/2,-z+1/21
crystal symmetry operation11_555-x+1/2,y,-z+1/21
crystal symmetry operation14_555-x+1/2,-y+1/2,z1
Buried area21310 Å2
ΔGint-121 kcal/mol
Surface area39650 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)148.400, 295.900, 71.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Atom site foot note1: CIS PROLINE - PRO T 126 / 2: CIS PROLINE - PRO R 126
DetailsTHIS CRYSTAL STRUCTURE REFERENCES THE REGULAR 1:1 COMPLEX OF T-STATE (LOW AFFINITY TO SUBSTRATE) AND R-STATE (HIGH AFFINITY TO SUBSTRATE) TETRAMERS OF L-LACTATE DEHYDROGENASE FROM BIFIDOBACTERIUM LONGUM. THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS ONE T-STATE SUBUNIT AND ONE R-STATE SUBUNIT ASSIGNED CHAIN IDENTIFIERS "T" AND "R", RESPECTIVELY. SYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. APPLIED TO RESIDUES: T 6 .. T 321 FORMATION OF THE P-AXIS RELATED SUBUNIT OF THE T-STATE TETRAMER SYMMETRY1 1 1.000000 0.000000 0.000000 0.00000 SYMMETRY2 1 0.000000 -1.000000 0.000000 0.00000 SYMMETRY3 1 0.000000 0.000000 -1.000000 0.00000 APPLIED TO RESIDUES: T 6 .. T 321 FORMATION OF THE Q-AXIS RELATED SUBUNIT OF THE T-STATE TETRAMER SYMMETRY1 2 -1.000000 0.000000 0.000000 0.00000 SYMMETRY2 2 0.000000 1.000000 0.000000 0.00000 SYMMETRY3 2 0.000000 0.000000 -1.000000 0.00000 APPLIED TO RESIDUES: T 6 .. T 321 FORMATION OF THE R-AXIS RELATED SUBUNIT OF THE T-STATE TETRAMER SYMMETRY1 3 -1.000000 0.000000 0.000000 0.00000 SYMMETRY2 3 0.000000 -1.000000 0.000000 0.00000 SYMMETRY3 3 0.000000 0.000000 1.000000 0.00000 APPLIED TO RESIDUES: R 6 .. R 322 FORMATION OF THE P-AXIS RELATED SUBUNIT OF THE R-STATE TETRAMER SYMMETRY1 4 1.000000 0.000000 0.000000 0.00000 SYMMETRY2 4 0.000000 -1.000000 0.000000 147.92900 SYMMETRY3 4 0.000000 0.000000 -1.000000 35.46099 APPLIED TO RESIDUES: R 6 .. R 322 FORMATION OF THE Q-AXIS RELATED SUBUNIT OF THE R-STATE TETRAMER SYMMETRY1 5 -1.000000 0.000000 0.000000 74.18398 SYMMETRY2 5 0.000000 1.000000 0.000000 0.00000 SYMMETRY3 5 0.000000 0.000000 -1.000000 35.46099 APPLIED TO RESIDUES: R 6 .. R 322 FORMATION OF THE R-AXIS RELATED SUBUNIT OF THE R-STATE TETRAMER SYMMETRY1 6 -1.000000 0.000000 0.000000 74.18398 SYMMETRY2 6 0.000000 -1.000000 0.000000 147.92900 SYMMETRY3 6 0.000000 0.000000 1.000000 0.00000

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Components

#1: Protein L-LACTATE DEHYDROGENASE (T- AND R- STATE TETRAMER COMPLEX)


Mass: 34128.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum subsp. longum (bacteria)
Species: Bifidobacterium longum / Strain: subsp. longum / Gene: BIFIDOBACTERIUM LONGUM LDH GENE / Plasmid: PUBM9 (A DERIVATIVE OF PUC119) / Production host: Escherichia coli (E. coli)
References: UniProt: P19869, UniProt: E8ME30*PLUS, 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.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE T-STATE TETRAMERS, THAT BIND NADH AND FBP, ARE CENTERED AT THE ORIGIN AND ITS EQUIVALENTS. THE ...THE T-STATE TETRAMERS, THAT BIND NADH AND FBP, ARE CENTERED AT THE ORIGIN AND ITS EQUIVALENTS. THE R-STATE TETRAMERS, THAT BIND NADH, OXAMATE AND FBP, ARE CENTERED AT (1/4, 1/4, 1/4) AND ITS EQUIVALENTS. THE MOLECULAR DYADS OF THESE TETRAMERS LIE ON THE CRYSTALLOGRAPHIC TWO-FOLD AXES. THIS ENZYME IS A MUTANT WITH CYS 199 REPLACED BY SER. KINETIC PROPERTIES OF THE ENZYME ARE IDENTICAL WITH THOSE OF WILD-TYPE ENZYME.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal grow
*PLUS
Temperature: 10 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5 mMNADH1reservoir
22.5 mMoxamate1reservoir
30.5 mMFBP1reservoir
420 %PEG60001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 24341 / % possible obs: 89.1 % / Observed criterion σ(I): 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 100 Å / % possible obs: 97.6 % / Num. measured all: 115542 / Rmerge(I) obs: 0.055

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Processing

Software
NameVersionClassification
X-PLOR2.1model building
X-PLOR2.1refinement
X-PLOR2.1phasing
RefinementResolution: 2.5→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.188 --
obs0.188 21245 79.2 %
Displacement parametersBiso mean: 23.79 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4700 0 134 301 5135
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.631
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.59
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.598
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

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