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- PDB-1lld: MOLECULAR BASIS OF ALLOSTERIC ACTIVATION OF BACTERIAL L-LACTATE D... -

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Basic information

Entry
Database: PDB / ID: 1lld
TitleMOLECULAR BASIS OF ALLOSTERIC ACTIVATION OF BACTERIAL L-LACTATE DEHYDROGENASE
ComponentsL-LACTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / OXIDOREDUCTASE(CHOH (D)-NAD (A))
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-lactate dehydrogenase 2 / L-lactate dehydrogenase 2
Similarity search - Component
Biological speciesBifidobacterium longum subsp. longum (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsIwata, S. / Ohta, T.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Molecular basis of allosteric activation of bacterial L-lactate dehydrogenase.
Authors: Iwata, S. / Ohta, T.
#1: Journal: FARADAY DISC.CHEM.SOC / Year: 1992
Title: Mechanism of Allosteric Transition of Bacterial L-Lactate Dehydrogenase
Authors: Iwata, S. / Ohta, T.
#2: 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.
#3: 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.
#4: Journal: J.Biochem.(Tokyo) / Year: 1989
Title: Crystallization of and Preliminary Crystallographic Data for Allosteric L-Lactate Dehydrogenase from Bifidobacterium Longum
Authors: Wata, S. / Minowa, T. / Mikami, B. / Morita, Y. / Ohta, T.
History
DepositionJun 8, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
Remark 650HELIX THE HELIX NAMES USED IN EARLIER LDH ENTRIES BY M.G.ROSSMANN ET AL. ARE GIVEN IN THE REMARK ...HELIX THE HELIX NAMES USED IN EARLIER LDH ENTRIES BY M.G.ROSSMANN ET AL. ARE GIVEN IN THE REMARK FIELD OF THE HELIX RECORDS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-LACTATE DEHYDROGENASE
B: L-LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5844
Polymers68,2582
Non-polymers1,3272
Water3,999222
1
A: L-LACTATE DEHYDROGENASE
B: L-LACTATE DEHYDROGENASE
hetero molecules

A: L-LACTATE DEHYDROGENASE
B: L-LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,1698
Polymers136,5154
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area16240 Å2
ΔGint-114 kcal/mol
Surface area45060 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)105.800, 131.400, 63.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: CIS PROLINE - PRO A 126 / 2: CIS PROLINE - PRO B 126
3: RESIDUES A 86 - A 88, B 86 - B 93, A 232 - A 234, AND B 232 - B 234 ARE DISORDERED. ALTHOUGH THE COORDINATES OF THESE RESIDUES ARE INCLUDED IN THIS ENTRY, THEY ARE LESS RELIABLE THAN THOSE OF OTHER RESIDUES.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.309, 0.951, -0.003), (0.951, 0.309, -0.003), (-0.002, -0.004, -1)
Vector: 6.835, -4.92, 46.534)
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS TWO SUBUNITS OF THE TETRAMER. THESE SUBUNITS HAVE BEEN ASSIGNED CHAIN IDENTIFIERS "A" AND "B". THE RESIDUES IN EACH CHAIN ARE NUMBERED SEQUENTIALLY FROM 1 - 319. THERE IS NO SIGNIFICANT DIFFERENCE BETWEEN THE TWO SUBUNIT STRUCTURES. THE TETRAMER CAN BE GENERATED FROM THE DIMER IN THIS ENTRY BY ROTATING 180 DEGREES ABOUT THE CRYSTALLOGRAPHIC DIAD PARALLEL TO Z AXIS THROUGH THE POINT (1/2,1/2,1/2). THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*.

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Components

#1: Protein L-LACTATE DEHYDROGENASE


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
References: UniProt: P19869, UniProt: E8ME30*PLUS, L-lactate dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS ENZYME IS A MUTANT WITH CYS 199 REPLACED BY SER. THIS MUTATION IS FOR THE HEAVY-ATOM ...THIS ENZYME IS A MUTANT WITH CYS 199 REPLACED BY SER. THIS MUTATION IS FOR THE HEAVY-ATOM DERIVATIVE PREPARATION, THE 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: 3.25 Å3/Da / Density % sol: 62.12 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Details: taken from Iwata, S. et al (1989). J. Biochem., 106-558-559.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18.2 mg/mlprotein1drop
25 mMTris-HCl1drop
3150 mM1dropNaCl
410 %(v/v)PEG60001reservoir
550 mMMES1reservoir
62.5 mMNADH1reservoir
72.5 mMsodium oxamate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 64557 / % possible obs: 77 % / Rmerge(I) obs: 0.061

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2→10 Å / σ(F): 1
Details: RESIDUES A 86 - A 88, B 86 - B 93, A 232 - A 234, AND B 232 - B 234 ARE DISORDERED. ALTHOUGH THE COORDINATES OF THESE RESIDUES ARE INCLUDED IN THIS ENTRY, THEY ARE LESS RELIABLE THAN THOSE OF OTHER RESIDUES.
RfactorNum. reflection
obs0.179 47766
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4700 0 88 222 5010
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.015
X-RAY DIFFRACTIONp_angle_d0.0370.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0520.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.691
X-RAY DIFFRACTIONp_mcangle_it3.381.5
X-RAY DIFFRACTIONp_scbond_it3.631
X-RAY DIFFRACTIONp_scangle_it4.81.5
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.1830.15
X-RAY DIFFRACTIONp_singtor_nbd0.1961
X-RAY DIFFRACTIONp_multtor_nbd0.3031
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2011
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.43
X-RAY DIFFRACTIONp_staggered_tor23.115
X-RAY DIFFRACTIONp_orthonormal_tor27.620
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / Num. reflection obs: 47766 / σ(F): 1 / Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS

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