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- PDB-1bdm: THE STRUCTURE AT 1.8 ANGSTROMS RESOLUTION OF A SINGLE SITE MUTANT... -

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Basic information

Entry
Database: PDB / ID: 1bdm
TitleTHE STRUCTURE AT 1.8 ANGSTROMS RESOLUTION OF A SINGLE SITE MUTANT (T189I) OF MALATE DEHYDROGENASE FROM THERMUS FLAVUS WITH INCREASED ENZYMATIC ACTIVITY
ComponentsMALATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE(NAD(A)-CHOH(D))
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / tricarboxylic acid cycle
Similarity search - Function
Malate dehydrogenase, type 2 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / 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 ...Malate dehydrogenase, type 2 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / 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
Chem-NAX / Malate dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsKelly, C.A. / Birktoft, J.J.
Citation
Journal: Biochemistry / Year: 1993
Title: Determinants of protein thermostability observed in the 1.9-A crystal structure of malate dehydrogenase from the thermophilic bacterium Thermus flavus.
Authors: Kelly, C.A. / Nishiyama, M. / Ohnishi, Y. / Beppu, T. / Birktoft, J.J.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Preliminary X-Ray Diffraction Analysis of a Crystallizable Mutant of Malate Dehydrogenase from the Thermophile Thermus Flavus
Authors: Kelly, C.A. / Sarfaty, S. / Nishiyama, M. / Beppu, T. / Birktoft, J.J.
#2: Journal: J.Biol.Chem. / Year: 1991
Title: Role of Threonine 190 in Modulating the Catalytic Function of Malate Dehydrogenase from a Thermophile Thermus Flavus
Authors: Nishiyama, M. / Shimada, K. / Horinouchi, S. / Beppu, T.
#3: Journal: Biochemistry / Year: 1989
Title: Refined Crystal Structure of Cytoplasmic Malate Dehydrogenase at 2.5-Angstroms Resolution
Authors: Birktoft, J.J. / Rhodes, G. / Banaszak, L.J.
#4: Journal: J.Biol.Chem. / Year: 1986
Title: Nucleotide Sequence of the Malate Dehydrogenase Gene of Thermus Flavus and its Mutation Directing an Increase in Enzyme Activity
Authors: Nishiyama, M. / Matsubara, N. / Yamamoto, K. / Iijima, S. / Uozumi, T. / Beppu, T.
#5: Journal: The Pyridine Nucleotide Coenzymes / Year: 1982
Title: Chemistry and Solution Conformation of the Pyridine Coenzymes
Authors: Oppenheimer, N.J.
#6: Journal: The Enzymes,Third Edition / Year: 1975
Title: Malate Dehydrogenase
Authors: Banaszak, L.J. / Bradshaw, R.A.
History
DepositionFeb 16, 1993Processing site: BNL
Revision 1.0Dec 20, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 7, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MALATE DEHYDROGENASE
B: MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2964
Polymers70,9292
Non-polymers1,3672
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-24 kcal/mol
Surface area24680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.750, 88.640, 118.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO A 131 / 2: CIS PROLINE - PRO B 131
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.6098, 0.0011, -0.7926), (0.0067, -1, -0.0066), (-0.7926, -0.0094, 0.6097)
Vector: 81.3223, 51.7046, 40.4052)
DetailsTHE ASYMMETRIC UNIT CONTAINS TWO SUBUNITS WHICH HAVE BEEN ASSIGNED CHAIN IDENTIFIERS *A* AND *B*. THEY ARE RELATED BY A NON-CRYSTALLOGRAPHIC SYMMETRY AXIS WITH A ROTATION ANGLE OF 180.0 DEGREES. THE TRANSFORMATION PROVIDED ON THE *MTRIX* RECORDS BELOW YIELDS OPTIMAL SUPERPOSITION OF SUBUNIT A UPON SUBUNIT B BASED UPON ALL ALPHA CARBON ATOMS.

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Components

#1: Protein MALATE DEHYDROGENASE


Mass: 35464.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / References: UniProt: P10584, malate dehydrogenase
#2: Chemical ChemComp-NAX / BETA-6-HYDROXY-1,4,5,6-TETRHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE


Mass: 683.456 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H31N7O15P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsWHILE THE ENZYME WAS CRYSTALLIZED AT PH 7.5 IN THE PRESENCE OF THE REDUCED COENZYME NADH, THE ...WHILE THE ENZYME WAS CRYSTALLIZED AT PH 7.5 IN THE PRESENCE OF THE REDUCED COENZYME NADH, THE ELECTRON DENSITY MAP WAS BEST FIT BY THE MODIFIED COENZYME REFERRED TO AS NADHX.
Sequence detailsTHE NUMBERING SYSTEM IS THE SAME AS THAT USED FOR THE CYTOPLASMIC MALATE DEHYDROGENASE STRUCTURE. ...THE NUMBERING SYSTEM IS THE SAME AS THAT USED FOR THE CYTOPLASMIC MALATE DEHYDROGENASE STRUCTURE. THE DELETION REGIONS IN TMDH-T189I, 201 - 204, 213 AND 276, LEAD TO DISCONTINUITIES IN THE TMDH NUMBERING; HOWEVER, THESE DO NOT REPRESENT BREAKS IN THE PEPTIDE CHAIN. SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: MDH_THEFL SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE LYS 75 ASP A 74 CROSS REFERENCE TO SEQUENCE DATABASE SWISS-PROT ENTRY NAME PDB ENTRY CHAIN NAME MDH_THEFL B SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: MDH_THEFL SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE LYS 75 ASP B 74 THE SEQUENCE PRESENTED IN THE ENTRY FITS THE OBSERVED DENSITY BETTER THAN THE PUBLISHED SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
113-15 mg/mlprotein1drop
20.1 MTris-HCl1reservoir
320-24 %PEG33501reservoir
4200-800 mM1reservoirNaCl
520 mMoxaloacetate1reservoir
60.2-0.5 mMNADH1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. obs: 63904 / Num. measured all: 376446 / Rmerge(I) obs: 0.071

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementRfactor Rwork: 0.169 / Rfactor obs: 0.169 / Highest resolution: 1.8 Å
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4905 0 90 202 5197
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2.77
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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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