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- PDB-1o0s: Crystal Structure of Ascaris suum Malic Enzyme Complexed with NADH -

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Basic information

Entry
Database: PDB / ID: 1o0s
TitleCrystal Structure of Ascaris suum Malic Enzyme Complexed with NADH
ComponentsNAD-dependent malic enzyme
KeywordsOXIDOREDUCTASE / Oxidative decarboxylase / Rossmann Fold / Malate dehydrogenase / Ascaris suum
Function / homology
Function and homology information


malate dehydrogenase (oxaloacetate-decarboxylating) / malate dehydrogenase (decarboxylating) (NAD+) activity / oxaloacetate decarboxylase activity / metabolic process / NAD binding / mitochondrial matrix / metal ion binding
Similarity search - Function
Hemocyanin, N-terminal domain - #30 / arginine biosynthesis bifunctional protein fold / arginine biosynthesis bifunctional protein fold - #10 / Malic enzyme, N-terminal domain / Malic enzyme, conserved site / Malic enzymes signature. / Malic oxidoreductase / Malic enzyme, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding ...Hemocyanin, N-terminal domain - #30 / arginine biosynthesis bifunctional protein fold / arginine biosynthesis bifunctional protein fold - #10 / Malic enzyme, N-terminal domain / Malic enzyme, conserved site / Malic enzymes signature. / Malic oxidoreductase / Malic enzyme, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding / Malic enzyme, N-terminal domain superfamily / Malic enzyme, N-terminal domain / Malic enzyme, NAD binding domain / Malic enzyme, NAD binding domain / Hemocyanin, N-terminal domain / Aminoacid dehydrogenase-like, N-terminal domain superfamily / Other non-globular / Special / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / TARTRONATE / NAD-dependent malic enzyme, mitochondrial
Similarity search - Component
Biological speciesAscaris suum (pig roundworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRao, G.S. / Coleman, D.E. / Karsten, W.E. / Cook, P.F. / Harris, B.G.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Crystallographic studies on Ascaris suum NAD-malic enzyme bound to reduced cofactor and identification of an effector site.
Authors: Rao, G.S. / Coleman, D.E. / Karsten, W.E. / Cook, P.F. / Harris, B.G.
#1: Journal: Biochemistry / Year: 2002
Title: Crystal Structure of the Malic Enzyme from Ascaris suum Complexed with Nicotinamide Adenine Dinucleotide at 2.3 A Resolution
Authors: Coleman, D.E. / Rao, G.S.J. / Goldsmith, E.J. / Cook, P.F. / Harris, B.G.
History
DepositionFeb 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Aug 16, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_remark / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 400COMPOUND STRUCTURE REVEALS A DIFFERENT ORIENTATION OF THE NICOTINAMIDE RING, COMPARED TO ITS ...COMPOUND STRUCTURE REVEALS A DIFFERENT ORIENTATION OF THE NICOTINAMIDE RING, COMPARED TO ITS POSITION IN THE ENZYME_NAD COMPLEX. STRUCTURE ALSO REVEALS THE BINDING OF TARTRONATE IN AN ALLOSTERIC SITE.
Remark 999 SEQUENCE THE NUMBERING SYSTEM USED FOR THE COORDINATES CORRESPONDS TO THE NUMBERING SYSTEM USED IN ... SEQUENCE THE NUMBERING SYSTEM USED FOR THE COORDINATES CORRESPONDS TO THE NUMBERING SYSTEM USED IN PUBLISHED MUTATIONAL STUDIES, WHERE RESIDUE 1 (LYS) IS THE FIRST RESIDUE PRESENT IN THE FULLY PROCESSED PROTEIN CHAIN. A 12 RESIDUE MITOCHONDRIAL TRANSPORT SEQUENCE IS PRESENT IN THE UNPROCESSED PROTEIN, BUT IS ABSENT FROM PROCESSED PROTEIN AND THE PROTEIN PRESENT IN THE CRYSTALS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD-dependent malic enzyme
B: NAD-dependent malic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,6806
Polymers137,1132
Non-polymers1,5674
Water12,881715
1
A: NAD-dependent malic enzyme
B: NAD-dependent malic enzyme
hetero molecules

A: NAD-dependent malic enzyme
B: NAD-dependent malic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,36012
Polymers274,2264
Non-polymers3,1348
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area28060 Å2
ΔGint-130 kcal/mol
Surface area88170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)130.947, 130.947, 149.128
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein NAD-dependent malic enzyme / NAD-ME


Mass: 68556.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ascaris suum (pig roundworm)
References: UniProt: P27443, malate dehydrogenase (oxaloacetate-decarboxylating)
#2: Chemical ChemComp-TTN / TARTRONATE


Mass: 118.045 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O5
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 715 / 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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 4000, sodium acetate, sodium tartronate, NADH, magnesium sulphate, mercaptoethanol, tris, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 7.3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMTris-SO41reservoirpH7.3
2100 mMsodium acetate1reservoir
315 %PEG40001reservoir
45 mMNADH1reservoir
510 mMtartronate1reservoir
620 mM1reservoirMgSO4
710 mM2-mercaptoethanol1reservoir
80.02 %sodium azide1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.992 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 18, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.992 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 98317 / Num. obs: 98317 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 6.75 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 21.6
Reflection shellResolution: 2→2.09 Å / Redundancy: 2.74 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.77 / Num. unique all: 12159 / % possible all: 98.4
Reflection
*PLUS
Num. obs: 104791 / % possible obs: 98.7 % / Num. measured all: 693156 / Rmerge(I) obs: 0.056

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LLQ

1llq


Resolution: 2→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Reflections with F<0.0 not used. Bulk solvent correction used throughtout.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 4104 -RANDOM
Rwork0.221 ---
all0.223 98317 --
obs0.223 82205 82.2 %-
Displacement parametersBiso mean: 39.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9516 0 104 715 10335
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.559
X-RAY DIFFRACTIONc_dihedral_angle_d22.156
X-RAY DIFFRACTIONc_improper_angle_d0.976
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection% reflection
Rfree0.37 283 -
Rwork0.317 --
obs-6698 67.5 %
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.272 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.156
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.976

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