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- PDB-7x12: Crystal structure of ME1 in complex with NADPH -

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Basic information

Entry
Database: PDB / ID: 7x12
TitleCrystal structure of ME1 in complex with NADPH
ComponentsNADP-dependent malic enzyme
KeywordsOXIDOREDUCTASE / malic enzyme / complex
Function / homology
Function and homology information


malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) / regulation of NADP metabolic process / malic enzyme activity / malate dehydrogenase (decarboxylating) (NADP+) activity / nucleotide biosynthetic process / NFE2L2 regulating TCA cycle genes / oxaloacetate decarboxylase activity / Pyruvate metabolism / malate metabolic process / NADP metabolic process ...malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) / regulation of NADP metabolic process / malic enzyme activity / malate dehydrogenase (decarboxylating) (NADP+) activity / nucleotide biosynthetic process / NFE2L2 regulating TCA cycle genes / oxaloacetate decarboxylase activity / Pyruvate metabolism / malate metabolic process / NADP metabolic process / response to carbohydrate / NADH metabolic process / pyruvate metabolic process / response to hormone / PPARA activates gene expression / ADP binding / NAD binding / NADP binding / manganese ion binding / protein homotetramerization / carbohydrate metabolic process / electron transfer activity / magnesium ion binding / mitochondrion / identical protein binding / cytoplasm / cytosol
Similarity search - Function
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 ...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 / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / Chem-NDP / NADP-dependent malic enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsAmano, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochemistry / Year: 2022
Title: Discovery and Characterization of a Novel Allosteric Small-Molecule Inhibitor of NADP + -Dependent Malic Enzyme 1.
Authors: Yoshida, T. / Kawabe, T. / Cantley, L.C. / Lyssiotis, C.A.
History
DepositionFeb 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADP-dependent malic enzyme
B: NADP-dependent malic enzyme
C: NADP-dependent malic enzyme
D: NADP-dependent malic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,09512
Polymers256,8944
Non-polymers3,2018
Water8,737485
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23490 Å2
ΔGint-111 kcal/mol
Surface area80650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.285, 181.594, 116.821
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
NADP-dependent malic enzyme / NADP-ME / Malic enzyme 1


Mass: 64223.383 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ME1 / Production host: Escherichia coli (E. coli)
References: UniProt: P48163, malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+)
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.94 Å3/Da / Density % sol: 58.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: HEPES, ammonium chloride, PEG 3350

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→47.43 Å / Num. obs: 175249 / % possible obs: 95.7 % / Redundancy: 5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.044 / Rrim(I) all: 0.101 / Net I/σ(I): 11.8 / Num. measured all: 881596 / Scaling rejects: 59
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.07-2.1150.9174436788050.6540.4451.0241.998
11.34-47.435.40.021581610830.9990.010.02340.787.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WJA

3wja


Resolution: 2.07→45.18 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.002 / SU ML: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 8760 5 %RANDOM
Rwork0.2159 ---
obs0.218 166417 95.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 144.13 Å2 / Biso mean: 39.777 Å2 / Biso min: 17.96 Å2
Baniso -1Baniso -2Baniso -3
1-2.33 Å2-0 Å20 Å2
2---1.2 Å20 Å2
3----1.13 Å2
Refinement stepCycle: final / Resolution: 2.07→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17804 0 196 485 18485
Biso mean--40.47 37.19 -
Num. residues----2256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01218360
X-RAY DIFFRACTIONr_angle_refined_deg1.491.65424888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44752252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33422.917960
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.489153228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.23115112
X-RAY DIFFRACTIONr_chiral_restr0.1090.22412
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214048
LS refinement shellResolution: 2.07→2.124 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 612 -
Rwork0.297 12567 -
all-13179 -
obs--97.81 %

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