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- PDB-1pjl: Crystal structure of human m-NAD-ME in ternary complex with NAD a... -

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Basic information

Entry
Database: PDB / ID: 1pjl
TitleCrystal structure of human m-NAD-ME in ternary complex with NAD and Lu3+
ComponentsNAD-dependent malic enzyme, mitochondrial
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


malate dehydrogenase (oxaloacetate-decarboxylating) / regulation of NADP metabolic process / malate dehydrogenase (decarboxylating) (NAD+) activity / malic enzyme activity / malate dehydrogenase (decarboxylating) (NADP+) activity / oxaloacetate decarboxylase activity / malate metabolic process / pyruvate metabolic process / Pyruvate metabolism / Mitochondrial protein degradation ...malate dehydrogenase (oxaloacetate-decarboxylating) / regulation of NADP metabolic process / malate dehydrogenase (decarboxylating) (NAD+) activity / malic enzyme activity / malate dehydrogenase (decarboxylating) (NADP+) activity / oxaloacetate decarboxylase activity / malate metabolic process / pyruvate metabolic process / Pyruvate metabolism / Mitochondrial protein degradation / NAD binding / electron transfer activity / mitochondrial matrix / intracellular membrane-bounded organelle / mitochondrion / metal ion binding
Similarity search - Function
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, 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 / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD-dependent malic enzyme, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsYang, Z. / Batra, R. / Floyd, D.L. / Hung, H.-C. / Chang, G.-G. / Tong, L.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2000
Title: Potent and competitive inhibition of malic enzymes by lanthanide ions
Authors: Yang, Z. / Batra, R. / Floyd, D.L. / Hung, H.-C. / Chang, G.-G. / Tong, L.
History
DepositionJun 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent malic enzyme, mitochondrial
B: NAD-dependent malic enzyme, mitochondrial
C: NAD-dependent malic enzyme, mitochondrial
D: NAD-dependent malic enzyme, mitochondrial
E: NAD-dependent malic enzyme, mitochondrial
F: NAD-dependent malic enzyme, mitochondrial
G: NAD-dependent malic enzyme, mitochondrial
H: NAD-dependent malic enzyme, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)541,81432
Polymers529,7998
Non-polymers12,01524
Water1,13563
1
A: NAD-dependent malic enzyme, mitochondrial
B: NAD-dependent malic enzyme, mitochondrial
C: NAD-dependent malic enzyme, mitochondrial
D: NAD-dependent malic enzyme, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,90716
Polymers264,9004
Non-polymers6,00712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21950 Å2
ΔGint-114 kcal/mol
Surface area80050 Å2
MethodPISA
2
E: NAD-dependent malic enzyme, mitochondrial
F: NAD-dependent malic enzyme, mitochondrial
G: NAD-dependent malic enzyme, mitochondrial
H: NAD-dependent malic enzyme, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,90716
Polymers264,9004
Non-polymers6,00712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22110 Å2
ΔGint-108 kcal/mol
Surface area80110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.3, 119.0, 125.9
Angle α, β, γ (deg.)116.5, 94.8, 102.8
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
NAD-dependent malic enzyme, mitochondrial / NAD-ME / Malic enzyme 2


Mass: 66224.875 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ME2 / Production host: Escherichia coli (E. coli)
References: UniProt: P23368, malate dehydrogenase (oxaloacetate-decarboxylating)
#2: Chemical
ChemComp-LU / LUTETIUM (III) ION / LU


Mass: 174.967 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Lu
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 54.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Hepes, 6% PEG8000, 5% MPD, 0.5 mM LuCl3, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 mg/mlprotein1drop
215 mMTris1droppH7.4
3120 mM1dropKCl
46 mMdithiothreitol1drop
50.2 mMEDTA1drop
63 mMNAD+1drop
7100 mMHEPES1reservoirpH7.0
86 %PEG80001reservoir
95 %MPD1reservoir
1010 mMtartronate1reservoir
110.5 mM1reservoirLuCl3
125 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 122000 / Num. obs: 105876 / % possible obs: 0.82 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.053
Reflection
*PLUS
Num. measured all: 306727

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.263 7500 random
Rwork0.204 --
all0.204 122000 -
obs0.204 100233 -
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34752 0 712 63 35527
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_d1.3
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 20 Å / Num. reflection all: 122000 / Num. reflection obs: 100233 / σ(F): 2 / Num. reflection Rfree: 7500 / % reflection Rfree: 7.5 % / Rfactor all: 0.204 / Rfactor obs: 0.204 / Rfactor Rfree: 0.263 / Rfactor Rwork: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.3

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