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- PDB-1gz3: Molecular mechanism for the regulation of human mitochondrial NAD... -

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Basic information

Entry
Database: PDB / ID: 1gz3
TitleMolecular mechanism for the regulation of human mitochondrial NAD(P)+-dependent malic enzyme by ATP and fumarate
ComponentsNAD-dependent malic enzyme, mitochondrial
KeywordsOXIDOREDUCTASE / ALLOSTERIC REGULATION / ENERGY METABOLISM / KINETICS
Function / homology
Function and homology information


malate dehydrogenase (oxaloacetate-decarboxylating) / malate dehydrogenase (decarboxylating) (NAD+) activity / regulation of NADP metabolic process / malate dehydrogenase (decarboxylating) (NADP+) activity / malic enzyme activity / oxaloacetate decarboxylase activity / Citric acid cycle (TCA cycle) / malate metabolic process / pyruvate metabolic process / NAD binding ...malate dehydrogenase (oxaloacetate-decarboxylating) / malate dehydrogenase (decarboxylating) (NAD+) activity / regulation of NADP metabolic process / malate dehydrogenase (decarboxylating) (NADP+) activity / malic enzyme activity / oxaloacetate decarboxylase activity / Citric acid cycle (TCA cycle) / malate metabolic process / pyruvate metabolic process / 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
ADENOSINE-5'-TRIPHOSPHATE / FUMARIC ACID / : / OXALATE ION / NAD-dependent malic enzyme, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYang, Z. / Lanks, C.W. / Tong, L.
CitationJournal: Structure / Year: 2002
Title: Molecular Mechanism for the Regulation of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme by ATP and Fumarate
Authors: Yang, Z. / Lanks, C.W. / Tong, L.
History
DepositionMay 14, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2003Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Sep 19, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_gen / entity_src_nat / struct_ref / struct_ref_seq_dif
Item: _citation.page_last / _entity.pdbx_description ..._citation.page_last / _entity.pdbx_description / _entity.src_method / _entity_name_com.name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,70620
Polymers248,6424
Non-polymers3,06516
Water20,8431157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22690 Å2
ΔGint-83.8 kcal/mol
Surface area76370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.815, 192.653, 110.161
Angle α, β, γ (deg.)90.00, 89.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 62160.414 Da / Num. of mol.: 4 / Fragment: RESIDUES 20-573 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ME2 / Organelle: MITOCHONDRION / Production host: Escherichia coli (E. coli)
References: UniProt: P23368, malate dehydrogenase (oxaloacetate-decarboxylating)

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Non-polymers , 5 types, 1173 molecules

#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2O4
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Chemical
ChemComp-FUM / FUMARIC ACID / Fumaric acid


Mass: 116.072 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H4O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1157 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 197 TO GLN ENGINEERED RESIDUE IN CHAIN A, ARG 542 TO VAL ...ENGINEERED RESIDUE IN CHAIN A, ARG 197 TO GLN ENGINEERED RESIDUE IN CHAIN A, ARG 542 TO VAL ENGINEERED RESIDUE IN CHAIN A, ARG 556 TO GLN ENGINEERED RESIDUE IN CHAIN B, ARG 197 TO GLN ENGINEERED RESIDUE IN CHAIN B, ARG 542 TO VAL ENGINEERED RESIDUE IN CHAIN B, ARG 556 TO GLN ENGINEERED RESIDUE IN CHAIN C, ARG 197 TO GLN ENGINEERED RESIDUE IN CHAIN C, ARG 542 TO VAL ENGINEERED RESIDUE IN CHAIN C, ARG 556 TO GLN ENGINEERED RESIDUE IN CHAIN D, ARG 197 TO GLN ENGINEERED RESIDUE IN CHAIN D, ARG 542 TO VAL ENGINEERED RESIDUE IN CHAIN D, ARG 556 TO GLN

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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: 3.06 Å3/Da / Density % sol: 59.87 %
Crystal growpH: 6 / Details: 9% PEG20K, PH 5.5 NA CITRATE, 5% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.979
DetectorDate: Feb 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 250429 / % possible obs: 91 % / Redundancy: 2.1 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.087 / Mean I/σ(I) obs: 11 / % possible all: 78

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DO8_D

Resolution: 2.3→20 Å / Rfactor Rfree error: 0.002 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.233 8984 7.5 %RANDOM
Rwork0.194 ---
obs0.194 119325 91 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.1 Å2 / ksol: 0.442 e/Å3
Displacement parametersBiso mean: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.61 Å20 Å2-0.74 Å2
2---6.14 Å20 Å2
3---1.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17477 0 184 1157 18818
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.3→2.32 Å / Rfactor Rfree error: 0.2 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.255 156 8.1 %
Rwork0.213 1762 -
obs--72.4 %

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