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- PDB-1dig: HUMAN METHYLENETETRAHYDROFOLATE DEHYDROGENASE / CYCLOHYDROLASE CO... -

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Basic information

Entry
Database: PDB / ID: 1dig
TitleHUMAN METHYLENETETRAHYDROFOLATE DEHYDROGENASE / CYCLOHYDROLASE COMPLEXED WITH NADP AND INHIBITOR LY374571
ComponentsMETHYLENETETRAHYDROFOLATE DEHYDROGENASE / CYCLOHYDROLASE
KeywordsOXIDOREDUCTASE / HYDROLASE / TETRAHYDROFOLATE / DEHYDROGENASE / CYCLOHYDROLASE / NADP / INHIBITOR / ROSSMANN FOLD
Function / homology
Function and homology information


methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity / serine family amino acid biosynthetic process / 10-formyltetrahydrofolate biosynthetic process / serine family amino acid metabolic process / embryonic neurocranium morphogenesis / methylenetetrahydrofolate dehydrogenase (NAD+) activity / formate-tetrahydrofolate ligase activity / formate-tetrahydrofolate ligase / embryonic viscerocranium morphogenesis / methylenetetrahydrofolate dehydrogenase (NADP+) ...methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity / serine family amino acid biosynthetic process / 10-formyltetrahydrofolate biosynthetic process / serine family amino acid metabolic process / embryonic neurocranium morphogenesis / methylenetetrahydrofolate dehydrogenase (NAD+) activity / formate-tetrahydrofolate ligase activity / formate-tetrahydrofolate ligase / embryonic viscerocranium morphogenesis / methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase / methenyltetrahydrofolate cyclohydrolase activity / methylenetetrahydrofolate dehydrogenase (NADP+) activity / methionine metabolic process / somite development / Metabolism of folate and pterines / methionine biosynthetic process / purine nucleotide biosynthetic process / histidine biosynthetic process / tetrahydrofolate interconversion / neural tube closure / one-carbon metabolic process / heart development / mitochondrion / extracellular exosome / membrane / ATP binding / cytosol
Similarity search - Function
Formate--tetrahydrofolate ligase signature 1. / Formate--tetrahydrofolate ligase / Formate-tetrahydrofolate ligase, FTHFS, conserved site / Formate-tetrahydrofolate ligase, FTHFS / Formate--tetrahydrofolate ligase signature 2. / Tetrahydrofolate dehydrogenase/cyclohydrolase signature 1. / Tetrahydrofolate dehydrogenase/cyclohydrolase signature 2. / Tetrahydrofolate dehydrogenase/cyclohydrolase, conserved site / Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain ...Formate--tetrahydrofolate ligase signature 1. / Formate--tetrahydrofolate ligase / Formate-tetrahydrofolate ligase, FTHFS, conserved site / Formate-tetrahydrofolate ligase, FTHFS / Formate--tetrahydrofolate ligase signature 2. / Tetrahydrofolate dehydrogenase/cyclohydrolase signature 1. / Tetrahydrofolate dehydrogenase/cyclohydrolase signature 2. / Tetrahydrofolate dehydrogenase/cyclohydrolase, conserved site / Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain / Tetrahydrofolate dehydrogenase/cyclohydrolase / Leucine Dehydrogenase, chain A, domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-L37 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / C-1-tetrahydrofolate synthase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsSchmidt, A. / Wu, H. / MacKenzie, R.E. / Chen, V.J. / Bewly, J.R. / Ray, J.E. / Toth, J.E. / Cygler, M.
Citation
Journal: Biochemistry / Year: 2000
Title: Structures of three inhibitor complexes provide insight into the reaction mechanism of the human methylenetetrahydrofolate dehydrogenase/cyclohydrolase.
Authors: Schmidt, A. / Wu, H. / MacKenzie, R.E. / Chen, V.J. / Bewly, J.R. / Ray, J.E. / Toth, J.E. / Cygler, M.
#1: Journal: Structure / Year: 1998
Title: The 3-D Structure of a Folate-Dependent Dehydrogenase/Cyclohydrolase Bifunctional Enzyme at 1.5 A Resolution
Authors: Allaire, M. / Li, Y. / MacKenzie, R.E. / Cygler, M.
History
DepositionNov 29, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / Item: _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METHYLENETETRAHYDROFOLATE DEHYDROGENASE / CYCLOHYDROLASE
B: METHYLENETETRAHYDROFOLATE DEHYDROGENASE / CYCLOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6566
Polymers66,6772
Non-polymers1,9794
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-19 kcal/mol
Surface area24120 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)67.889, 136.419, 61.579
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsDC301 forms dimers, the two monomers (chains A and B) being related by a noncrystallographic twofold axis in the crystal structure.

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Components

#1: Protein METHYLENETETRAHYDROFOLATE DEHYDROGENASE / CYCLOHYDROLASE / DC301


Mass: 33338.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P11586, methylenetetrahydrofolate dehydrogenase (NADP+), methenyltetrahydrofolate cyclohydrolase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-L37 / [[N'-(2,5-DIAMINO-6-HYDROXY-PYRIMIDIN-4-YL)-UREAYL]-PHEN-4-YL]-CARBONYL-GLUTAMIC ACID / LY374571


Mass: 433.375 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N7O7
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.14 Å3/Da / Density % sol: 42.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: PEG 3350, GLYCEROL, SODIUM CITRATE, AMMONIUM ACETATE, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
Method: vapor diffusion / Details: protein/inhibitor ratio is 1:10
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 %(w/v)PEG33501reservoir
20.2 Mammonium acetate1reservoir
35 %glycerol1reservoir
40.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 30, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. all: 29810 / Num. obs: 29810 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 7
Reflection shellResolution: 2.2→2.23 Å / Redundancy: 5 % / Rmerge(I) obs: 0.147 / % possible all: 98.2
Reflection
*PLUS
Num. obs: 29628 / Redundancy: 5 % / Num. measured all: 238477
Reflection shell
*PLUS
% possible obs: 98.2 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.2→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: BULK SOLVENT CORRECTION APPLIED
RfactorNum. reflection% reflectionSelection details
Rfree0.267 2900 -RANDOM
Rwork0.226 ---
obs0.226 29650 99.8 %-
all-29650 --
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4402 0 131 218 4751
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 26225
Solvent computation
*PLUS
Displacement parameters
*PLUS

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