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- PDB-1e7w: One active site, two modes of reduction correlate the mechanism o... -

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Basic information

Entry
Database: PDB / ID: 1e7w
TitleOne active site, two modes of reduction correlate the mechanism of leishmania pteridine reductase with pterin metabolism and antifolate drug resistance in trpanosomes
ComponentsPTERIDINE REDUCTASE
KeywordsOXIDOREDUCTASE / DIHYDROFOLATE REDUCTASE / PTERIDINE REDUCTASE / SHORTCHAIN DEHYDROGENASE / METHOTREXATE RESISTANCE
Function / homology
Function and homology information


pteridine reductase / 6,7-dihydropteridine reductase activity / pteridine reductase activity / tetrahydrobiopterin biosynthetic process / response to methotrexate / oxidoreductase activity / cytosol
Similarity search - Function
Pteridine reductase / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
METHOTREXATE / Chem-NDP / Pteridine reductase 1 / Pteridine reductase 1
Similarity search - Component
Biological speciesLEISHMANIA MAJOR (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsGourley, D.G. / Hunter, W.N.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Pteridine Reductase Mechanism Correlates Pterin Metabolism with Drug Resistance in Trypanosomatid Parasites.
Authors: Gourley, D.G. / Schuttelkopf, A. / Leonard, G. / Luba, J. / Hardy, L. / Beverley, S. / Hunter, W.N.
History
DepositionSep 11, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PTERIDINE REDUCTASE
B: PTERIDINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0329
Polymers61,4462
Non-polymers2,5867
Water8,575476
1
A: PTERIDINE REDUCTASE
B: PTERIDINE REDUCTASE
hetero molecules

A: PTERIDINE REDUCTASE
B: PTERIDINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,06318
Polymers122,8914
Non-polymers5,17214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)80.312, 80.800, 90.747
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.493, 0.87), (0.87, 0.493, -0.005), (-0.004, -0.002, -1)
Vector: 0.02054, 0.04453, 41.8347)
DetailsBIOMOLECULE

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Components

#1: Protein PTERIDINE REDUCTASE /


Mass: 30722.850 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / Strain: CC-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834
References: UniProt: Q9U1F8, UniProt: Q01782*PLUS, EC: 1.1.1.253
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-MTX / METHOTREXATE / Methotrexate


Mass: 454.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22N8O5 / Comment: chemotherapy*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 476 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsEXTRA GLY-SER-HIS SEQUENCE EXTENSION ON N-TERMINAL DISCREPANCIES WITH SEQUENCE IN DATA BASE AS ...EXTRA GLY-SER-HIS SEQUENCE EXTENSION ON N-TERMINAL DISCREPANCIES WITH SEQUENCE IN DATA BASE AS ERROR REVEALLED IN ORIGINAL SEQUENCE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growpH: 5.4 / Details: pH 5.40

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87, 0.886, 0.97950, 0.97960
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.871
20.8861
30.97951
40.97961
ReflectionResolution: 1.75→30 Å / Num. obs: 59475 / % possible obs: 98.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 25.7 Å2 / Rsym value: 0.45 / Net I/σ(I): 24.6

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Processing

SoftwareName: REFMAC / Classification: refinement
RefinementMethod to determine structure: MAD / Resolution: 1.75→30 Å / SU B: 2.827 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.127
RfactorNum. reflection% reflectionSelection details
Rfree0.244 3016 5 %RANDOM
Rwork0.196 ---
obs-56168 98.2 %-
Displacement parametersBiso mean: 32.5 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3917 0 174 476 4567
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0320.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.7992
X-RAY DIFFRACTIONp_mcangle_it3.5643
X-RAY DIFFRACTIONp_scbond_it3.2292
X-RAY DIFFRACTIONp_scangle_it4.3753
X-RAY DIFFRACTIONp_plane_restr0.0030.01
X-RAY DIFFRACTIONp_chiral_restr0.2220.15
X-RAY DIFFRACTIONp_singtor_nbd0.1820.3
X-RAY DIFFRACTIONp_multtor_nbd0.280.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1440.3
X-RAY DIFFRACTIONp_planar_tor2.6293
X-RAY DIFFRACTIONp_staggered_tor14.77615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor27.61520
X-RAY DIFFRACTIONp_special_tor

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