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- PDB-1typ: SUBSTRATE INTERACTIONS BETWEEN TRYPANOTHIONE REDUCTASE AND N1-GLU... -

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Basic information

Entry
Database: PDB / ID: 1typ
TitleSUBSTRATE INTERACTIONS BETWEEN TRYPANOTHIONE REDUCTASE AND N1-GLUTATHIONYLSPERMIDINE DISULPHIDE AT 0.28-NM RESOLUTION
ComponentsTRYPANOTHIONE REDUCTASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


trypanothione-disulfide reductase / trypanothione-disulfide reductase (NADPH) activity / glutathione-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / cytosol
Similarity search - Function
Trypanothione reductase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain ...Trypanothione reductase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / GLUTATHIONE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / SPERMIDINE / Trypanothione reductase
Similarity search - Component
Biological speciesCrithidia fasciculata (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsBailey, S. / Hunter, W.N.
Citation
Journal: Eur.J.Biochem. / Year: 1993
Title: Substrate interactions between trypanothione reductase and N1-glutathionylspermidine disulphide at 0.28-nm resolution.
Authors: Bailey, S. / Smith, K. / Fairlamb, A.H. / Hunter, W.N.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Active Site of Trypanothione Reductase: A Target for Rational Drug Design
Authors: Hunter, W.N. / Bailey, S. / Habash, J. / Harrop, S.J. / Helliwell, J.R. / Abogye-Kwarteng, T. / Smith, K. / Fairlamb, A.H.
#2: Journal: Science / Year: 1992
Title: Crystal Structures of Two Viral Peptides in Complex with Murine Mhc Class I H-2KB
Authors: Fremont, D.H. / Matsumura, M. / Stura, E.A. / Peterson, P.A. / Wilson, I.A.
#3: Journal: J.Mol.Biol. / Year: 1990
Title: Initiating a Crystallographic Study of Trypanothione Reductase
Authors: Hunter, W.N. / Smith, K. / Derewenda, Z. / Harrop, S.J. / Habash, J. / Islam, M.S. / Helliwell, J.R. / Fairlamb, A.H.
#4: Journal: Nature / Year: 1984
Title: A Large Increase in Enzyme-Substrate Affinity by Protein Engineering
Authors: Wilkinson, A.J. / Fersht, A.R. / Blow, D.M. / Carter, P. / Winter, G.
History
DepositionJun 29, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_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_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: TRYPANOTHIONE REDUCTASE
B: TRYPANOTHIONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,67214
Polymers105,8042
Non-polymers4,86812
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16290 Å2
ΔGint-92 kcal/mol
Surface area33850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.800, 128.800, 92.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Atom site foot note1: CIS PROLINE - PRO A 43 / 2: CIS PROLINE - PRO A 370 / 3: CIS PROLINE - PRO A 462 / 4: CIS PROLINE - PRO B 43 / 5: CIS PROLINE - PRO B 370 / 6: CIS PROLINE - PRO B 462

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein TRYPANOTHIONE REDUCTASE


Mass: 52901.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crithidia fasciculata (eukaryote) / References: UniProt: P39040, EC: 1.6.4.8

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Non-polymers , 5 types, 412 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#5: Chemical
ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H19N3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsN1-GLUTATHIONYLSPERMIDINE IS REPRESENTED BY GLUTATHIONE AND SPERMIDINE ON THE HETATM RECORDS BELOW.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.62 Å3/Da / Density % sol: 66.07 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118 mg/mlenzyme solution1drop
20.1 Mpotasssium phosphate1drop
350 %(w/v)ammonium sulfate1drop
480 %satammonium sulphate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 8.85 Å / Num. obs: 35848 / % possible obs: 70 % / Rmerge(I) obs: 0.096
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.95 Å / % possible obs: 36.9 % / Num. possible: 5076 / Rmerge(I) obs: 0.24

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.8→8 Å / σ(F): 1
Details: REFERENCE 1 DESCRIBES THE STRUCTURE SOLUTION BY MOLECULAR REPLACEMENT AND PARTIAL REFINEMENT TO ALLOW DETAILS OF THE ACTIVE SITE TO BE PRESENTED.
RfactorNum. reflection
Rwork0.148 -
obs0.148 32393
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7418 0 318 400 8136
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 8 Å / Num. reflection obs: 32393 / σ(F): 1 / Rfactor obs: 0.148
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.3

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