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- PDB-2npx: NADH BINDING SITE AND CATALYSIS OF NADH PEROXIDASE -

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Basic information

Entry
Database: PDB / ID: 2npx
TitleNADH BINDING SITE AND CATALYSIS OF NADH PEROXIDASE
ComponentsNADH PEROXIDASE
KeywordsOXIDOREDUCTASE(H2O2(A))
Function / homology
Function and homology information


NADH peroxidase / NADH peroxidase activity
Similarity search - Function
: / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD-linked reductase, C-terminal dimerisation domain / 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 ...: / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD-linked reductase, C-terminal dimerisation domain / 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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NADH peroxidase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsStehle, T. / Claiborne, A. / Schulz, G.E.
Citation
Journal: Eur.J.Biochem. / Year: 1993
Title: NADH binding site and catalysis of NADH peroxidase.
Authors: Stehle, T. / Claiborne, A. / Schulz, G.E.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: The Structure of Nadh Peroxidase from Streptococcus Faecalis 10C1 Refined at 2.16 Angstroms Resolution
Authors: Stehle, T. / Ahmed, S.A. / Claiborne, A. / Schulz, G.E.
#2: Journal: FEBS Lett. / Year: 1990
Title: The Structure of Nadh Peroxidase from Streptococcus Faecalis at 3.3 Angstroms Resolution
Authors: Stehle, T. / Ahmed, S.A. / Claiborne, A. / Schulz, G.E.
History
DepositionMay 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: Derived calculations / Version format compliance
Revision 2.0Jun 5, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _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: NADH PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1003
Polymers49,6511
Non-polymers1,4492
Water6,071337
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: NADH PEROXIDASE
hetero molecules

A: NADH PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,2006
Polymers99,3022
Non-polymers2,8984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area11480 Å2
ΔGint-58 kcal/mol
Surface area32220 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)77.200, 134.500, 145.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: RESIDUE CYS 42 IS A SULFONIC ACID (CYS42-SO3H).
Components on special symmetry positions
IDModelComponents
11A-842-

HOH

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Components

#1: Protein NADH PEROXIDASE


Mass: 49651.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / References: UniProt: P37062, NADH peroxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE STRUCTURE IS A COMPLEX BETWEEN NADH PEROXIDASE AND ITS SUBSTRATE NADH. THE ENZYME IS IN A NON- ...THE STRUCTURE IS A COMPLEX BETWEEN NADH PEROXIDASE AND ITS SUBSTRATE NADH. THE ENZYME IS IN A NON-NATIVE FORM IN WHICH THE CATALYTICALLY ACTIVE CYS 42 RESIDUE IS OXIDIZED TO A SULFONIC ACID (CYS42-SO3H). THIS IS REPRESENTED BY STORING THE ATOMS OF CYSTEINE AS CYS 42 AND THE THREE ADDITIONAL OXYGENS AS HET GROUP CYO AT THE END OF THE CHAIN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.82 Å3/Da / Density % sol: 67.78 %
Crystal grow
*PLUS
Temperature: 20-24 ℃ / pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
30.5 mMEDTA1drop
42 mMdithiothreitol1drop
60.5 mMEDTA1reservoir
72 mMdithiothreitol1reservoir
82.05 Mammonium sulfate1reservoir
90.005 mMFAD1reservoir
2potasssium phosphate1drop
5potassium phosphate1reservoir
103 mM1reservoirNaN3

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. obs: 27682 / % possible obs: 95.4 % / Rmerge(I) obs: 0.071

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.159 / Rfactor obs: 0.159 / Highest resolution: 2.4 Å
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3493 0 97 337 3927
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
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: 2.4 Å / Rfactor obs: 0.159
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3

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