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- PDB-1cyf: IDENTIFYING THE PHYSIOLOGICAL ELECTRON TRANSFER SITE OF CYTOCHROM... -

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Entry
Database: PDB / ID: 1cyf
TitleIDENTIFYING THE PHYSIOLOGICAL ELECTRON TRANSFER SITE OF CYTOCHROME C PEROXIDASE BY STRUCTURE-BASED ENGINEERING
ComponentsCYTOCHROME C PEROXIDASE
KeywordsOXIDOREDUCTASE (H2O2(A))
Function / homology
Function and homology information


cytochrome-c peroxidase / cytochrome-c peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / mitochondrial intermembrane space / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Class I peroxidase / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. ...Class I peroxidase / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.35 Å
AuthorsMiller, M.A. / Han, G.W. / Kraut, J.
Citation
Journal: Biochemistry / Year: 1996
Title: Identifying the physiological electron transfer site of cytochrome c peroxidase by structure-based engineering.
Authors: Miller, M.A. / Geren, L. / Han, G.W. / Saunders, A. / Beasley, J. / Pielak, G.J. / Durham, B. / Millett, F. / Kraut, J.
#1: Journal: Biochemistry / Year: 1990
Title: X-Ray Structures of Recombinant Yeast Cytochrome C Peroxidase and Three Heme-Cleft Mutants Prepared by Site-Directed Mutagenesis
Authors: Wang, J. / Mauro, J.M. / Edwards, S.L. / Oatley, S.J. / Fishel, L.A. / Ashford, V.A. / Xuong, N.-H. / Kraut, J.
#2: Journal: J.Biol.Chem. / Year: 1984
Title: Crystal Structure of Yeast Cytochrome C Peroxidase Refined at 1.7 Angstroms Resolution
Authors: Finzel, B.C. / Poulos, T.L. / Kraut, J.
History
DepositionJul 3, 1995Processing site: BNL
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME C PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3862
Polymers33,7701
Non-polymers6161
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.330, 73.880, 45.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYTOCHROME C PEROXIDASE


Mass: 33769.605 Da / Num. of mol.: 1 / Mutation: INS(MET ILE AT N-TERMINUS), C128A, A193C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P00431, cytochrome-c peroxidase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE SIDE CHAIN AT CYS 193 IS DISORDERED, AND NO INTERPRETABLE DENSITY WAS FOUND BEYOND SG OF CYS ...THE SIDE CHAIN AT CYS 193 IS DISORDERED, AND NO INTERPRETABLE DENSITY WAS FOUND BEYOND SG OF CYS 193. HOWEVER, THE PRESENCE OF THE SIDE CHAIN WAS CONFIRMED UNAMBIGUOUSLY USING ELECTROSPRAY MASS SPECTROSCOPY.
Sequence detailsTHIS CYTOCHROME C PEROXIDASE DIFFERS FROM A PREVIOUSLY DEPOSITED STRUCTURE (PROTEIN DATA BANK ENTRY ...THIS CYTOCHROME C PEROXIDASE DIFFERS FROM A PREVIOUSLY DEPOSITED STRUCTURE (PROTEIN DATA BANK ENTRY 2CYP) BY TWO STRAIN-RELATED SEQUENCE DIFFERENCES - THR 53 TO ILE AND ASP 152 TO GLY, AND THE ADDITION OF MET-ILE AT THE N-TERMINUS, HENCE CCP(MI). THE OVERALL STRUCTURE IS THE SAME AS THE PREVIOUSLY DEPOSITED ONE BUT IN A DIFFERENT SPACE GROUP. THE SEQUENCE DIFFERS FROM THAT REPORTED FOR 2CYP AT RESIDUE 272. IN THE PRESENT ENTRY, THIS RESIDUE IS REPORTED AS ASN. THIS CORRECTS AN ERROR INTRODUCED IN 2CYP, WHERE THE RESIDUE IS INCORRECTLY REPORTED TO BE ASP. RESIDUES ARE NUMBERED TO BE CONSISTENT WITH THE SEQUENCE OF THE NATIVE (2CYP) STRUCTURE. THUS THE FIRST TWO RESIDUES HAVE RESIDUE NUMBERS -1 AND 0, RESPECTIVELY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal grow
*PLUS
Method: unknown

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.35→20 Å / Isotropic thermal model: 0 / σ(F): 0
Stereochemistry target values: D.E. TRONRUD ET AL., ACTA CRYST. A43, 489 (1987)
Details: THE ADDITION OF A BULKY GROUP AT POSITION 193 MAKES IT IMPOSSIBLE FOR THE ENZYME TO CRYSTALLIZE IN A FORM THAT IS ISOMORPHOUS WITH THE CCP(MI) PARENT. THIS IS BECAUSE CB OF ALA 193 IN THE ...Details: THE ADDITION OF A BULKY GROUP AT POSITION 193 MAKES IT IMPOSSIBLE FOR THE ENZYME TO CRYSTALLIZE IN A FORM THAT IS ISOMORPHOUS WITH THE CCP(MI) PARENT. THIS IS BECAUSE CB OF ALA 193 IN THE PARENT MAKES A CRYSTAL CONTACT WITH THE SIDE CHAIN OF THR 275. THE MUTANT ENZYME ADOPTS A NEW CRYSTAL PACKING THAT ALLOWS RESIDUE 193 TO PROJECT INTO AN OTHERWISE UNOCCUPIED AREA. THE MODEL WAS CREATED INITIALLY USING MOLECULAR REPLACEMENT WITH THE CCP(MI) PARENT AS THE SEARCH MODEL. TRANSLATION FUNCTIONS WERE CALCULATED BY SAMPLING A TRANSLATION VECTOR ON A 1 ANGSTROM GRID, UTILIZING DATA BETWEEN 8 AND 4 ANGSTROM RESOLUTION. THE TRANSLATION VECTOR WAS FURTHER REFINED BY AN R-FACTOR MINIMIZATION PROCEDURE WITH STEPS OF 0.1 ANGSTROM, RESULTING IN AN R-FACTOR OF 0.283 FOR DATA TO 4 ANGSTROMS RESOLUTION. UNLIKE THE CCP(MI) PARENT, COORDINATES FOR RESIDUES -1, 0, AND 1 - 3 ARE INCLUDED IN THIS ENTRY BECAUSE THESE RESIDUES COULD BE RESOLVED IN THE FINAL ELECTRON DENSITY MAPS. WATER MOLECULES WITH B-FACTORS GREATER THAN 80. WERE NOT INCLUDED.
RfactorNum. reflection% reflection
obs0.166 12243 84 %
Solvent computationSolvent model: MOEW & KRETSINGER, JMB 91, 211-228 (1975) / Bsol: 91.17 Å2 / ksol: 0.67 e/Å3
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2410 0 83 145 2638
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0124801
X-RAY DIFFRACTIONt_angle_deg2.933421.35
X-RAY DIFFRACTIONt_dihedral_angle_d16.614070
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.02751
X-RAY DIFFRACTIONt_gen_planes0.00635410
X-RAY DIFFRACTIONt_it3.8924800.04
X-RAY DIFFRACTIONt_nbd0.0236710

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