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- PDB-1bes: INTERACTION BETWEEN PROXIMAL AND DISTALS REGIONS OF CYTOCHROME C ... -

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Entry
Database: PDB / ID: 1bes
TitleINTERACTION BETWEEN PROXIMAL AND DISTALS REGIONS OF CYTOCHROME C PEROXIDASE
ComponentsCYTOCHROME C PEROXIDASE
KeywordsPEROXIDASE / OXIDOREDUCTASE
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 Å
AuthorsMiller, M.A. / Kraut, J.
Citation
Journal: To be Published
Title: Interaction between Proximal and Distals Regions of Cytochrome C Peroxidase
Authors: Miller, M.A. / Han, G.W. / Kraut, J.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: A Ligand-Gated, Hinged Loop Rearrangement Opens a Channel to a Buried Artificial Protein Cavity
Authors: Fitzgerald, M.M. / Musah, R.A. / Mcree, D.E. / Goodin, D.B.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: A Cation Binding Motif Stabilizes the Compound I Radical of Cytochrome C Peroxidase
Authors: Miller, M.A. / Han, G.W. / Kraut, J.
#3: 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.M. / Mauro, M. / Edwards, S.L. / Oatley, S.J. / Fishel, L.A. / Ashford, V.A. / Xuong, N.H. / Kraut, J.
#4: Journal: Biochemistry / Year: 1987
Title: Yeast Cytochrome C Peroxidase: Mutagenesis and Expression in Escherichia Coli Show Tryptophan-51 is not the Radical Site in Compound I
Authors: Fishel, L.A. / Villafranca, J.E. / Mauro, J.M. / Kraut, J.
#5: Journal: J.Biol.Chem. / Year: 1984
Title: Crystal Structure of Yeast Cytochrome C Peroxidase Refined at 1.7-A Resolution
Authors: Finzel, B.C. / Poulos, T.L. / Kraut, J.
History
DepositionMay 16, 1998Processing site: BNL
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: CYTOCHROME C PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0514
Polymers33,2041
Non-polymers8473
Water3,045169
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.295, 74.256, 45.107
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: 33203.887 Da / Num. of mol.: 1 / Mutation: MET ILE ADDED AT N-TERMINUS, W191Y
Source method: isolated from a genetically manipulated source
Details: FE(III)-CL COMPLEX, WITH A MES (+) ZWITTERION BOUND IN THE PROXIMAL REGION
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PUC8 / Production host: Escherichia coli (E. coli) / References: UniProt: P00431, cytochrome-c peroxidase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE MUTATION INFLUENCES THE COORDINATION STATE OF THE ENZYME. THE BINDING OF MES FROM BUFFER TENDS ...THE MUTATION INFLUENCES THE COORDINATION STATE OF THE ENZYME. THE BINDING OF MES FROM BUFFER TENDS TO PROMOTE ANION BINDING AT THE IRON. THE INCREASED AFFINITY FOR ANIONS CAUSES CL TO BIND AT IRON, CREATING A 6C-HS FERRIC HEME. THE TRP 191 TO TYR SUBSTITUTION CREATES AN UNSTABLE CONFORMATION OF THE 191 LOOP. THE ORIENTATION OF TYR 191 CAN ALLOW K+ BINDING IN KPO4 BUFFER. IN MES BUFFER (THIS STRUCTURE), THE 191 LOOP ROTATES TOWARD THE MOLECULAR SURFACE, AND A MES MOLECULE TO BIND TO THE RESULTING CAVITY.
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 PACKING. 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 54 %
Crystal growpH: 6 / Details: 30% MPD, 20 MM TRIS/MES PH 6.0, 150 MM NACL

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceWavelength: 1.5418
DetectorDate: Nov 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2 Å / Num. obs: 21914 / % possible obs: 90 % / Rsym value: 0.065

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Processing

SoftwareName: TNT / Version: 1 / Classification: refinement
RefinementResolution: 2→20 Å / Isotropic thermal model: TNT BCORREL.DAT / σ(F): 2 / Stereochemistry target values: TNT PROTGEO
Details: RESTRAINTS WERE RELAXED FOR PLANARITY OF THE BACKBONE UNITS FOR RESIDUES 191-195, OTHERWISE THE DENSITY COULD NOT BE MODELLED PROPERLY. THE PLANARITY OF THE PEPTIDE BOND WAS RELAXED FOR ...Details: RESTRAINTS WERE RELAXED FOR PLANARITY OF THE BACKBONE UNITS FOR RESIDUES 191-195, OTHERWISE THE DENSITY COULD NOT BE MODELLED PROPERLY. THE PLANARITY OF THE PEPTIDE BOND WAS RELAXED FOR RESIDUES 190-194 BECAUSE IT WAS THE ONLY WAY THE MODEL COULD BE FITTED INTO THE DENSITY. THE DENSITY WAS CONTINUOUS THROUGH THIS REGION, AND SO THE AUTHORS CHOSE TO MODEL INTO THE DENSITY RATHER THAN TO PRESERVE THE REQUIREMENT FOR PLANARITY OF OMEGA. COORDINATES FOR RESIDUES -1, 0, AND 1 - 3 ARE NOT INCLUDED IN THIS ENTRY BECAUSE THESE RESIDUES COULD NOT BE RESOLVED IN THE FINAL ELECTRON DENSITY MAPS. WATER MOLECULES WITH B-FACTORS GREATER THAN 80 WERE NOT INCLUDED IN THE MODEL.
Num. reflection% reflection
obs21970 90 %
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2324 0 56 169 2549
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.009
X-RAY DIFFRACTIONt_angle_deg2.317
X-RAY DIFFRACTIONt_dihedral_angle_d17.46
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.009
X-RAY DIFFRACTIONt_gen_planes0.007
X-RAY DIFFRACTIONt_it4.36
X-RAY DIFFRACTIONt_nbd0.021

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