Effect of mutation at valine 61 on the three-dimensional structure, stability, and redox potential of cytochrome b5.


Abstract

To elucidate the role played by Val61 of cytochrome b(5), this residue of the tryptic fragment of bovine liver cytochrome b(5) was chosen for replacement with tyrosine (Val61Tyr), histidine (Val61His), glutamic acid (Val61Glu), and lysine (Val61Lys) by means of site-directed mutagenesis. The mutants Val61Tyr, Val61Glu, Val61His, and Val61Lys exhibit electronic spectra identical to that of the wild type, suggesting that mutation at Val61 did not affect the overall protein structure significantly. The redox potentials determined by differential pulse voltammetry were -10 (wild type), -25 (Val61Glu), -33 (Val61Tyr), 12 (Val61His), and 17 mV (Val61Lys) versus NHE. The thermal stabilities and urea-mediated denaturation of wild-type cytochrome b(5) and its mutants were in the following order: wild type > Val61Glu > Val61Tyr > Val61His > Val61Lys. The kinetics of denaturation of cytochrome b(5) by urea was also analyzed. The first-order rate constants of heme transfer between cytochrome b(5) and apomyoglobin at 20 +/- 0.2 degrees C were 0.25 +/- 0.01 (wild type), 0.42 +/- 0.02 (Val61Tyr), 0.93 +/- 0.04 (Val61Glu), 2.88 +/- 0.01 (Val61His), and 3.88 +/- 0.02 h(-)(1) (Val61Lys). The crystal structure of Val61His was determined using the molecular replacement method and refined at 2.1 A resolution, showing that the imidazole side chain of His61 points away from the heme-binding pocket and extends into the solvent, the coordination distances from Fe to NE2 atoms of two axial ligands are approximately 0.6 A longer than the reported value, and the hydrogen bond network involving Val61, the heme propionates, and three water molecules no longer exists. We conclude that the conserved residue Val61 is located at one of the key positions, the "electrostatic potential" around the heme-exposed area and the hydrophobicity of the heme pocket are determinant factors modulating the redox potential of cytochrome b(5), and the hydrogen bond network around the exposed heme edge is also an important factor affecting the heme stability. Study holds ProTherm entries: 6554, 6555, 6556, 6557, 6558, 6560, 6561, 6562, 6563, 14323, 14324, 14325, 14326 Extra Details: electronic spectra; protein structur; first-order rate constant;,heme-binding pocket; electrostatic potential; hydrophobicity

Submission Details

ID: vbnLMZb5

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:32 p.m.

Version: 1

Publication Details
Xue LL;Wang YH;Xie Y;Yao P;Wang WH;Qian W;Huang ZX;Wu J;Xia ZX,Biochemistry (1999) Effect of mutation at valine 61 on the three-dimensional structure, stability, and redox potential of cytochrome b5. PMID:10508399
Additional Information

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
2M33 2013-02-06 Solution NMR structure of full-length oxidized microsomal rabbit cytochrome b5
1B5B 1998-06-17 RAT FERROCYTOCHROME B5 B CONFORMATION, NMR, 1 STRUCTURE
1I5U 2001-03-21 SOLUTION STRUCTURE OF CYTOCHROME B5 TRIPLE MUTANT (E48A/E56A/D60A)
1AQA 1997-09-17 SOLUTION STRUCTURE OF REDUCED MICROSOMAL RAT CYTOCHROME B5, NMR, MINIMIZED AVERAGE STRUCTURE
1IET 1997-04-21 APOCYTOCHROME B5, PH 6.2, 298 K, NMR, MINIMIZED AVERAGE STRUCTURE
1DO9 2000-01-05 SOLUTION STRUCTURE OF OXIDIZED MICROSOMAL RABBIT CYTOCHROME B5. FACTORS DETERMINING THE HETEROGENEOUS BINDING OF THE HEME.
1SH4 2004-08-10 Solution structure of oxidized bovine microsomal cytochrome B5 Mutant V45H
2AXX 1998-03-04 THE SOLUTION STRUCTURE OF OXIDIZED RAT MICROSOMAL CYTOCHROME B5, NMR, 21 STRUCTURES
5XE4 2018-02-14 NMR solution structure of the aromatic mutant H43W H67F cytochrome b5
1IEU 1997-04-21 APOCYTOCHROME B5, PH 6.2, 298 K, NMR, 10 STRUCTURES
1MNY 2002-11-13 Dimethyl propionate ester heme-containing cytochrome b5
1BLV 1998-07-29 SOLUTION STRUCTURE OF OXIDIZED RAT MICROSOMAL CYTOCHROME B5 IN THE PRESENCE OF 2 M GUANIDINIUM CHLORIDE: MONITORING THE EARLY STEPS IN PROTEIN UNFOLDING
1AW3 1998-02-04 THE SOLUTION NMR STRUCTURE OF OXIDIZED RAT MICROSOMAL CYTOCHROME B5, MINIMIZED AVERAGE STRUCTURE
1JEX 2001-07-11 SOLUTION STRUCTURE OF A67V MUTANT OF RAT FERRO CYTOCHROME B5
2I96 2007-09-04 Solution structure of the oxidized microsomal human cytochrome b5
1BFX 1998-08-12 THE SOLUTION NMR STRUCTURE OF THE B FORM OF OXIDIZED RAT MICROSOMAL CYTOCHROME B5, MINIMIZED AVERAGE STRUCTURE
1F04 2000-06-21 SOLUTION STRUCTURE OF OXIDIZED BOVINE MICROSOMAL CYTOCHROME B5 MUTANT (E44A, E48A, E56A, D60A) AND ITS INTERACTION WITH CYTOCHROME C
5XEE 2018-02-14 NMR solution structure of the aromatic mutant H43F H67F cytochrome b5
1J0Q 2003-08-12 Solution Structure of Oxidized Bovine Microsomal Cytochrome b5 mutant V61H
1F03 2000-06-21 SOLUTION STRUCTURE OF OXIDIZED BOVINE MICROSOMAL CYTOCHROME B5 MUTANT (E44A, E48A, E56A, D60A) AND ITS INTERACTION WITH CYTOCHROME C
1B5A 1998-06-17 RAT FERROCYTOCHROME B5 A CONFORMATION, NMR, 1 STRUCTURE
1I87 2001-05-16 SOLUTION STRUCTURE OF THE WATER-SOLUBLE FRAGMENT OF RAT HEPATIC APOCYTOCHROME B5
1NX7 2004-06-15 Solution Structure of Oxidized Bovine Microsomal Cytochrome B5
1IB7 2001-04-04 SOLUTION STRUCTURE OF F35Y MUTANT OF RAT FERRO CYTOCHROME B5, A CONFORMATION, ENSEMBLE OF 20 STRUCTURES
1HKO 2003-03-18 NMR structure of bovine cytochrome b5
1I8C 2001-05-16 SOLUTION STRUCTURE OF THE WATER-SOLUBLE FRAGMENT OF RAT HEPATIC APOCYTOCHROME B5
1AXX 1998-03-04 THE SOLUTION STRUCTURE OF OXIDIZED RAT MICROSOMAL CYTOCHROME B5, NMR, 19 STRUCTURES
3X34 2015-07-15 0.76 Crystal structure of the reduced form of the solubilized domain of porcine cytochrome b5 in form 1 crystal
3X32 2015-07-15 0.83 Crystal structure of the oxidized form of the solubilized domain of porcine cytochrome b5 in form 1 crystal
3X33 2015-07-15 0.93 Crystal structure of the oxidized form of the solubilized domain of porcine cytochrome b5 in form 2 crystal
3X35 2015-07-15 0.95 Crystal structure of the reduced form of the solubilized domain of porcine cytochrome b5 in form 2 crystal
1CYO 1994-11-30 1.5 BOVINE CYTOCHROME B(5)
3OZZ 2011-09-14 1.7 Structure of a cytochrome b5 core-swap mutant
1LQX 2002-09-04 1.8 Crystal structure of V45E mutant of cytochrome b5
1M2I 2003-03-18 1.8 Crystal structure of E44A/E56A mutant of cytochrome b5
1M2M 2003-03-18 1.8 Crystal structure of E44A/E48A/E56A/D60A mutant of cytochrome b5
1M20 2002-09-11 1.8 Crystal Structure of F35Y Mutant of Trypsin-solubilized Fragment of Cytochrome b5
1U9U 2005-02-01 1.86 Crystal structure of F58Y mutant of cytochrome b5
1LR6 2002-09-04 1.9 Crystal structure of V45Y mutant of cytochrome b5
1M59 2003-03-18 1.9 Crystal Structure of P40V Mutant of Trypsin-solubilized Fragment of Cytochrome b5
1EHB 2000-08-09 1.9 CRYSTAL STRUCTURE OF RECOMBINANT TRYPSIN-SOLUBILIZED FRAGMENT OF CYTOCHROME B5
1U9M 2005-02-01 2.0 Crystal structure of F58W mutant of cytochrome b5
1ES1 2000-08-09 2.1 CRYSTAL STRUCTURE OF VAL61HIS MUTANT OF TRYPSIN-SOLUBILIZED FRAGMENT OF CYTOCHROME B5
4HIN 2013-10-16 2.4 2.4A Resolution Structure of Bovine Cytochrome b5 (S71L)

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
92.9 Cytochrome b5 P00168 CYB5_ALOSE
90.2 Cytochrome b5 P56395 CYB5_MOUSE
91.3 Cytochrome b5 P00173 CYB5_RAT
90.2 Cytochrome b5 P00167 CYB5_HUMAN
91.3 Cytochrome b5 P00169 CYB5_RABIT
91.3 Cytochrome b5 P00170 CYB5_HORSE
96.7 Cytochrome b5 P00172 CYB5_PIG
100.0 Cytochrome b5 P00171 CYB5_BOVIN