The adaptability of Escherichia coli thioredoxin to non-conservative amino acid substitutions.
Abstract
The adaptability of Escherichia coli thioredoxin to the substitution of a series of non-natural amino acids has been investigated. Different thiosulfonated alkyl groups were inserted into the hydrophobic core of the protein in position 78 via disulfide bonding with a buried cysteine residue as previously described (Wynn R, Richards FM. 1993. Unnatural amino acid packing mutants of Escherichia coli thioredoxin produced by combined mutagenesis/chemical modification techniques. Protein Sci 2:395-403). The side chains added to the cysteine included methyl, ethyl, n-propyl, n-butyl, n-pentyl, and cyclo-pentyl derivatives. The side chains appear to exploit the presence of the large cavities to incorporate these variant forms, enabling the protein to fold and have some activity. Solution structural and kinetic data suggested that these substitutions had little effect on the overall fold of the protein. Thermodynamic data revealed that the entropic effect of restricting the side chains in the folded protein has an effect on the stability. The variant forms of thioredoxin have different propensities to form dimers despite the limited structural perturbations. Molecular modeling studies allow the conformation of the side chains to be assessed. Study holds ProTherm entries: 9392, 9393, 9394, 9395, 9396, 9397, 9398, 9399, 9400, 9401, 9402, 9403, 9404, 9405, 9406, 9407, 9408, 9409, 9410, 9411, 9412 Extra Details: calorimetry; cysteine modification; differential scanning; kinetics; protein folding; thermodynamics: thioredoxin; unnatural amino acids
Submission Details
ID: kHz5G3mZ3
Submitter: Connie Wang
Submission Date: April 24, 2018, 8:38 p.m.
Version: 1
Publication Details
O'Brien R;Wynn R;Driscoll PC;Davis B;Plaxco KW;Sturtevant JM;Ladbury JE,Protein Sci. (1997) The adaptability of Escherichia coli thioredoxin to non-conservative amino acid substitutions. PMID:9194193Additional Information
Study Summary
Structure view and single mutant data analysis
Study data
| 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 |
|---|---|---|---|
| 1M7T | 2002-09-25 | Solution Structure and Dynamics of the Human-Escherichia coli Thioredoxin Chimera: Insights into Thermodynamic Stability | |
| 1XOA | 1996-06-10 | THIOREDOXIN (OXIDIZED DISULFIDE FORM), NMR, 20 STRUCTURES | |
| 1XOB | 1996-06-10 | THIOREDOXIN (REDUCED DITHIO FORM), NMR, 20 STRUCTURES | |
| 4HUA | 2013-05-29 | 1.1 | E. coli thioredoxin variant with (4R)-FluoroPro76 as single proline residue |
| 5HR3 | 2017-02-22 | 1.1 | Crystal structure of thioredoxin N106A mutant |
| 5HR2 | 2017-02-22 | 1.2 | Crystal structure of thioredoxin L94A mutant |
| 5HR0 | 2017-02-22 | 1.31 | Crystal structure of thioredoxin E101G mutant |
| 4HU7 | 2013-05-29 | 1.4 | E. coli thioredoxin variant with Pro76 as single proline residue |
| 4HU9 | 2013-05-29 | 1.55 | E. coli thioredoxin variant with (4S)-FluoroPro76 as single proline residue |
| 4X43 | 2015-06-24 | 1.65 | Structure of proline-free E. coli Thioredoxin |
| 2TRX | 1991-10-15 | 1.68 | CRYSTAL STRUCTURE OF THIOREDOXIN FROM ESCHERICHIA COLI AT 1.68 ANGSTROMS RESOLUTION |
| 1KEB | 2002-11-13 | 1.8 | Crystal Structure of Double Mutant M37L,P40S E.coli Thioredoxin |
| 2EIQ | 2007-09-11 | 1.9 | Design of Disulfide-linked Thioredoxin Dimers and Multimers Through Analysis of Crystal Contacts |
| 2TIR | 1993-10-31 | 2.0 | CRYSTAL STRUCTURE ANALYSIS OF A MUTANT ESCHERICHIA COLI THIOREDOXIN IN WHICH LYSINE 36 IS REPLACED BY GLUTAMIC ACID |
| 3DYR | 2009-01-27 | 2.0 | Crystal structure of E. coli thioredoxin mutant I76T in its oxidized form |
| 6GD1 | 2018-10-31 | 2.01 | Structure of HuR RRM3 |
| 1X9M | 2004-10-26 | 2.1 | T7 DNA polymerase in complex with an N-2-acetylaminofluorene-adducted DNA |
| 5HR1 | 2017-02-22 | 2.14 | Crystal structure of thioredoxin L107A mutant |
| 1SL1 | 2004-07-06 | 2.2 | Binary 5' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template |
| 2H71 | 2007-05-15 | 2.2 | Crystal Structure of Thioredoxin Mutant D47E in Hexagonal (p61) Space Group |
| 1T7P | 1998-02-25 | 2.2 | T7 DNA POLYMERASE COMPLEXED TO DNA PRIMER/TEMPLATE,A NUCLEOSIDE TRIPHOSPHATE, AND ITS PROCESSIVITY FACTOR THIOREDOXIN |
| 2H75 | 2007-05-15 | 2.2 | Crystal Structure of Thioredoxin Mutant D13E in Hexagonal (p61) Space Group |
| 3DXB | 2008-10-28 | 2.2 | Structure of the UHM domain of Puf60 fused to thioredoxin |
| 1TXX | 1999-09-13 | 2.2 | ACTIVE-SITE VARIANT OF E.COLI THIOREDOXIN |
| 1TK5 | 2004-08-31 | 2.2 | T7 DNA polymerase binary complex with 8 oxo guanosine in the templating strand |
| 2H76 | 2007-05-15 | 2.25 | Crystal Structure of Thioredoxin Mutant D10E in Hexagonal (p61) Space Group |
| 2H6Z | 2007-05-15 | 2.25 | Crystal Structure of Thioredoxin Mutant E44D in Hexagonal (p61) Space Group |
| 2H72 | 2007-05-15 | 2.25 | Crystal Structure of Thioredoxin mutant E85D in Hexagonal (p61) Space Group |
| 1SKS | 2004-07-06 | 2.3 | Binary 3' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template |
| 1X9W | 2004-10-26 | 2.3 | T7 DNA polymerase in complex with a primer/template DNA containing a disordered N-2 aminofluorene on the template, crystallized with dideoxy-ATP as the incoming nucleotide. |
| 1SL2 | 2004-07-06 | 2.3 | Ternary 5' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template and an incoming nucleotide |
| 1THO | 1993-10-31 | 2.3 | CRYSTAL STRUCTURE OF A MUTANT ESCHERICHIA COLI THIOREDOXIN WITH AN ARGININE INSERTION IN THE ACTIVE SITE |
| 1TK0 | 2004-08-31 | 2.3 | T7 DNA polymerase ternary complex with 8 oxo guanosine and ddCTP at the insertion site |
| 1SKW | 2004-07-06 | 2.3 | Binary 3' complex of T7 DNA polymerase with a DNA primer/template containing a disordered cis-syn thymine dimer on the template |
| 1ZCP | 2005-08-09 | 2.3 | Crystal Structure of a catalytic site mutant E. coli TrxA (CACA) |
| 2H6Y | 2007-05-15 | 2.4 | Crystal Structure of Thioredoxin Mutant E48D in Hexagonal (p61) Space Group |
| 1SKR | 2004-07-06 | 2.4 | T7 DNA Polymerase Complexed To DNA Primer/Template and ddATP |
| 5XOC | 2018-03-28 | 2.4 | Crystal structure of human Smad3-FoxH1 complex |
| 2H74 | 2007-05-15 | 2.4 | Crystal Structure of Thioredoxin Mutant D2E in Hexagonal (p61) Space Group |
| 2FD3 | 2005-12-27 | 2.45 | Crystal Structure of Thioredoxin Mutant P34H |
| 2H73 | 2007-05-15 | 2.45 | Crystal Structure of Thioredoxin Mutant D43E in Hexagonal (p61) Space Group |
| 1TKD | 2004-08-31 | 2.49 | T7 DNA polymerase ternary complex with 8 oxo guanosine and dCMP at the elongation site |
| 1ZZY | 2005-07-19 | 2.5 | Crystal Structure of Thioredoxin Mutant L7V |
| 2BTO | 2005-06-23 | 2.5 | Structure of BtubA from Prosthecobacter dejongeii |
| 1TK8 | 2004-08-31 | 2.5 | T7 DNA polymerase ternary complex with 8 oxo guanosine and dAMP at the elongation site |
| 2EIR | 2007-09-11 | 2.5 | Design of Disulfide-linked Thioredoxin Dimers and Multimers Through Analysis of Crystal Contacts |
| 6H7N | 2018-10-17 | 2.5 | ACTIVATED TURKEY BETA1 ADRENOCEPTOR WITH BOUND PARTIAL AGONIST XAMOTEROL AND NANOBODY Nb6B9 |
| 1T8E | 2004-10-12 | 2.54 | T7 DNA Polymerase Ternary Complex with dCTP at the Insertion Site. |
| 2H6X | 2007-05-15 | 2.6 | Crystal Structure of Thioredoxin Wild Type in Hexagonal (p61) Space Group |
| 2AJQ | 2006-09-26 | 2.6 | Structure of replicative DNA polymerase provides insigts into the mechanisms for processivity, frameshifting and editing |
| 2EIO | 2007-09-11 | 2.6 | Design of Disulfide-linked Thioredoxin Dimers and Multimers Through Analysis of Crystal Contacts |
| 2FCH | 2005-12-27 | 2.6 | Crystal Structure of Thioredoxin Mutant G74S |
| 1X9S | 2004-10-26 | 2.7 | T7 DNA polymerase in complex with a primer/template DNA containing a disordered N-2 aminofluorene on the template, crystallized with dideoxy-CTP as the incoming nucleotide. |
| 2H70 | 2007-05-15 | 2.7 | Crystal Structure of Thioredoxin Mutant D9E in Hexagonal (p61) Space Group |
| 6H7L | 2018-10-17 | 2.7 | ACTIVATED TURKEY BETA1 ADRENOCEPTOR WITH BOUND PARTIAL AGONIST DOBUTAMINE AND NANOBODY Nb6B9 |
| 6IBL | 2019-01-09 | 2.7 | ACTIVATED TURKEY BETA1 ADRENOCEPTOR WITH BOUND AGONIST FORMOTEROL AND NANOBODY Nb80 |
| 1ZYQ | 2005-11-22 | 2.7 | T7 DNA polymerase in complex with 8oG and incoming ddATP |
| 6H7M | 2018-10-17 | 2.76 | ACTIVATED TURKEY BETA1 ADRENOCEPTOR WITH BOUND PARTIAL AGONIST SALBUTAMOL AND NANOBODY Nb6B9 |
| 1OAZ | 2004-01-15 | 2.78 | IgE Fv SPE7 complexed with a recombinant thioredoxin |
| 5E4W | 2015-12-02 | 2.8 | Crystal structure of cpSRP43 chromodomains 2 and 3 in complex with the Alb3 tail |
| 6H7J | 2018-10-17 | 2.8 | ACTIVATED TURKEY BETA1 ADRENOCEPTOR WITH BOUND AGONIST ISOPRENALINE AND NANOBODY Nb80 |
| 6H7O | 2018-10-17 | 2.8 | ACTIVATED TURKEY BETA1 ADRENOCEPTOR WITH BOUND WEAK PARTIAL AGONIST CYANOPINDOLOL AND NANOBODY Nb6B9 |
| 1SRX | 1976-05-19 | 2.8 | THREE-DIMENSIONAL STRUCTURE OF ESCHERICHIA COLI THIOREDOXIN-S2 TO 2.8 ANGSTROMS RESOLUTION |
| 1F6M | 2000-08-30 | 2.95 | CRYSTAL STRUCTURE OF A COMPLEX BETWEEN THIOREDOXIN REDUCTASE, THIOREDOXIN, AND THE NADP+ ANALOG, AADP+ |
| 6H1Y | 2019-02-06 | 2.99 | CRYSTAL STRUCTURE OF A CHIMERIC VARIANT OF THIOREDOXIN FROM ESCHERICHIA COLI |
| 2O8V | 2007-03-27 | 3.0 | PAPS reductase in a covalent complex with thioredoxin C35A |
| 1SL0 | 2004-07-06 | 3.2 | Ternary 3' complex of T7 DNA polymerase with a DNA primer/template containing a disordered cis-syn thymine dimer on the template and an incoming nucleotide |
| 6GDG | 2018-05-16 | 4.11 | Cryo-EM structure of the adenosine A2A receptor bound to a miniGs heterotrimer |
| 6N7W | 2019-03-06 | 4.5 | Structure of bacteriophage T7 leading-strand DNA polymerase (D5A/E7A)/Trx in complex with a DNA fork and incoming dTTP (from multiple lead complexes) |
| 5IKN | 2016-12-07 | 4.8 | Crystal Structure of the T7 Replisome in the Absence of DNA |