Mutagenic analysis of the interior packing of an alpha/beta barrel protein. Effects on the stabilities and rates of interconversion of the native and partially folded forms of the alpha subunit of tryptophan synthase.
Abstract
A series of single and double amino acid replacements in four beta strands of the alpha subunit of tryptophan synthase from Salmonella typhimurium, and alpha/beta barrel protein, was made to study the interior packing of the barrel and to clarify its folding mechanism. The urea-induced unfolding of the alpha subunit is thought to involve a stable intermediate in which the amino folding unit (residues 1-188; helices 0-5, strands 1-6) remains folded while the carboxy folding unit (residues 189-268; helices 6-8, strands 7-8) becomes disordered [Beasty, A. M., & Matthews, C. R. (1985) Biochemistry 24, 3547; Miles, E. W., Yutani, K., & Ogasahara, K. (1982) Biochemistry 21, 2586]. Mutations in strands 1 (A18G and A18V), 6 (Y175Q), 7 (L209V), and 8 (G230A, G230V, and I232V) at the interface between these two folding units show that the effects on the stabilities of the native and intermediate conformations critically depend on the site of the replacement. Although all of these mutations decrease the stability of the native conformation, only the replacements in strand 6, Y175Q, and possibly strand 8, I232V, also perturb the intermediate. Comparisons of the effects of three pairs of double mutants with the effects of the constituent single mutants on stability show that strands 6 and 7 interact in both the intermediate and native conformations, while strands 1 and 8 interact only in the native conformation. Kinetic studies of unfolding indicate that the interactions which occur in the native conformation arise in the preceding transition state. These results demonstrate that the carboxy folding unit adopts an organized structure in the intermediate, contrary to our previous interpretation. The general implication is that the state of folding of one segment of a protein can depend on the presence of another, more stable element of structure. Study holds ProTherm entries: 2551, 2552, 2553, 2554, 2555, 2556, 2557, 2558, 2559, 2560, 2561, 2562, 2563, 2564, 2565, 2566, 2567, 2568 Extra Details: additive : EDTA(0.2 mM),Transition is from Native to Intermediate,dG and ddG were measured in the presence of [urea]50% tryptophan synthase alpha subunit; interior packing; stability;,alpha/beta barrel protein; folding mechanism
Submission Details
ID: HvhYDKkA3
Submitter: Connie Wang
Submission Date: April 24, 2018, 8:19 p.m.
Version: 1
Publication Details
Tsuji T;Chrunyk BA;Chen X;Matthews CR,Biochemistry (1993) Mutagenic analysis of the interior packing of an alpha/beta barrel protein. Effects on the stabilities and rates of interconversion of the native and partially folded forms of the alpha subunit of tryptophan synthase. PMID:8504078Additional 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 UniProtKB Entries
| Percent Identity | Matching Chains | Protein | Accession | Entry Name |
|---|---|---|---|---|
| 100.0 | Tryptophan synthase alpha chain | P00929 | TRPA_SALTY | |
| 99.6 | Tryptophan synthase alpha chain | B5F4M3 | TRPA_SALA4 | |
| 99.6 | Tryptophan synthase alpha chain | B5FU65 | TRPA_SALDC | |
| 99.6 | Tryptophan synthase alpha chain | B5R3P3 | TRPA_SALEP | |
| 99.6 | Tryptophan synthase alpha chain | B5R6M4 | TRPA_SALG2 | |
| 99.6 | Tryptophan synthase alpha chain | B4TJK9 | TRPA_SALHS | |
| 99.6 | Tryptophan synthase alpha chain | B4T6X2 | TRPA_SALNS | |
| 99.6 | Tryptophan synthase alpha chain | A9MWR3 | TRPA_SALPB | |
| 99.6 | Tryptophan synthase alpha chain | Q8Z7E0 | TRPA_SALTI | |
| 99.3 | Tryptophan synthase alpha chain | Q57NT2 | TRPA_SALCH | |
| 99.3 | Tryptophan synthase alpha chain | C0Q3N3 | TRPA_SALPC | |
| 99.3 | Tryptophan synthase alpha chain | Q5PNM0 | TRPA_SALPA | |
| 99.3 | Tryptophan synthase alpha chain | B5BIC0 | TRPA_SALPK | |
| 98.9 | Tryptophan synthase alpha chain | B4TX39 | TRPA_SALSV | |
| 95.1 | Tryptophan synthase alpha chain | A9MPY6 | TRPA_SALAR | |
| 99.7 | B | Tryptophan synthase alpha chain | B5F4M4 | TRPB_SALA4 |
| 99.7 | B | Tryptophan synthase alpha chain | B5FU66 | TRPB_SALDC |
| 99.7 | B | Tryptophan synthase alpha chain | B5R3P4 | TRPB_SALEP |
| 99.7 | B | Tryptophan synthase alpha chain | B5R6M5 | TRPB_SALG2 |
| 99.7 | B | Tryptophan synthase alpha chain | B4TJK8 | TRPB_SALHS |
| 99.7 | B | Tryptophan synthase alpha chain | B4T6X1 | TRPB_SALNS |
| 99.7 | B | Tryptophan synthase alpha chain | Q5PD17 | TRPB_SALPA |
| 99.7 | B | Tryptophan synthase alpha chain | A9MWR4 | TRPB_SALPB |
| 99.7 | B | Tryptophan synthase alpha chain | C0Q3N4 | TRPB_SALPC |
| 99.7 | B | Tryptophan synthase alpha chain | B5BIC1 | TRPB_SALPK |
| 99.7 | B | Tryptophan synthase alpha chain | B4TX38 | TRPB_SALSV |
| 99.7 | B | Tryptophan synthase alpha chain | P0A2K2 | TRPB_SALTI |
| 99.7 | B | Tryptophan synthase alpha chain | P0A2K1 | TRPB_SALTY |
| 99.5 | B | Tryptophan synthase alpha chain | Q57NT3 | TRPB_SALCH |
| 98.2 | B | Tryptophan synthase alpha chain | A9MPY7 | TRPB_SALAR |
| 96.7 | B | Tryptophan synthase alpha chain | A8AG61 | TRPB_CITK8 |
| 97.0 | B | Tryptophan synthase alpha chain | B7LS19 | TRPB_ESCF3 |
| 96.7 | B | Tryptophan synthase alpha chain | Q8X7B6 | TRPB_ECO57 |
| 96.7 | B | Tryptophan synthase alpha chain | B5YZP1 | TRPB_ECO5E |
| 96.7 | B | Tryptophan synthase alpha chain | Q3Z109 | TRPB_SHISS |
| 96.7 | B | Tryptophan synthase alpha chain | B7UR67 | TRPB_ECO27 |
| 96.7 | B | Tryptophan synthase alpha chain | B7NVN1 | TRPB_ECO7I |
| 96.7 | B | Tryptophan synthase alpha chain | B7MUA0 | TRPB_ECO81 |
| 96.7 | B | Tryptophan synthase alpha chain | Q0TIA9 | TRPB_ECOL5 |
| 96.7 | B | Tryptophan synthase alpha chain | Q8FHV9 | TRPB_ECOL6 |
| 96.7 | B | Tryptophan synthase alpha chain | B1LH31 | TRPB_ECOSM |
| 96.7 | B | Tryptophan synthase alpha chain | Q32GS9 | TRPB_SHIDS |
| 96.5 | B | Tryptophan synthase alpha chain | A7ZL79 | TRPB_ECO24 |
| 96.5 | B | Tryptophan synthase alpha chain | B7L493 | TRPB_ECO55 |
| 96.5 | B | Tryptophan synthase alpha chain | B7LY17 | TRPB_ECO8A |
| 96.5 | B | Tryptophan synthase alpha chain | B1XBL0 | TRPB_ECODH |
| 96.5 | B | Tryptophan synthase alpha chain | A7ZZJ7 | TRPB_ECOHS |
| 96.5 | B | Tryptophan synthase alpha chain | B1ITJ4 | TRPB_ECOLC |
| 96.5 | B | Tryptophan synthase alpha chain | P0A879 | TRPB_ECOLI |
| 96.5 | B | Tryptophan synthase alpha chain | B6I9X5 | TRPB_ECOSE |
| 96.5 | B | Tryptophan synthase alpha chain | Q0T5D5 | TRPB_SHIF8 |
| 96.5 | B | Tryptophan synthase alpha chain | P0A880 | TRPB_SHIFL |
| 96.5 | B | Tryptophan synthase alpha chain | B7ML77 | TRPB_ECO45 |
| 96.5 | B | Tryptophan synthase alpha chain | A1AAN1 | TRPB_ECOK1 |
| 96.5 | B | Tryptophan synthase alpha chain | Q1RCA6 | TRPB_ECOUT |
| 96.5 | B | Tryptophan synthase alpha chain | B7N474 | TRPB_ECOLU |
| 96.5 | B | Tryptophan synthase alpha chain | B2U0F2 | TRPB_SHIB3 |
| 96.5 | B | Tryptophan synthase alpha chain | Q31ZV4 | TRPB_SHIBS |
| 93.7 | B | Tryptophan synthase alpha chain | B5XT02 | TRPB_KLEP3 |
| 93.7 | B | Tryptophan synthase alpha chain | A6T7W6 | TRPB_KLEP7 |
| 92.7 | B | Tryptophan synthase alpha chain | A4WB02 | TRPB_ENT38 |
| 93.2 | B | Tryptophan synthase alpha chain | A7MMG1 | TRPB_CROS8 |
| 91.6 | B | Tryptophan synthase alpha chain | C6DGZ5 | TRPB_PECCP |
| 91.1 | B | Tryptophan synthase alpha chain | A8GF82 | TRPB_SERP5 |
| 90.9 | B | Tryptophan synthase alpha chain | Q6D4U0 | TRPB_PECAS |
| 90.1 | B | Tryptophan synthase alpha chain | B2VKT2 | TRPB_ERWT9 |