Detection of rare partially folded molecules in equilibrium with the native conformation of RNaseH.
Abstract
Despite the general observation that single domain proteins denature in a completely cooperative manner, amide hydrogen exchange of ribonuclease H in low levels of denaturant demonstrates the existence of two partially folded species. The structures of these marginally stable species resemble kinetic folding intermediates and the molten globule state of the protein. These data suggest that the first region to fold is the thermodynamically most stable portion of the protein and that the molten globule is a high free energy conformation present at equilibrium in the native state. Study holds ProTherm entries: 9931, 9932, 9933, 9934, 9935, 9936, 9937, 9938, 9939, 9940, 9941, 9942, 9943, 9944, 9945, 9946, 9947, 9948, 9949, 9950, 9951, 9952, 9953, 9954, 9955, 9956, 9957, 9958, 9959, 9960, 9961, 9962, 9963, 9964, 9965, 9966, 9967, 9968, 9969, 9970, 9971, 9972, 9973, 9974, 9975, 9976 Extra Details: amide proton exchange in Ile7 single domain proteins; cooperative manner; partially folded species;,molten globule; free energy conformation
Submission Details
ID: DkAw9nS94
Submitter: Connie Wang
Submission Date: April 24, 2018, 8:39 p.m.
Version: 1
Publication Details
Chamberlain AK;Handel TM;Marqusee S,Nat. Struct. Biol. (1996) Detection of rare partially folded molecules in equilibrium with the native conformation of RNaseH. PMID:8784352Additional Information
Study Summary
| Number of data points | 46 |
| Proteins | Ribonuclease HI ; Ribonuclease HI |
| Unique complexes | 1 |
| Assays/Quantities/Protocols | Experimental Assay: dG_H2O buffers:Sodium acetate: 100mM ; Experimental Assay: dG_H2O buffers:Sodium acetate: 100 mM |
| Libraries | Mutations for sequence MLKQVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHCEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERCDELARAAAMNPTLEDTGYQVEV |
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 |
|---|---|---|---|
| 1RCH | 1997-02-12 | SOLUTION NMR STRUCTURE OF RIBONUCLEASE HI FROM ESCHERICHIA COLI, 8 STRUCTURES | |
| 1JL1 | 2002-02-27 | 1.3 | D10A E. coli ribonuclease HI |
| 2YV0 | 2008-03-18 | 1.4 | Structural and Thermodynamic Analyses of E. coli ribonuclease HI Variant with Quintuple Thermostabilizing Mutations |
| 1F21 | 2000-12-06 | 1.4 | DIVALENT METAL COFACTOR BINDING IN THE KINETIC FOLDING TRAJECTORY OF E. COLI RIBONUCLEASE HI |
| 3QIO | 2011-04-20 | 1.4 | Crystal Structure of HIV-1 RNase H with engineered E. coli loop and N-hydroxy quinazolinedione inhibitor |
| 2RN2 | 1993-10-31 | 1.48 | STRUCTURAL DETAILS OF RIBONUCLEASE H FROM ESCHERICHIA COLI AS REFINED TO AN ATOMIC RESOLUTION |
| 1JXB | 2002-03-06 | 1.6 | I53A, a point mutant of the cysteine-free variant of E. coli Rnase HI |
| 3QIN | 2011-04-20 | 1.7 | Crystal Structure of HIV-1 RNase H p15 with engineered E. coli loop and pyrimidinol carboxylic acid inhibitor |
| 3HYF | 2009-10-20 | 1.7 | Crystal structure of HIV-1 RNase H p15 with engineered E. coli loop and active site inhibitor |
| 1JL2 | 2002-01-18 | 1.76 | Crystal structure of TCEO RNase H-a chimera combining the folding core from T. thermophilus RNase H and the remaining region of E. coli RNase H |
| 3AA4 | 2010-10-06 | 1.79 | A52V E.coli RNase HI |
| 1LAV | 1993-10-31 | 1.8 | STABILIZATION OF ESCHERICHIA COLI RIBONUCLEASE HI BY CAVITY-FILLING MUTATIONS WITHIN A HYDROPHOBIC CORE |
| 1KVA | 1997-03-12 | 1.8 | E. COLI RIBONUCLEASE HI D134A MUTANT |
| 1RBU | 1994-01-31 | 1.8 | STRUCTURAL STUDY OF MUTANTS OF ESCHERICHIA COLI RIBONUCLEASE HI WITH ENHANCED THERMOSTABILITY |
| 1RBV | 1994-01-31 | 1.8 | STRUCTURAL STUDY OF MUTANTS OF ESCHERICHIA COLI RIBONUCLEASE HI WITH ENHANCED THERMOSTABILITY |
| 1LAW | 1993-10-31 | 1.8 | STABILIZATION OF ESCHERICHIA COLI RIBONUCLEASE HI BY CAVITY-FILLING MUTATIONS WITHIN A HYDROPHOBIC CORE |
| 1RBR | 1994-01-31 | 1.8 | STRUCTURAL STUDY OF MUTANTS OF ESCHERICHIA COLI RIBONUCLEASE HI WITH ENHANCED THERMOSTABILITY |
| 1RBT | 1994-01-31 | 1.8 | STRUCTURAL STUDY OF MUTANTS OF ESCHERICHIA COLI RIBONUCLEASE HI WITH ENHANCED THERMOSTABILITY |
| 1RBS | 1994-01-31 | 1.8 | STRUCTURAL STUDY OF MUTANTS OF ESCHERICHIA COLI RIBONUCLEASE HI WITH ENHANCED THERMOSTABILITY |
| 1RDB | 1993-10-31 | 1.9 | CRYSTAL STRUCTURES OF RIBONUCLEASE HI ACTIVE SITE MUTANTS FROM ESCHERICHIA COLI |
| 3AA2 | 2010-10-06 | 1.9 | A52I E. coli RNase HI |
| 1GOA | 1994-01-31 | 1.9 | COOPERATIVE STABILIZATION OF ESCHERICHIA COLI RIBONUCLEASE HI BY INSERTION OF GLY-80B AND GLY-77-> ALA SUBSTITUTION |
| 1G15 | 2001-03-14 | 1.9 | CO-CRYSTAL OF E. COLI RNASE HI WITH TWO MN2+ IONS BOUND IN THE THE ACTIVE SITE |
| 1KVC | 1997-03-12 | 1.9 | E. COLI RIBONUCLEASE HI D134N MUTANT |
| 1KVB | 1997-03-12 | 1.9 | E. COLI RIBONUCLEASE HI D134H MUTANT |
| 1GOC | 1994-01-31 | 2.0 | COOPERATIVE STABILIZATION OF ESCHERICHIA COLI RIBONUCLEASE HI BY INSERTION OF GLY-80B AND GLY-77-> ALA SUBSTITUTION |
| 1GOB | 1994-01-31 | 2.0 | COOPERATIVE STABILIZATION OF ESCHERICHIA COLI RIBONUCLEASE HI BY INSERTION OF GLY-80B AND GLY-77-> ALA SUBSTITUTION |
| 1RNH | 1991-10-15 | 2.0 | STRUCTURE OF RIBONUCLEASE H PHASED AT 2 ANGSTROMS RESOLUTION BY MAD ANALYSIS OF THE SELENOMETHIONYL PROTEIN |
| 4Z0U | 2015-04-29 | 2.0 | RNase HI/SSB-Ct complex |
| 2Z1I | 2007-11-13 | 2.0 | Crystal structure of E.coli RNase HI surface charged mutant(Q4R/T40E/Q72H/Q76K/Q80E/T92K/Q105K/Q113R/Q115K) |
| 3AA5 | 2010-10-06 | 2.1 | A52F E.coli RNase HI |
| 2Z1G | 2007-11-13 | 2.1 | Crystal structure of E.coli RNase HI surface charged mutant(Q4R/T40E/Q72H/Q76K/Q80E/T92K/Q105K) |
| 1RDA | 1993-10-31 | 2.15 | CRYSTAL STRUCTURES OF RIBONUCLEASE HI ACTIVE SITE MUTANTS FROM ESCHERICHIA COLI |
| 1WSG | 2005-02-08 | 2.2 | Co-crystal structure of E.coli RNase HI active site mutant (E48A/D134N*) with Mn2+ |
| 3AA3 | 2010-10-06 | 2.2 | A52L E. coli RNase HI |
| 1WSE | 2005-02-08 | 2.3 | Co-crystal structure of E.coli RNase HI active site mutant (E48A*) with Mn2+ |
| 1WSF | 2005-02-08 | 2.3 | Co-crystal structure of E.coli RNase HI active site mutant (D134A*) with Mn2+ |
| 1RDC | 1993-10-31 | 2.3 | CRYSTAL STRUCTURES OF RIBONUCLEASE HI ACTIVE SITE MUTANTS FROM ESCHERICHIA COLI |
| 2Z1J | 2007-11-13 | 2.38 | Crystal structure of E.coli RNase HI surface charged mutant(Q4R/T40E/Q72H/Q76K/Q80E/T92K/Q105K/Q113R/Q115K/N143K/T145K) |
| 2Z1H | 2007-11-13 | 2.6 | Crystal structure of E.coli RNase HI surface charged mutant(Q4R/T92K/Q105K/Q113R/Q115K/N143K/T145K) |
| 1RDD | 1993-10-31 | 2.8 | CRYSTAL STRUCTURE OF ESCHERICHIA COLI RNASE HI IN COMPLEX WITH MG2+ AT 2.8 ANGSTROMS RESOLUTION: PROOF FOR A SINGLE MG2+ SITE |
Relevant UniProtKB Entries
| Percent Identity | Matching Chains | Protein | Accession | Entry Name |
|---|---|---|---|---|
| 90.9 | Ribonuclease HI | A6T512 | RNH_KLEP7 | |
| 90.9 | Ribonuclease HI | B5Y1G2 | RNH_KLEP3 | |
| 92.9 | Ribonuclease HI | C0Q6N2 | RNH_SALPC | |
| 93.5 | Ribonuclease HI | P0A2B9 | RNH_SALTY | |
| 93.5 | Ribonuclease HI | P0A2C0 | RNH_SALTI | |
| 93.5 | Ribonuclease HI | B4TYH0 | RNH_SALSV | |
| 93.5 | Ribonuclease HI | B5BDW5 | RNH_SALPK | |
| 93.5 | Ribonuclease HI | A9MZ19 | RNH_SALPB | |
| 93.5 | Ribonuclease HI | Q5PFD8 | RNH_SALPA | |
| 93.5 | Ribonuclease HI | B4SV39 | RNH_SALNS | |
| 93.5 | Ribonuclease HI | B4TK85 | RNH_SALHS | |
| 93.5 | Ribonuclease HI | B5R5L3 | RNH_SALG2 | |
| 93.5 | Ribonuclease HI | B5R449 | RNH_SALEP | |
| 93.5 | Ribonuclease HI | B5FJ58 | RNH_SALDC | |
| 93.5 | Ribonuclease HI | Q57SZ6 | RNH_SALCH | |
| 93.5 | Ribonuclease HI | A9MPF1 | RNH_SALAR | |
| 93.5 | Ribonuclease HI | B5F8X2 | RNH_SALA4 | |
| 93.5 | Ribonuclease HI | A8AKR0 | RNH_CITK8 | |
| 99.4 | Ribonuclease HI | Q0TLC3 | RNH_ECOL5 | |
| 99.4 | Ribonuclease HI | A7ZWF6 | RNH_ECOHS | |
| 99.4 | Ribonuclease HI | B7LHC0 | RNH_ECO55 | |
| 99.4 | Ribonuclease HI | B7UJB0 | RNH_ECO27 | |
| 100.0 | Ribonuclease HI | Q3Z5E9 | RNH_SHISS | |
| 100.0 | Ribonuclease HI | P0A7Y7 | RNH_SHIFL | |
| 100.0 | Ribonuclease HI | Q32JP9 | RNH_SHIDS | |
| 100.0 | Ribonuclease HI | Q325T2 | RNH_SHIBS | |
| 100.0 | Ribonuclease HI | B2U352 | RNH_SHIB3 | |
| 100.0 | Ribonuclease HI | B7LW89 | RNH_ESCF3 | |
| 100.0 | Ribonuclease HI | B1LHM3 | RNH_ECOSM | |
| 100.0 | Ribonuclease HI | B6HZS7 | RNH_ECOSE | |
| 100.0 | Ribonuclease HI | B7N876 | RNH_ECOLU | |
| 100.0 | Ribonuclease HI | P0A7Y4 | RNH_ECOLI | |
| 100.0 | Ribonuclease HI | B1IPU4 | RNH_ECOLC | |
| 100.0 | Ribonuclease HI | P0A7Y5 | RNH_ECOL6 | |
| 100.0 | Ribonuclease HI | B1XD78 | RNH_ECODH | |
| 100.0 | Ribonuclease HI | C4ZRV1 | RNH_ECOBW | |
| 100.0 | Ribonuclease HI | B7M213 | RNH_ECO8A | |
| 100.0 | Ribonuclease HI | B7MQ23 | RNH_ECO81 | |
| 100.0 | Ribonuclease HI | B7NKW4 | RNH_ECO7I | |
| 100.0 | Ribonuclease HI | B5Z0I8 | RNH_ECO5E | |
| 100.0 | Ribonuclease HI | P0A7Y6 | RNH_ECO57 | |
| 100.0 | Ribonuclease HI | B7MBJ0 | RNH_ECO45 | |
| 100.0 | Ribonuclease HI | A7ZHV1 | RNH_ECO24 |