The effects of multiple ancestral residues on the Thermus thermophilus 3-isopropylmalate dehydrogenase.

Abstract

Previously, we showed that mutants of Thermus thermophilus 3-isopropylmalate dehydrogenase (IPMDH) each containing a residue (ancestral residue) that had been predicted to exist in a postulated common ancestor protein often have greater thermal stabilities than does the contemporary wild-type enzyme. In this study, the combined effects of multiple ancestral residues were analyzed. Two mutants, containing multiple mutations, Sup3mut (Val181Thr/Pro324Thr/Ala335Glu) and Sup4mut (Leu134Asn/Val181Thr/Pro324Thr/Ala335Glu) were constructed and show greater thermal stabilities than the wild-type and single-point mutant IPMDHs do. Most of the mutants have similar or improved catalytic efficiencies at 70 degrees C when compared with the wild-type IPMDH. Study holds ProTherm entries: 22914, 22915, 22916, 22917 Extra Details: 0.5 mM EDTA was added in the experiment Ancestral residue; Protein stability; 3-Isopropylmalate dehydrogenase; Thermus thermophilus

Submission Details

ID: PVqRqV6H3

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:54 p.m.

Version: 1

Publication Details
Watanabe K;Yamagishi A,FEBS Lett. (2006) The effects of multiple ancestral residues on the Thermus thermophilus 3-isopropylmalate dehydrogenase. PMID:16797545
Additional Information

Study Summary

Number of data points 8
Proteins 3-isopropylmalate dehydrogenase ; 3-isopropylmalate dehydrogenase
Unique complexes 2
Assays/Quantities/Protocols Experimental Assay: Tm details:Additives , prot_conc:5.4 microM, buffers:phosphate: 20 mM ; Experimental Assay: Tm prot_conc:10.9 microM, buffers:potassium phosphate: 20 mM, details:Additives EDTA (0.5 mM), ; Derived Quantity: dTm details:Additives , prot_conc:5.4 microM, buffers:phosphate: 20 mM ; Derived Quantity: dTm prot_conc:10.9 microM, buffers:potassium phosphate: 20 mM, details:Additives EDTA (0.5 mM),
Libraries Mutations for sequence MKVAVLPGDGIGPEVTEAALKVLRALDEAEGLGLAYEVFPFGGAAIDAFGEPFPEPTRKGVEEAEAVLLGSVGGPKWDGLPRKIRPETGLLSLRKSQDLFANLRPAKVFPGLERLSPLKEEIARGVDVLIVRELTGGIYFGEPRGMSEAEAWNTERYSKPEVERVARVAFEAARKRRKHVVSVDKANVLEVGEFWRKTVEEVGRGYPDVALEHQYVDAMAMHLVRSPARFDVVVTGNIFGDILSDLASVLPGSLGLLPSASLGRGTPVFEPVHGSAPDIAGKGIANPTAAILSAAMMLEHAFGLVELARKVEDAVAKALLETPPPDLGGSAGTEAFTATVLRHLA

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
2Y3Z 2011-01-19 1.83 Structure of Isopropylmalate dehydrogenase from Thermus thermophilus - apo enzyme
4F7I 2012-06-13 2.0 Structure of Isopropylmalate dehydrogenase from Thermus thermophilus in complex with IPM, Mn and NADH
4WUO 2014-11-12 2.05 Structure of the E270A Mutant Isopropylmalate dehydrogenase from Thermus thermophilus in complex with IPM, Mn and NADH
1XAC 1996-04-03 2.1 CHIMERA ISOPROPYLMALATE DEHYDROGENASE BETWEEN BACILLUS SUBTILIS (M) AND THERMUS THERMOPHILUS (T) FROM N-TERMINAL: 20% T MIDDLE 20% M RESIDUAL 60% T, MUTATED AT S82R. LOW TEMPERATURE (100K) STRUCTURE.
1XAA 1996-04-03 2.1 3-ISOPROPYLMALATE DEHYDROGENASE, LOW TEMPERATURE (100K) STRUCTURE
1G2U 2000-11-01 2.1 THE STRUCTURE OF THE MUTANT, A172V, OF 3-ISOPROPYLMALATE DEHYDROGENASE FROM THERMUS THERMOPHILUS HB8 : ITS THERMOSTABILITY AND STRUCTURE.
1XAB 1996-04-03 2.1 3-ISOPROPYLMALATE DEHYDROGENASE, LOW TEMPERATURE (150K) STRUCTURE
1XAD 1996-04-03 2.1 CHIMERA ISOPROPYLMALATE DEHYDROGENASE BETWEEN BACILLUS SUBTILIS (M) AND THERMUS THERMOPHILUS (T) FROM N-TERMINAL: 20% T MIDDLE 20% M RESIDUAL 60% T, MUTATED AT S82R. LOW TEMPERATURE (150K) STRUCTURE.
1IPD 1993-10-31 2.2 THREE-DIMENSIONAL STRUCTURE OF A HIGHLY THERMOSTABLE ENZYME, 3-ISOPROPYLMALATE DEHYDROGENASE OF THERMUS THERMOPHILUS AT 2.2 ANGSTROMS RESOLUTION
2Y41 2011-01-19 2.2 Structure of Isopropylmalate dehydrogenase from Thermus thermophilus - complex with IPM and MN
1DR0 2000-01-19 2.2 STRUCTURE OF MODIFIED 3-ISOPROPYLMALATE DEHYDROGENASE AT THE C-TERMINUS, HD708
1IDM 1995-09-15 2.2 3-ISOPROPYLMALATE DEHYDROGENASE, LOOP-DELETED CHIMERA
1WAL 1999-05-25 2.27 3-ISOPROPYLMALATE DEHYDROGENASE (IPMDH) MUTANT (M219A)FROM THERMUS THERMOPHILUS
1GC9 2000-09-27 2.3 THE CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS 3-ISOPROPYLMALATE DEHYDROGENASE MUTATED AT 172TH FROM ALA TO GLY
1OSJ 1997-01-27 2.35 STRUCTURE OF 3-ISOPROPYLMALATE DEHYDROGENASE
1HEX 1994-12-20 2.5 STRUCTURE OF 3-ISOPROPYLMALATE DEHYDROGENASE IN COMPLEX WITH NAD+: LIGAND-INDUCED LOOP-CLOSING AND MECHANISM FOR COFACTOR SPECIFICITY
2Y42 2011-01-19 2.5 Structure of Isopropylmalate dehydrogenase from Thermus thermophilus - complex with NADH and Mn
1GC8 2000-09-27 2.5 THE CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS 3-ISOPROPYLMALATE DEHYDROGENASE MUTATED AT 172TH FROM ALA TO PHE
2Y40 2011-01-19 2.5 Structure of Isopropylmalate dehydrogenase from Thermus thermophilus - complex with Mn
1DR8 2000-01-19 2.7 STRUCTURE OF MODIFIED 3-ISOPROPYLMALATE DEHYDROGENASE AT THE C-TERMINUS, HD177
2ZTW 2009-10-13 2.79 Structure of 3-isopropylmalate dehydrogenase in complex with the inhibitor and NAD+
1DPZ 2000-01-12 2.8 STRUCTURE OF MODIFIED 3-ISOPROPYLMALATE DEHYDROGENASE AT THE C-TERMINUS, HD711
1OSI 1997-01-27 3.0 STRUCTURE OF 3-ISOPROPYLMALATE DEHYDROGENASE

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
91.9 3-isopropylmalate dehydrogenase P24098 LEU3_THEAQ
100.0 3-isopropylmalate dehydrogenase P61495 LEU3_THETH
99.4 3-isopropylmalate dehydrogenase P61494 LEU3_THET2
100.0 3-isopropylmalate dehydrogenase Q5SIY4 LEU3_THET8