Conserved residues and their role in the structure, function, and stability of acyl-coenzyme A binding protein.


Abstract

In the family of acyl-coenzyme A binding proteins, a subset of 26 sequence sites are identical in all eukaryotes and conserved throughout evolution of the eukaryotic kingdoms. In the context of the bovine protein, the importance of these 26 sequence positions for structure, function, stability, and folding has been analyzed using single-site mutations. A total of 28 mutant proteins were analyzed which covered 17 conserved sequence positions and three nonconserved positions. As a first step, the influence of the mutations on the protein folding reaction has been probed, revealing a folding nucleus of eight hydrophobic residues formed between the N- and C-terminal helices [Kragelund, B. B., et al. (1999) Nat. Struct. Biol. (In press)]. To fully analyze the role of the conserved residues, the function and the stability have been measured for the same set of mutant proteins. Effects on function were measured by the extent of binding of the ligand dodecanoyl-CoA using isothermal titration calorimetry, and effects on protein stability were measured with chemical denaturation followed by intrinsic tryptophan and tyrosine fluorescence. The sequence sites that have been conserved for direct functional purposes have been identified. These are Phe5, Tyr28, Tyr31, Lys32, Lys54, and Tyr73. Binding site residues are mainly polar or charged residues, and together, four of these contribute approximately 8 kcal mol-1 of the total free energy of binding of 11 kcal mol-1. The sequence sites conserved for stability of the structure have likewise been identified and are Phe5, Ala9, Val12, Leu15, Leu25, Tyr28, Lys32, Gln33, Tyr73, Val77, and Leu80. Essentially, all of the conserved residues that maintain the stability are hydrophobic residues at the interface of the helices. Only one conserved polar residue, Gln33, is involved in stability. The results indicate that conservation of residues in homologous proteins may result from a summed optimization of an effective folding reaction, a stable native protein, and a fully active binding site. This is important in protein design strategies, where optimization of one of these parameters, typically function or stability, may influence any of the others markedly. Study holds ProTherm entries: 5569, 5570, 5571, 5572, 5573, 5574, 5575, 5576, 5577, 5578, 5579, 5580, 5581, 5582, 5583, 5584, 5585, 5586, 5587, 5588, 5589, 5590, 5591, 5592, 5593, 5594, 5595, 5596, 5597 Extra Details: conserved sequence position; protein folding; charged residue;,free energy of binding; hydrophobic

Submission Details

ID: 4z5Ciqox3

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:30 p.m.

Version: 1

Publication Details
Kragelund BB;Poulsen K;Andersen KV;Baldursson T;Krøll JB;Neergård TB;Jepsen J;Roepstorff P;Kristiansen K;Poulsen FM;Knudsen J,Biochemistry (1999) Conserved residues and their role in the structure, function, and stability of acyl-coenzyme A binding protein. PMID:10029532
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
1ACA 1994-01-31 THREE-DIMENSIONAL STRUCTURE OF THE COMPLEX BETWEEN ACYL-COENZYME A BINDING PROTEIN AND PALMITOYL-COENZYME A
1NTI 2004-05-18 RDC-refined NMR structure of bovine Acyl-coenzyme A Binding Protein, ACBP
2ABD 1993-07-15 THE THREE-DIMENSIONAL STRUCTURE OF ACYL-COENZYME A BINDING PROTEIN FROM BOVINE LIVER. STRUCTURAL REFINEMENT USING HETERONUCLEAR MULTIDIMENSIONAL NMR SPECTROSCOPY
1NVL 2004-05-11 RDC-refined NMR structure of bovine Acyl-coenzyme A Binding Protein, ACBP, in complex with palmitoyl-coenzyme A
2CB8 2006-10-25 1.4 High resolution crystal structure of liganded human L-ACBP
2FJ9 2006-10-31 1.6 High resolution crystal structure of the unliganded human ACBP
1HB6 2002-03-11 2.0 Structure of bovine Acyl-CoA binding protein in orthorhombic crystal form
1HB8 2002-03-11 2.0 Structure of bovine Acyl-CoA binding protein in tetragonal crystal form
2FDQ 2006-10-24 3.5 crystal structure of ACBP from Armadillo Harderian Gland

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
92.0 Acyl-CoA-binding protein P12026 ACBP_PIG
93.1 Acyl-CoA-binding protein P07108 ACBP_HUMAN
95.4 Acyl-CoA-binding protein P82934 ACBP_CHAVI
100.0 Acyl-CoA-binding protein P07107 ACBP_BOVIN