Evolution of protein function, from a structural perspective

doi:10.1016/S1367-5931(99)00007-1

Current Opinion in Chemical Biology

Volume 3, Issue 5, 1 October 1999, Pages 548-556

https://doi.org/10.1016/S1367-5931(99)00007-1 Get rights and content

Abstract

The recent growth in structural data, and ensuing analyses, have revealed the structural and functional versatility of protein families. With respect to enzymes, local active-site mutations, variations in surface loops and recruitment of additional domains accommodate the diverse substrate specificities and catalytic activities observed within several superfamilies. Conversely, some functions have more than one structural solution, having evolved independently several times during evolution. Combined with the existence of multi-functional genes, which have arisen by gene recruitment, these phenomena must be considered in the process of genome annotation.

Introduction

Evolutionary relationships are often exploited to provide insights into the biological role of uncharacterised proteins. Properties are inferred on the basis that protein family members commonly exhibit some similarity in function. With the proliferation of sequence, structural and biochemical data in recent years, however, scientists have identified many remarkable examples of protein evolution: relatives sharing high structural, and even sequence similarity can perform disparate functions, and conversely, proteins having dissimilar structures can have identical biochemical roles. A complete understanding of these complexities at the molecular level requires detailed structural analyses, since function and three-dimensional structure are inherently linked.

These observations are exemplified by two well studied cases. Lysozyme and α-lactalbumin share high sequence and structural similarity, yet α-lactalbumin does not exhibit the O-glycosyl hydrolase activity of lysozyme, and instead regulates the substrate specificity of galactosyltransferase [1]. The sugar-binding site of α-lactalbumin has remained during evolution whilst the catalytic residues have changed. The classic example of functional convergence is that of subtilisin and chymotrypsin. They have different structural folds, yet they have the same Ser–His–Asp catalytic triad and both function as serine proteases via the same catalytic mechanism [2].

Evolutionary relationships are traditionally detected by sequence similarity, but structural comparison is a far more powerful method, since protein structure is conserved even after all trace of sequence similarity disappears. This observation, combined with the growth in the protein data bank (pdb) [3], has allowed biologists to classify proteins into structural evolutionary families 4, 5, many of which are now well populated. Individually, protein structures may provide details of binding, catalysis and signalling. Collectively, in the context of sequence information, structural relatives can reveal the underlying mechanisms of evolving new functions from a structural standpoint. Similarly, with the atomic comparison of functional analogues such as chymotrypsin and subtilisin one can identify the common structural motif to which their functional similarity can be attributed.

Here we discuss recent, novel fold/function analyses, and then focus on the various mechanisms of evolving new functions with reference to recent examples in the literature. The review centres on enzymes; nevertheless, many points raised are applicable to proteins in general.

Section snippets

Enzyme structure/function relationships

Recent analyses have provided insights into novel structure/function relationships, and have highlighted the functional versatility of protein structures within homologues families, folds and secondary structure classes. With few consistent descriptors for other functional types, emphasis is placed on enzymes as the hierarchical Enzyme Classification (EC) scheme [6] facilitates the systematic comparisons of enzyme function.

Mechanisms of functional evolution

Given the versatility of folds and functions, how is function modulated through gene structure, sequence and thus three-dimensional-structural changes? A simple schematic diagram of the possible routes to new functions is given in Figure 5.

Gene fusion

Given that there are a limited number of folds, probably a few thousand at most 9, 37, yet an immeasurable number of functions required to sustain life, modular construction has been an important mechanism for the evolution of new gene functions. This is illustrated by the high percentage (30%) of polypeptide chains within the pdb that comprise more than one domain [38], and this percentage represents a lower limit since for many proteins, the structure of only one domain of several has been

Gene recruitment

Gene recruitment refers to the acquisition of a new function by an existing gene. This evolutionary strategy is exemplified by the recruitment of enzymes as crystallins, the structural proteins in the eye lens [45]. These new roles were acquired by modifications in gene expression.

Following recruitment, multi-functional genes are subject to two or more selective pressures, resulting in constraints on adaptability. As noted by Piatigorsky and Wistow [46], such pressures can lead to one of three

Conclusions

An understanding of the biological role of all gene products is the principal objective of genome analysis. How these functions have evolved is also of major intellectual and scientific interest. At the molecular level, three-dimensional structures facilitate the detection of distant evolutionary relationships, which can reveal how function is modified during evolution by sequence and structural changes. Understanding this evolution of function will provide clues for the design of proteins with

Acknowledgements

Annabelle E Todd is supported by a BBSRC special studentship and is sponsored by Oxford Molecular. Christine A Orengo is supported by the Medical Research Council. We also acknowledge support from the Bloomsbury Structural Biology Centre.

References and recommended reading

Papers of particular interest, published within the annual period of review, have been highlighted as:

• of special interest
•• of outstanding interest

References (47)

FC Bernstein et al.
The protein data bank: a computer based archival file for macromolecular structures
J Mol Biol
(1977)
AG Murzin et al.
SCOP – A structural classification of proteins database for the investigation of sequences and structures
J Mol Biol
(1995)
ACR Martin et al.
Protein folds and functions
Structure
(1998)
H Hegyi et al.
The relationship between protein structure and function: a comprehensive survey with application to the yeast genome
J Mol Biol
(1999)
PC Babbitt et al.
Understanding enzyme superfamilies: chemistry as the fundamental determinant in the evolution of new catalytic activities
J Biol Chem
(1997)
JA Gerlt et al.
Mechanistically diverse enzyme superfamilies: the importance of chemistry in the evolution of catalysis
Curr Opin Chem Biol
(1998)
P Bork et al.
From genome sequences to protein function
Curr Opin Struct Biol
(1994)
P Bork et al.
Predicting function: from genes to genomes and back
J Mol Biol
(1998)
JS Richardson
The anatomy and taxonomy of protein structure
Adv Protein Chem
(1981)
CA Orengo et al.
From protein structure to function
Curr Opin Struct Biol
(1999)

JJ Perona et al.

Evolutionary divergence of substrate specificity within the chymotrypsin-like serine protease fold

J Biol Chem

(1997)

S Oue et al.

Redesigning the substrate specificity of an enzyme by cumulative effects of the mutations of non-active site residues

J Biol Chem

(1999)

L Demetrius

Role of enzyme-substrate flexibility in catalytic activity: an evolutionary perspective

J Theor Biol

(1998)

GA Petsko et al.

On the origin of enzymatic species

Trends Biochem Sci

(1993)

AD McLachlan

Gene duplication in the structural evolution of chymotrypsin

J Mol Biol

(1979)

MR Singleton et al.

Structure of the adenylation domain of an NAD⁺-dependent DNA ligase

Structure

(1999)

KR Acharya et al.

Crystal structure of human α-lactalbumin at 1.7 Å resolution

J Mol Biol

(1991)

AC Wallace et al.

Derivation of 3D coordinate templates for searching structural databases: application to the Ser-His-Asp catalytic triads of the serine proteinases and lipases

Protein Sci

(1996)

CA Orengo et al.

CATH – a hierarchic classification of protein domain structures

Structure

(1997)

Enzyme Nomenclature 1992

(1992)

CA Orengo et al.

Protein superfamilies and domain superfolds

Nature

(1994)

L Holm et al.

An evolutionary treasure: unification of a broad set of amidohydrolases related to urease

Proteins

(1997)

B Zhang et al.

From fold predictions to function predictions: automation of functional site conservation analysis for functional genome predictions

Protein, Sci

(1999)

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ReviewEvolution of protein function, from a structural perspective

Abstract

Introduction

Section snippets

Enzyme structure/function relationships

Mechanisms of functional evolution

Gene fusion

Gene recruitment

Conclusions

Acknowledgements

References and recommended reading

J Mol Biol

J Mol Biol

Structure

J Mol Biol

J Biol Chem

Curr Opin Chem Biol

Curr Opin Struct Biol

J Mol Biol

Adv Protein Chem

Curr Opin Struct Biol

J Biol Chem

J Biol Chem

J Theor Biol

Trends Biochem Sci

J Mol Biol

Structure

Crystal structure of human α-lactalbumin at 1.7 Å resolution

J Mol Biol

Derivation of 3D coordinate templates for searching structural databases: application to the Ser-His-Asp catalytic triads of the serine proteinases and lipases

Protein Sci

CATH – a hierarchic classification of protein domain structures

Structure

Enzyme Nomenclature 1992

Protein superfamilies and domain superfolds

Nature

An evolutionary treasure: unification of a broad set of amidohydrolases related to urease

Proteins

From fold predictions to function predictions: automation of functional site conservation analysis for functional genome predictions

Protein, Sci

Review
Evolution of protein function, from a structural perspective