Small but versatile: the extraordinary functional and structural diversity of the β-grasp fold View Full Text


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Article Info

DATE

2007-07-02

AUTHORS

A Maxwell Burroughs, S Balaji, Lakshminarayan M Iyer, L Aravind

ABSTRACT

BACKGROUND: The beta-grasp fold (beta-GF), prototyped by ubiquitin (UB), has been recruited for a strikingly diverse range of biochemical functions. These functions include providing a scaffold for different enzymatic active sites (e.g. NUDIX phosphohydrolases) and iron-sulfur clusters, RNA-soluble-ligand and co-factor-binding, sulfur transfer, adaptor functions in signaling, assembly of macromolecular complexes and post-translational protein modification. To understand the basis for the functional versatility of this small fold we undertook a comprehensive sequence-structure analysis of the fold and developed a natural classification for its members. RESULTS: As a result we were able to define the core distinguishing features of the fold and numerous elaborations, including several previously unrecognized variants. Systematic analysis of all known interactions of the fold showed that its manifold functional abilities arise primarily from the prominent beta-sheet, which provides an exposed surface for diverse interactions or additionally, by forming open barrel-like structures. We show that in the beta-GF both enzymatic activities and the binding of diverse co-factors (e.g. molybdopterin) have independently evolved on at least three occasions each, and iron-sulfur-cluster-binding on at least two independent occasions. Our analysis identified multiple previously unknown large monophyletic assemblages within the beta-GF, including one which unifies versions found in the fasciclin-1 superfamily, the ribosomal protein L25, the phosphoribosyl AMP cyclohydrolase (HisI) and glutamine synthetase. We also uncovered several new groups of beta-GF domains including a domain found in bacterial flagellar and fimbrial assembly components, and 5 new UB-like domains in the eukaryotes. CONCLUSION: Evolutionary reconstruction indicates that the beta-GF had differentiated into at least 7 distinct lineages by the time of the last universal common ancestor of all extant organisms, encompassing much of the structural diversity observed in extant versions of the fold. The earliest beta-GF members were probably involved in RNA metabolism and subsequently radiated into various functional niches. Most of the structural diversification occurred in the prokaryotes, whereas the eukaryotic phase was mainly marked by a specific expansion of the ubiquitin-like beta-GF members. The eukaryotic UB superfamily diversified into at least 67 distinct families, of which at least 19-20 families were already present in the eukaryotic common ancestor, including several protein and one lipid conjugated forms. Another key aspect of the eukaryotic phase of evolution of the beta-GF was the dramatic increase in domain architectural complexity of proteins related to the expansion of UB-like domains in numerous adaptor roles. More... »

PAGES

18-18

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    PUBMED

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    30 schema:description BACKGROUND: The beta-grasp fold (beta-GF), prototyped by ubiquitin (UB), has been recruited for a strikingly diverse range of biochemical functions. These functions include providing a scaffold for different enzymatic active sites (e.g. NUDIX phosphohydrolases) and iron-sulfur clusters, RNA-soluble-ligand and co-factor-binding, sulfur transfer, adaptor functions in signaling, assembly of macromolecular complexes and post-translational protein modification. To understand the basis for the functional versatility of this small fold we undertook a comprehensive sequence-structure analysis of the fold and developed a natural classification for its members. RESULTS: As a result we were able to define the core distinguishing features of the fold and numerous elaborations, including several previously unrecognized variants. Systematic analysis of all known interactions of the fold showed that its manifold functional abilities arise primarily from the prominent beta-sheet, which provides an exposed surface for diverse interactions or additionally, by forming open barrel-like structures. We show that in the beta-GF both enzymatic activities and the binding of diverse co-factors (e.g. molybdopterin) have independently evolved on at least three occasions each, and iron-sulfur-cluster-binding on at least two independent occasions. Our analysis identified multiple previously unknown large monophyletic assemblages within the beta-GF, including one which unifies versions found in the fasciclin-1 superfamily, the ribosomal protein L25, the phosphoribosyl AMP cyclohydrolase (HisI) and glutamine synthetase. We also uncovered several new groups of beta-GF domains including a domain found in bacterial flagellar and fimbrial assembly components, and 5 new UB-like domains in the eukaryotes. CONCLUSION: Evolutionary reconstruction indicates that the beta-GF had differentiated into at least 7 distinct lineages by the time of the last universal common ancestor of all extant organisms, encompassing much of the structural diversity observed in extant versions of the fold. The earliest beta-GF members were probably involved in RNA metabolism and subsequently radiated into various functional niches. Most of the structural diversification occurred in the prokaryotes, whereas the eukaryotic phase was mainly marked by a specific expansion of the ubiquitin-like beta-GF members. The eukaryotic UB superfamily diversified into at least 67 distinct families, of which at least 19-20 families were already present in the eukaryotic common ancestor, including several protein and one lipid conjugated forms. Another key aspect of the eukaryotic phase of evolution of the beta-GF was the dramatic increase in domain architectural complexity of proteins related to the expansion of UB-like domains in numerous adaptor roles.
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    38 L25
    39 RNA
    40 RNA metabolism
    41 Ub-like domain
    42 ability
    43 active site
    44 activity
    45 adaptor function
    46 adaptor role
    47 analysis
    48 ancestor
    49 architectural complexity
    50 aspects
    51 assemblages
    52 assembly
    53 assembly components
    54 barrel-like structure
    55 basis
    56 beta-GF domains
    57 beta-GF members
    58 beta-grasp fold
    59 binding
    60 biochemical functions
    61 classification
    62 clusters
    63 common ancestor
    64 complexes
    65 complexity
    66 components
    67 comprehensive sequence-structure analysis
    68 conjugated forms
    69 core distinguishing features
    70 cyclohydrolase
    71 different enzymatic active sites
    72 distinct families
    73 distinct lineages
    74 distinguishing features
    75 diverse interactions
    76 diverse range
    77 diversification
    78 diversity
    79 domain
    80 domain architectural complexity
    81 dramatic increase
    82 earliest beta-GF members
    83 elaboration
    84 enzymatic active site
    85 enzymatic activity
    86 eukaryotes
    87 eukaryotic common ancestor
    88 eukaryotic phase
    89 eukaryotic ubiquitin
    90 evolution
    91 evolutionary reconstruction
    92 expansion
    93 extant organisms
    94 extant versions
    95 family
    96 fasciclin-1
    97 features
    98 fimbrial assembly components
    99 folds
    100 form
    101 function
    102 functional ability
    103 functional niches
    104 functional versatility
    105 glutamine synthetase
    106 grasp fold
    107 group
    108 increase
    109 independent occasions
    110 interaction
    111 iron-sulfur clusters
    112 key aspects
    113 large monophyletic assemblages
    114 last universal common ancestor
    115 lineages
    116 lipid conjugated forms
    117 macromolecular complexes
    118 manifold functional abilities
    119 members
    120 metabolism
    121 modification
    122 monophyletic assemblage
    123 natural classification
    124 new UB-like domains
    125 new group
    126 niche
    127 numerous adaptor roles
    128 numerous elaborations
    129 occasions
    130 open barrel-like structures
    131 organisms
    132 phase
    133 phosphoribosyl AMP cyclohydrolase
    134 post-translational protein modification
    135 prokaryotes
    136 protein
    137 protein L25
    138 protein modification
    139 range
    140 reconstruction
    141 results
    142 ribosomal protein L25
    143 role
    144 scaffolds
    145 sequence-structure analysis
    146 sites
    147 small folds
    148 specific expansion
    149 structural diversification
    150 structural diversity
    151 structure
    152 sulfur transfer
    153 surface
    154 synthetase
    155 systematic analysis
    156 time
    157 transfer
    158 ubiquitin
    159 ubiquitin-like beta-GF members
    160 universal common ancestor
    161 unknown large monophyletic assemblages
    162 variants
    163 versatility
    164 version
    165 schema:name Small but versatile: the extraordinary functional and structural diversity of the β-grasp fold
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