1s5p
From Proteopedia
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| , resolution 1.96Å | |||||||
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| Ligands: | |||||||
| Gene: | NPDA, COBB, B1120 (Escherichia coli) | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Structure and substrate binding properties of cobB, a Sir2 homolog protein deacetylase from Eschericia coli.
Overview
Sirtuins are NAD+-dependent protein deacetylase enzymes that are broadly conserved from bacteria to human, and have been implicated to play important roles in gene regulation, metabolism and longevity. cobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase (Acs) at an active site lysine to stimulate its enzymatic activity. Here, we report the structure of cobB bound to an acetyl-lysine containing non-cognate histone H4 substrate. A comparison with the previously reported archaeal and eukaryotic sirtuin structures reveals the greatest variability in a small zinc-binding domain implicated to play a particularly important role in substrate-specific binding by the sirtuin proteins. Comparison of the cobB/histone H4 complex with other sirtuin proteins in complex with acetyl-lysine containing substrates, further suggests that contacts to the acetyl-lysine side-chain and beta-sheet interactions with residues directly C-terminal to the acetyl-lysine represent conserved features of sirtuin-substrate recognition. Isothermal titration calorimetry studies were used to compare the affinity of cobB for a variety of cognate and non-cognate acetyl-lysine-bearing peptides revealing an exothermic reaction with relatively little discrimination between substrates. In contrast, similar studies employing intact acetylated Acs protein as a substrate reveal a binding reaction that is endothermic, suggesting that cobB recognition of substrate involves a burial of hydrophobic surface and/or structural rearrangement involving substrate regions distal to the acetyl-lysine-binding site. Together, these studies suggest that substrate-specific binding by sirtuin proteins involves contributions from the zinc-binding domain of the enzyme and substrate regions distal to the acetyl-lysine-binding site.
About this Structure
1S5P is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
Structure and substrate binding properties of cobB, a Sir2 homolog protein deacetylase from Escherichia coli., Zhao K, Chai X, Marmorstein R, J Mol Biol. 2004 Mar 26;337(3):731-41. PMID:15019790
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