An active site at work – the role of key residues in C. diphteriae coproheme decarboxylase

dUTPases are a ubiquitous family of enzymes that are essential for all organisms and catalyse the breakdown of 2-deoxyuridine triphosphate (dUTP). InBacillus subtilisthere are two homotrimeric dUTPases: a genomic and a prophage form. Here, the structures of the genomic dUTPase and of its complex with the substrate analogue dUpNHpp and calcium are described, both at 1.85 Å resolution. The overall fold resembles that of previously solved trimeric dUTPases. The C-terminus, which contains one of the conserved sequence motifs, is disordered in both structures. The crystal of the complex contains six independent protomers which accommodate six dUpNHpp molecules, with three triphosphates in thetransconformation and the other three in the activegaucheconformation. The structure of the complex confirms the role of several key residues that are involved in ligand binding and the position of the catalytic water. Asp82, which has previously been proposed to act as a general base, points away from the active site. In the complex Ser64 reorients in order to hydrogen bond the phosphate chain of the substrate. A novel feature has been identified: the position in the sequence of the `Phe-lid', which packs against the uracil moiety, is adjacent to motif III, whereas in all other dUTPase structures the lid is in a conserved position in motif V of the flexible C-terminal arm. This requires a reconsideration of some aspects of the accepted mechanism.

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The functional role of the key residues in the active site of peroxidases

Biochemical Society Transactions ◽

10.1042/bst0230240 ◽

1995 ◽

Vol 23 (2) ◽

pp. 240-244 ◽

Cited By ~ 5

Author(s):

G. Smulevich

Keyword(s):

Active Site ◽

Functional Role ◽

Key Residues

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Faculty Opinions recommendation of Role of an active site guanine in hairpin ribozyme catalysis probed by exogenous nucleobase rescue.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1019915.242452 ◽

2004 ◽

Author(s):

Donald Burke

Keyword(s):

Active Site ◽

Hairpin Ribozyme

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Faculty Opinions recommendation of Structural and kinetic evidence for an extended hydrogen-bonding network in catalysis of methyl group transfer. Role of an active site asparagine residue in activation of methyl transfer by methyltransferases.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1067744.520660 ◽

2007 ◽

Author(s):

Rowena Matthews

Keyword(s):

Hydrogen Bonding ◽

Active Site ◽

Methyl Group ◽

Group Transfer ◽

Methyl Transfer ◽

Hydrogen Bonding Network ◽

Asparagine Residue ◽

Methyl Group Transfer

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HPF1 remodels the active site of PARP1 to enable the serine ADP-ribosylation of histones

Nature Communications ◽

10.1038/s41467-021-21302-4 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Fa-Hui Sun ◽

Peng Zhao ◽

Nan Zhang ◽

Lu-Lu Kong ◽

Catherine C. L. Wong ◽

...

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Active Site ◽

Negative Charge ◽

Structural Data ◽

Dna Breaks ◽

Adp Ribosylation ◽

Local Conformation ◽

Key Residues ◽

Structural Insights

AbstractUpon binding to DNA breaks, poly(ADP-ribose) polymerase 1 (PARP1) ADP-ribosylates itself and other factors to initiate DNA repair. Serine is the major residue for ADP-ribosylation upon DNA damage, which strictly depends on HPF1. Here, we report the crystal structures of human HPF1/PARP1-CAT ΔHD complex at 1.98 Å resolution, and mouse and human HPF1 at 1.71 Å and 1.57 Å resolution, respectively. Our structures and mutagenesis data confirm that the structural insights obtained in a recent HPF1/PARP2 study by Suskiewicz et al. apply to PARP1. Moreover, we quantitatively characterize the key residues necessary for HPF1/PARP1 binding. Our data show that through salt-bridging to Glu284/Asp286, Arg239 positions Glu284 to catalyze serine ADP-ribosylation, maintains the local conformation of HPF1 to limit PARP1 automodification, and facilitates HPF1/PARP1 binding by neutralizing the negative charge of Glu284. These findings, along with the high-resolution structural data, may facilitate drug discovery targeting PARP1.

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