Ydc2 protein domain

Protein domain

Ydc2 protein domain

Crystal structure of the yeast mitochondrial Holliday junction resolvase, YDC2

Identifiers
Symbol| Ydc2-catalyst
Pfam| PF09159
Pfam clan| CL0219
InterPro| IPR015242
SCOP2| 1kcf / SCOPe / SUPFAM
CDD| cd00529
| Available protein structures:

Pfam  | structures / ECOD
PDB| RCSB PDB; PDBe; PDBj
PDBsum| structure summary

In molecular biology, the protein domain, Ydc2 (also known as SpCce1), is a Holliday junction resolvase from the fission yeast Schizosaccharomyces pombe that is involved in the maintenance of mitochondrial DNA.

## Function

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In molecular biology, the Ydc2 domains are enzymes, or in other words biological catalysts, capable of resolving Holliday junctions into separate DNA duplexes by cleaving DNA after 5'-CT-3, and 5'-TT-3, sequences.

## Properties

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The junction resolving enzymes are very diverse, but have the following properties in common:

* high structure specificity for binding
* metal dependent, sequence specific cleavage activity[1]

Essentially, they are highly specific.

## Limiting factors

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Furthermore, the cleavage efficiency is affected by:

* strand type (continuous or exchange)
* nucleotide sequence at cleavage site[1]

## Structure

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This protein domain forms a ribonuclease H fold consisting of two beta sheets and one alpha helix, arranged as a beta-alpha-beta motif. Each beta sheet has five strands, arranged in a 32145 order, with the second strand being antiparallel to the rest.[2]

## References

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1. ^ a b White MF, Lilley DM (1998). "Interaction of the resolving enzyme YDC2 with the four-way DNA junction". Nucleic Acids Res. 26 (24): 5609–16\. doi:10.1093/nar/26.24.5609. PMC 148026. PMID 9837990.
2. ^ Ceschini S, Keeley A, McAlister MS, Oram M, Phelan J, Pearl LH, Tsaneva IR, Barrett TE (December 2001). "Crystal structure of the fission yeast mitochondrial Holliday junction resolvase Ydc2". EMBO J. 20 (23): 6601–11\. doi:10.1093/emboj/20.23.6601. PMC 125760. PMID 11726496.

This article incorporates text from the public domain Pfam and InterPro: IPR015242