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2  structures 108  species 1  interaction 128  sequences 6  architectures

Family: Ydc2-catalyt (PF09159)

Summary: Mitochondrial resolvase Ydc2 / RNA splicing MRS1

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This is the Wikipedia entry entitled "Ydc2 protein domain". More...

Ydc2 protein domain Edit Wikipedia article

Ydc2 protein domain
PDB 1kcf EBI.jpg
Crystal structure of the yeast mitochondrial Holliday junction resolvase, YDC2
Identifiers
Symbol Ydc2-catalyt
Pfam PF09159
Pfam clan CL0219
InterPro IPR015242
SCOP 1kcf
SUPERFAMILY 1kcf

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[edit]

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[edit]

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[edit]

Furthermore, the cleavage efficiency is affected by:

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

Structure[edit]

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[edit]

  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

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Mitochondrial resolvase Ydc2 / RNA splicing MRS1 Provide feedback

Members of this family adopt a secondary structure 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. Mitochondrial resolvase Ydc2 is capable of resolving Holliday junctions and cleaves DNA after 5'-CT-3' and 5'-TT-3' sequences [1]. This family also contains the mitochondrial RNA-splicing protein MRS1 which is involved in the excision of group I introns [2-3].

Literature references

  1. Ceschini S, Keeley A, McAlister MS, Oram M, Phelan J, Pearl LH, Tsaneva IR, Barrett TE; , EMBO J. 2001;20:6601-6611.: Crystal structure of the fission yeast mitochondrial Holliday junction resolvase Ydc2. PUBMED:11726496 EPMC:11726496

  2. Turk EM, Caprara MG;, J Biol Chem. 2010;285:8585-8594.: Splicing of yeast aI5beta group I intron requires SUV3 to recycle MRS1 via mitochondrial degradosome-promoted decay of excised intron ribonucleoprotein (RNP). PUBMED:20064926 EPMC:20064926

  3. Kreike J, Schulze M, Pillar T, Korte A, Rodel G;, Curr Genet. 1986;11:185-191.: Cloning of a nuclear gene MRS1 involved in the excision of a single group I intron (bI3) from the mitochondrial COB transcript in S. cerevisiae. PUBMED:2834089 EPMC:2834089


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR015242

This 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. They are capable of resolving Holliday junctions and cleave DNA after 5'-CT-3, and 5'-TT-3, sequences [PUBMED:11726496]. This entry also includes a domain found in the mitochondrial RNA-splicing protein MRS1 which is involved in the excision of group I introns [PUBMED:20064926, PUBMED:2834089].

Domain organisation

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Alignments

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(53)
Full
(128)
Representative proteomes NCBI
(123)
Meta
(59)
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(18)
RP35
(40)
RP55
(69)
RP75
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  Seed
(53)
Full
(128)
Representative proteomes NCBI
(123)
Meta
(59)
RP15
(18)
RP35
(40)
RP55
(69)
RP75
(83)
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  Seed
(53)
Full
(128)
Representative proteomes NCBI
(123)
Meta
(59)
RP15
(18)
RP35
(40)
RP55
(69)
RP75
(83)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: pdb_1kcf
Previous IDs: none
Type: Domain
Author: Sammut SJ
Number in seed: 53
Number in full: 128
Average length of the domain: 264.70 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 72.90 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.0 20.0
Trusted cut-off 20.0 20.7
Noise cut-off 19.8 19.9
Model length: 274
Family (HMM) version: 5
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Ydc2-catalyt

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Ydc2-catalyt domain has been found. There are 2 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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