defs for restriction enzyme complexes

[gocentral]

Hello,

In continuation of my work on the restriction terms, I'd like to request addition of and/or modfications to the definitions for the restriction enzyme complex terms:

1. type I site-specific deoxyribonuclease complex (GO:0019812) Currently this term is undefined. Proposed def: "This is a multisubunit complex composed of 2 copies of the "restiction" (R) subunit, 2 copies of the "methylation" (M) subunit, and 2 copy of the "specificity" (S) subunit. This complex recognizes specific short DNA sequences (through the S subunit), and binds to them. If the recognition site is hemimethylated the complex acts as a methyltransferase which modifies the recognition site. S-adenosylmethionine is the methyl donor. Only the M and S subunits are required for this reaction. If the complex binds to an un-methylated recognition site, then the complex translocates the DNA bi-directionally in an ATP-dependent manor. When the translocation is stalled by impact with another complex or unusual DNA structure, the enzyme functions as an endonuclease and cleavage of the DNA will occur. This will be hundreds or thousands of base pairs away from the recognition site. These DNA restriction systems are used by bacteria to defend against phage and other foreign DNA that may enter a cell." Def. taken from PMID:15788748 and PMID:12654995 Also, please add the synonym: "type I restriction enzyme complex" and the forms of the name with "Type" capitalized, since according to PMID:12654995, that is the "official" way to designate these.

2. type II site-specific deoxyribonuclease complex (GO:0009359) Currently this term is undefined. Proposed def: "These complexes may consist of dimers, tetramers and may also function as monomers and therefore not be contained in any complex. The complex functions as an endonuclease to cleave DNA at or near a specific recognition site, when that site is un-methylated. It is also possible for the endonuclease to be in a complex with the corresponding methyltransferase that methylates the recognition site. DNA restriction systems such as this are used by bacteria to defend against phage and other foreign DNA that may enter a cell."
   Def ref: PMID:12654995 Also, please add the synonym: "type II restriction enzyme complex" and the forms of the name with "Type" capitalized, since according to PMID:12654995, that is the "official" way to designate these.

3. type III site-specific deoxyribonuclease complex (GO:0019813) Proposed new def: "A heterodimeric enzyme complex composed of two subunits\, Res and Mod. Functions as an endonuclease and cleaves DNA. Cleavage will only occur when there are two un-methylated copies of a specific recognition site in an inverse orientation on the DNA. Cleavage occurs at a specific distance away from one of the recognition sites. The Mod subunit can act alone as a methyltansferase. DNA restriction systems such as this are used by bacteria to defend against phage and other foreign DNA that may enter a cell." Def ref: PMID:12654995 Also, please add the synonym: "type III restriction enzyme complex" and the forms of the name with "Type" capitalized, since according to PMID:12654995, that is the "official" way to designate these.

4. new term request: name: type IV site-specific deoxyribonuclease complex def: "A complex consisting of two proteins which acts as an endonuclease in DNA sequences containing a specific modified recognition site. Modifications may include methylation, hydroxymethylation, and glucosyl-hydroxymethylation. Some forms of the enzyme contain only one protein." Def ref: PMID:12654995 parent: intracellular (GO:0005622) Also, please add the synonym: "type IV restriction enzyme complex" and the forms of the name with "Type" capitalized, since according to PMID:12654995, that is the "official" way to designate these.

NOTE: all of these currently have "intracellular" as a parent - but I'm thinking they can all go under "cytoplasm".

Thanks, Michelle

Reported by: mlgwinn

Original Ticket: "geneontology/ontology-requests/3399":https://sourceforge.net/p/geneontology/ontology-requests/3399

[gocentral]

• assigned_to: nobody --> gomidori

Original comment by: mah11

[gocentral]

Logged In: YES user_id=436423

New definitions! thanks!

I've added Type IV site-specific deoxyribonuclease complex, GO:0032068, made the def changes with minor adjustments, and added synonyms (for 'Type' vs. 'type' I've just changed the case in the term name - the no- synonyms-only-for-case rule).

m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=482944

Sounds good - thanks Midori.

Michelle

Original comment by: mlgwinn

[gocentral]

Logged In: YES user_id=482944

Hi Midori,

I just noticed an error in my initial submission: Type I site-specific deoxyribonuclease complex (GO:0019812) - the def should say "...and 1 copy of the "specificity" (S) subunit..." .

Sorry about that.

Michelle

Original comment by: mlgwinn

[gocentral]

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OK; fixed (before I even committed the file from the previous edits).

m

Original comment by: mah11

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... and remembering to close this now ...

Original comment by: mah11

[gocentral]

• milestone: --> TermGenie
• status: open --> closed-accepted

Original comment by: mah11