User:Pakpoom Subsoontorn/Notebook/Genetically Encoded Memory/2008/10/10: Difference between revisions
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==Classification== | ==Classification== | ||
Keywords for classification, which can be overlapped | Keywords for classification, which can be overlapped | ||
*Tyrosine recombinase | *By Structure | ||
*Serine recombinase | **Tyrosine recombinase | ||
*Large Serine recombinase | **Serine recombinase | ||
*Integrase | **Large Serine recombinase | ||
*Excisionase | *By Function | ||
*Invertase | **Integrase | ||
*Resolvase | **Excisionase | ||
*Transposase | **Invertase | ||
*Integron | **Resolvase | ||
**Transposase | |||
*other stuffs | |||
**Integron | |||
==Site Specific recombinases== | ==Site Specific recombinases== |
Revision as of 18:56, 21 October 2008
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Summary Note on site-specific recombinase system
ClassificationKeywords for classification, which can be overlapped
Site Specific recombinasesName: lambda, Host: Escherichia Coli
length:: 356 aa. N-terminal 1-64 aa binds to arm-type site. C-terminal 65-169 aa binds to low affinity core-type site. 170-356 aa is the minimal catalytic domain which include catalytic tyrosine and RKHRK pentad crystal structure of C-terminal catalytic domain is known
attB:: has two inverted repeated sequence flanking an overlap region. inverted repeated sequence (core-type) is about 9-13 bps. The overlap region is about 6-8 bps and shares sequence with attP. Here is where crossing over occur. attP is more complicated, with arm-type sites flanking core-type site. overlap-region::TTTATAC
Mutation could change specificity to HK022's site
host factor (IHF, from HimA and hip genes) is required for sharp bending in DNA, allowing the integrase bound at arm-type site to also bind at the low affinity core-type sites.
the mutant works in mammalian cell (see more experiment detail)
Name: HK022, Host: Escherichia Coli
attB:: has two inverted repeated sequence flanking an overlap region. inverted repeated sequence (core-type). The overlap region shares sequence with attP. Crossing over occurs at the overlap region. overlap-region::AGGTGAA attP has arm-type sites flanking core-type site.
Integrases from lambda and HK022 recognize the same arm-type site. However, the integrases notice the difference in core-type site. IHF is required.
attB:: has two inverted repeated sequence flanking an overlap region. inverted repeated sequence (core-type). The overlap region shares sequence with attP. Crossing over occurs at the overlap region. overlap-region::TTCGTAA attP has arm-type sites flanking core-type site.
IHF is required.
Name: HP1, Host: Haemophilus influenzae
length:: 337 aa crystal structure of C-terminal catalytic domain is known
attB:: has two inverted repeated sequence flanking an overlap region. inverted repeated sequence (core-type). The overlap region shares sequence with attP. Crossing over occurs at the overlap region. overlap-region::TTTTAAA attP has arm-type sites flanking core-type site.
Name: L5, Host: Mycobacterium smegmatis
length:: 613 aa crystal structure is unknown.
attP:: has core-type sites and overlap region, without an arm-type site
Mutation/directed evolution could change specificity to pseudo attP site (HpsA, 44% identity)
Excisionase has not yet been found.
Integration works in E.coli, mammalian and in vitro
Name: R4, Host: Streptomyces
length:: 469 aa crystal structure is unknown.
attP:: has core-type sites and overlap region, without an arm-type site. Minimal attB and attP site is <56 bps.
Excisionase has not yet been found.
Integration works in mammalian cell.
length:: 485 aa. crystal structure is unknown.
attP:: has core-type sites and overlap region, without an arm-type site. Minimal attB and attP site is <56 bps
Integration works in E.coli, mammalian cell and in vitro.
Name: Cre (P1), Host: Escherichia coli
Name: XerC, Host: Escherichia coli
Name: Gamma-Delta, Host: Escherichia coli Action: resolvase
length:: 183 aa some crystal structure with res target have been identified.
Integration works in mammalian cell.
Name: Tn3, Host: Klebsiella pneumoniae Action: resolvase
questions/notes
DatabaseReference
335:667-678
improved genomic integration at a native human sequence. Nucl Acids Res, 29 5044-5051 |