User:Pakpoom Subsoontorn/Notebook/Genetically Encoded Memory/2008/10/10: Difference between revisions
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**Amino-Acid-Sequence | **Amino-Acid-Sequence | ||
**Domains | **Domains | ||
*** | *** six tyrosine kinase conserved residues: R212, K235, H308, R311, Y342, H308 (nucleophilic tyrosine and catalytic pentad) | ||
*Target sequence: two identical simple sequence < 50 bp | *Target sequence: two identical simple sequence < 50 bp | ||
*Mechanism: | *Mechanism: | ||
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Name: Gamma-Delta, Host: Escherichia coli | Name: Gamma-Delta, Host: Escherichia coli | ||
*Classification: serine resolvase | |||
* | *structure: | ||
**Length: 183 aa | |||
**Amino-Acid-Sequence | |||
*Target sequence: | **Domains | ||
* | *** Catalytic site has R8, S10, D67, R68 | ||
*** Li et al 2005 science | |||
*Target sequence: two identical simple sequence < 50 bp | |||
**res-I, res-II, res-III | |||
*Mechanism: | |||
**two dimer per site (see diagram from the ref) | |||
*Engineering | |||
**Mutation | |||
***Mutation could change specificity to HK022's site | |||
**Chimeric | |||
**Directed-Evolution | |||
*Exision: | |||
**Unnatural-Host | |||
Revision as of 20:10, 21 October 2008
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Summary Note on site-specific recombinase system
ClassificationKeywords for classification, which can be overlapped
Methods
Site Specific recombinasesName: lambda, Host: Escherichia Coli
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. Break one strand at the time. Tyrosine phosphate binds to 3'end . 5'OH is free. Integration involve holiday junction
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: FLP, Host: Saccharomyces cerevisiae
Name: Gamma-Delta, Host: Escherichia coli
Name: Tn3, Host: Klebsiella pneumoniae Action: resolvase
questions/notes
DatabaseReference
improved genomic integration at a native human sequence. Nucl Acids Res, 29 5044-5051
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