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Revision as of 16:57, 4 October 2022

1 DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX
2 UvrD
3 UvrD Binding Site for DNA
4 UvrD Binding Site with RNAP and nontemplate strand
5 UvrD Tudor-Domain

DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX

Structural highlights

1d66 is a 4 chain structure with sequence from Atcc 18824. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[GAL4_YEAST] This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which code for the enzymes used to convert galactose to glucose. It recognizes a 17 base pair sequence in (5'-CGGRNNRCYNYNCNCCG-3') the upstream activating sequence (UAS-G) of these genes.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

A specific DNA complex of the 65-residue, N-terminal fragment of the yeast transcriptional activator, GAL4, has been analysed at 2.7 A resolution by X-ray crystallography. The protein binds as a dimer to a symmetrical 17-base-pair sequence. A small, Zn(2+)-containing domain recognizes a conserved CCG triplet at each end of the site through direct contacts with the major groove. A short coiled-coil dimerization element imposes 2-fold symmetry. A segment of extended polypeptide chain links the metal-binding module to the dimerization element and specifies the length of the site. The relatively open structure of the complex would allow another protein to bind coordinately with GAL4.

: Zinc is responsible for maintaining the secondary structure.

Gal4 has lots of that interact with DNA

The Upstream activation sequence () for Gal 4.It only interacts with one strand of DNA sequence. The UAS is a 881 amino acid protein that binds to DNA, has dimerization, and recruits other transcriptional promoters. This needs galactose in order to be open.

It recognizes a 17 base pair sequence in (5'-CGGRNNRCYNYNCNCCG-3') the upstream activating sequence (UAS-G) of these genes. (This is what I found from sources)

i. I was searching for this, but I kind of struggled to find this when I was looking through the links. ii. The protein interacts with one strand of double stranded DNA.

DNA recognition by GAL4: structure of a protein-DNA complex.,Marmorstein R, Carey M, Ptashne M, Harrison SC Nature. 1992 Apr 2;356(6368):408-14. PMID:1557122^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Marmorstein R, Carey M, Ptashne M, Harrison SC. DNA recognition by GAL4: structure of a protein-DNA complex. Nature. 1992 Apr 2;356(6368):408-14. PMID:1557122 doi:http://dx.doi.org/10.1038/356408a0

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

UvrD

, also known as Helicase II, is one of many components responsible in repairing DNA damage. UvrD is involved in nucleotide excision repair (NER) and transcription-coupled DNA repair (TCR repair). TCR repair occurs during transcription when Helicase II binds to a RNA polymerase (RNAP) and slides backwards in order to fix the mismatched nucleotide. One of the main structural components of how UvrD binds to RNAP is by having a Tudor-domain like fold. This helps better explain the UvrD-RNAP interaction, which is a better explanation than just having nucleic-acid affinity. A main cause in damage to DNA, which requires for nucleotide excision repair is from UV radiation, which can come from multiple sources, including sunlight and UV light from tanning beds.

UvrD Binding Site for DNA

UvrD Binding Site with RNAP and nontemplate strand

is necessary for the backtracking over DNA to repair the mismatched nucleotide. The C-terminal Domain or CTD is an important structure that is thought of to be an important in the interaction between UvrD and RNAP.

UvrD Tudor-Domain

What is a Tudor Domain? It is a methyl-lysine and methyl arginine binding domain present in proteins.

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-	==UvrD Binding Site ~~for~~ RNAP==	+	==UvrD Binding Site with RNAP and nontemplate strand ==
-	UvrD-dependent binding for RNA polymerase is necessary for the backtracking over DNA to repair the mismatched nucleotide. The C-terminal Domain or CTD is an important structure that is thought of to be an important in the interaction between UvrD and RNAP.	+	<scene name='92/925553/Uvrd_with_rnap_and_nusa/1'>UvrD-dependent binding for RNA polymerase</scene> is necessary for the backtracking over DNA to repair the mismatched nucleotide. The C-terminal Domain or CTD is an important structure that is thought of to be an important in the interaction between UvrD and RNAP.

Sandbox reserved 1752

From Proteopedia

Revision as of 16:57, 4 October 2022

Contents

DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

UvrD

UvrD Binding Site for DNA

UvrD Binding Site with RNAP and nontemplate strand

UvrD Tudor-Domain

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