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

spinqualitylabelsall models PDB ID 1d66 Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image 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. See Also Gal3-Gal80-Gal4 Hydrogen in macromolecular models 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 Contents 1 Structural highlights 2 Function 3 Evolutionary Conservation 4 Publication Abstract from PubMed 5 See Also 6 References

UvrD

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, 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. Helicases use energy from nucleoside triphosphate hydrolysis to unwind double helices in metabolic pathways using nucleic acids. A nucleoside triphosphate (NTP) is a nucleotide with a nitrogenous base bound to a 5-carbon sugar with 3 phosphates attached. Phosphates are typically used to store energy that is released when breaking bonds to drive catabolic reactions. Helicases are also involved in multiple processes, including RNAs and DNAs, single stranded and double stranded. Helicases were found in the 1970’s to be DNA-dependent ATPases, meaning that they use ATP hydrolysis to complete its interactions with the different types of nucleic acids it comes into contact with. There are multiple types of helicases, with some being for RNA and DNA. Helicase II, also called UvrD is the founding member of SF1, one group of six superfamiliies used to identify helicases. SF1 and SF2 members share seven conserved sequence motifs that are involved in NTP binding. These are located between the two RecA-like domains in other group members of SF1 and SF2. UvrD is important in replication, recombination, and repair from ultraviolet damage and mismatched base pairs. Go into NER from the book..

There are 7 sequence motifs and a Q motif conserved among the SF1 and the SF2. I, Ia, II-VI) are involved in ATP binding. Motifs Ia, III, and V are also involved in ssDNA binding. Motif IV is reported to be unique in SF1. They found in their paper, seven new sequence motifs conserved among UvrD homologs. They are Ib, Ic, Id, IVb, IVc, Va, and VIa. These conserved residues are involved in DNA binding or domain 1B and 2B interactions.

UvrD Binding Site for DNA

UvrD Binding Site with RNAP and nontemplate strand

UvrD Binding Site for ATP analog

When determining the structure of UvrD, an ATP analog was used. They used an so that the last phosphate can't be cleaved. Using the unhydrolyzable analog is beneficial in locking in the structure to observe.

UvrD Tudor-Domain

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