1xyi
From Proteopedia
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|PDB= 1xyi |SIZE=350|CAPTION= <scene name='initialview01'>1xyi</scene>, resolution 1.45Å | |PDB= 1xyi |SIZE=350|CAPTION= <scene name='initialview01'>1xyi</scene>, resolution 1.45Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= sac7d ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2285 Sulfolobus acidocaldarius]) | |GENE= sac7d ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2285 Sulfolobus acidocaldarius]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1azp|1AZP]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xyi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xyi OCA], [http://www.ebi.ac.uk/pdbsum/1xyi PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1xyi RCSB]</span> | ||
}} | }} | ||
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[[Category: protein-dna complex]] | [[Category: protein-dna complex]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:56:25 2008'' |
Revision as of 21:56, 30 March 2008
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| , resolution 1.45Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||
| Gene: | sac7d (Sulfolobus acidocaldarius) | ||||||
| Related: | 1AZP
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Hyperthermophile chromosomal protein Sac7d double mutant Val26Ala/Met29Ala in complex with DNA GCGATCGC
Overview
Sac7d, a small, abundant, sequence-general DNA-binding protein from the hyperthermophilic archaeon Sulfolobus acidocaldarius, causes a single-step sharp kink in DNA (approximately 60 degrees) via the intercalation of both Val26 and Met29. These two amino acids were systematically changed in size to probe their effects on DNA kinking. Eight crystal structures of five Sac7d mutant-DNA complexes have been analyzed. The DNA-binding pattern of the V26A and M29A single mutants is similar to that of the wild-type, whereas the V26A/M29A protein binds DNA without side chain intercalation, resulting in a smaller overall bending (approximately 50 degrees). The M29F mutant inserts the Phe29 side chain orthogonally to the C2pG3 step without stacking with base pairs, inducing a sharp kink (approximately 80 degrees). In the V26F/M29F-GCGATCGC complex, Phe26 intercalates deeply into DNA bases by stacking with the G3 base, whereas Phe29 is stacked on the G15 deoxyribose, in a way similar to those used by the TATA box-binding proteins. All mutants have reduced DNA-stabilizing ability, as indicated by their lower T m values. The DNA kink patterns caused by different combinations of hydrophobic side chains may be relevant in understanding the manner by which other minor groove-binding proteins interact with DNA.
About this Structure
1XYI is a Single protein structure of sequence from Sulfolobus acidocaldarius. Full crystallographic information is available from OCA.
Reference
Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d., Chen CY, Ko TP, Lin TW, Chou CC, Chen CJ, Wang AH, Nucleic Acids Res. 2005 Jan 14;33(1):430-8. Print 2005. PMID:15653643
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