This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1akh

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 11:23, 22 December 2014

MAT A1/ALPHA2/DNA TERNARY COMPLEX

Structural highlights

1akh is a 4 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:	MAT A1 RESIDUES 66 - 126 (Saccharomyces cerevisiae), MAT ALPHA2 RESIDUES 128 - 210 (Saccharomyces cerevisiae)
Resources:	FirstGlance, OCA, RCSB, PDBsum

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

The crystal structure of the heterodimer formed by the DNA binding domains of the yeast mating type transcription factors, MATa1 and MATalpha2, bound to a 21 bp DNA fragment has been determined at 2.5 A resolution. The DNA fragment in the present study differs at four central base pairs from the DNA sequence used in the previously studied ternary complex. These base pair changes give rise to a (dA5).(dT5) tract without changing the overall base composition of the DNA. The resulting A-tract occurs near the center of the overall 60 degrees bend in the DNA. Comparison of the two structures shows that the structural details of the DNA bend are maintained despite the DNA sequence changes. Analysis of the A5-tract DNA subfragment shows that it contains a bend toward the minor groove centered at one end of the A-tract. The observed bend is larger than that observed in the crystal structures of A-tracts embedded in uncomplexed DNA, which are straight and have been presumed to be quite rigid. Variation of the central DNA base sequence reverses the two AT base pairs contacted in the minor groove by Arg7 of the alpha2 N-terminal arm without significantly altering the DNA binding affinity of the a1/alpha2 heterodimer. The Arg7 side chain accommodates the sequence change by forming alternate H bond interactions, in agreement with the proposal that minor groove base pair recognition is insensitive to base pair reversal. Furthermore, the minor groove spine of hydration, which stabilizes the narrowed minor groove caused by DNA bending, is conserved in both structures. We also find that many of the water-mediated hydrogen bonds between the a1 and alpha2 homeodomains and the DNA are highly conserved, indicating an important role for water in stabilization of the a1/alpha2-DNA complex.

Crystal structure of the MATa1/MATalpha2 homeodomain heterodimer in complex with DNA containing an A-tract.,Li T, Jin Y, Vershon AK, Wolberger C Nucleic Acids Res. 1998 Dec 15;26(24):5707-18. PMID:9838003^[1]

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

References

↑ Li T, Jin Y, Vershon AK, Wolberger C. Crystal structure of the MATa1/MATalpha2 homeodomain heterodimer in complex with DNA containing an A-tract. Nucleic Acids Res. 1998 Dec 15;26(24):5707-18. PMID:9838003

1 Structural highlights
2 Evolutionary Conservation
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1akh"

@@ Line 3: / Line 3: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[1akh]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AKH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AKH FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MAT A1 RESIDUES 66 - 126 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), MAT ALPHA2 RESIDUES 128 - 210 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
+</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MAT A1 RESIDUES 66 - 126 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), MAT ALPHA2 RESIDUES 128 - 210 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1akh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1akh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1akh RCSB], [http://www.ebi.ac.uk/pdbsum/1akh PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1akh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1akh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1akh RCSB], [http://www.ebi.ac.uk/pdbsum/1akh PDBsum]</span></td></tr>
-<table>
+</table>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 29: / Line 29: @@
 </StructureSection>
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Jin, Y.]]
+[[Category: Jin, Y]]
-[[Category: Li, T.]]
+[[Category: Li, T]]
-[[Category: Vershon, A K.]]
+[[Category: Vershon, A K]]
-[[Category: Wolberger, C.]]
+[[Category: Wolberger, C]]
 [[Category: Complex]]
 [[Category: Dna]]

1akh

From Proteopedia

Revision as of 11:23, 22 December 2014

MAT A1/ALPHA2/DNA TERNARY COMPLEX

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox