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| - | [[Image:1ahd.gif|left|200px]] | + | {{Seed}} |
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| | {{STRUCTURE_1ahd| PDB=1ahd | SCENE= }} | | {{STRUCTURE_1ahd| PDB=1ahd | SCENE= }} |
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| - | '''DETERMINATION OF THE NMR SOLUTION STRUCTURE OF AN ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX'''
| + | ===DETERMINATION OF THE NMR SOLUTION STRUCTURE OF AN ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX=== |
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| - | ==Overview==
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| - | The nuclear magnetic resonance (NMR) solution structure of a complex formed by the mutant Antennapedia homeodomain with Cys39 replaced by Ser, Antp(C39S), and a 14 base-pair DNA duplex containing the BS2 operator sequence was determined using uniform 13C and 15N-labeling of the protein. Two-dimensional nuclear Overhauser enhancement spectroscopy ([1H,1H]NOESY) with 15N(omega 2)-half-filter and 13C(omega 1, omega 2)-double-half-filter, and three-dimensional heteronuclear-correlated [1H,1H]NOESY yielded a total of 855 intramolecular NOE upper distance constraints in the homeodomain, 151 upper distance constraints within the DNA duplex, and 39 intermolecular protein-DNA upper distance constraints. These data were used as the input for the structure calculation with simulated annealing followed by molecular dynamics in a water bath and energy refinement. A group of 16 conformers was thus generated which represent the solution structure of the Antp(C39S) homeodomain-DNA complex. The new structure determination confirms the salient features reported previously from a preliminary investigation of the same complex, in particular the location of the recognition helix in the major groove with the turn of the helix-turn-helix motif outside the contact area with the DNA, and the N-terminal arm of the homeodomain contacting the minor groove of the DNA. In addition, distinct amino acid side-chain-DNA contacts could be identified, and evidence was found that the invariant residue Asn51 (and possibly also Gln50) is in a slow dynamic equilibrium between two or several different DNA contact sites. The molecular dynamics calculations in a water bath yielded structures with hydration water molecules in the protein-DNA interface, which coincides with direct NMR observations of hydration waters. In the Appendix the experimental data obtained with the Antp(C39S) homeodomain-DNA complex and the techniques used for the structure calculation are evaluated using a simulated input data set derived from the X-ray crystal structure of a DNA complex with a homologous homeodomain. This study indicates that a nearly complete set of NOE upper distance constraints for the Antp(C39S) homeodomain and the protein-DNA interface was presently obtained. It further shows that the structure calculation used here yields a precise reproduction of the crystal structure from the simulated input data, and also results in hydration of the protein-DNA interface in the recalculated complex. | + | The line below this paragraph, {{ABSTRACT_PUBMED_7903398}}, adds the Publication Abstract to the page |
| | + | (as it appears on PubMed at http://www.pubmed.gov), where 7903398 is the PubMed ID number. |
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| | + | {{ABSTRACT_PUBMED_7903398}} |
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| | ==About this Structure== | | ==About this Structure== |
| - | 1AHD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AHD OCA]. | + | 1AHD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AHD OCA]. |
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| | ==Reference== | | ==Reference== |
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| | [[Category: Wuthrich, K.]] | | [[Category: Wuthrich, K.]] |
| | [[Category: Dna binding protein/dna]] | | [[Category: Dna binding protein/dna]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 10:16:27 2008'' | + | |
| | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 16:51:11 2008'' |
Revision as of 13:51, 30 June 2008
Template:STRUCTURE 1ahd
DETERMINATION OF THE NMR SOLUTION STRUCTURE OF AN ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX
Template:ABSTRACT PUBMED 7903398
About this Structure
1AHD is a Single protein structure of sequence from Drosophila melanogaster. Full experimental information is available from OCA.
Reference
Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex., Billeter M, Qian YQ, Otting G, Muller M, Gehring W, Wuthrich K, J Mol Biol. 1993 Dec 20;234(4):1084-93. PMID:7903398
Page seeded by OCA on Mon Jun 30 16:51:11 2008
