1ewf
From Proteopedia
(New page: 200px<br /> <applet load="1ewf" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ewf, resolution 1.7Å" /> '''THE 1.7 ANGSTROM CRY...) |
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| - | [[Image:1ewf.gif|left|200px]]<br /> | + | [[Image:1ewf.gif|left|200px]]<br /><applet load="1ewf" size="350" color="white" frame="true" align="right" spinBox="true" |
| - | <applet load="1ewf" size=" | + | |
caption="1ewf, resolution 1.7Å" /> | caption="1ewf, resolution 1.7Å" /> | ||
'''THE 1.7 ANGSTROM CRYSTAL STRUCTURE OF BPI'''<br /> | '''THE 1.7 ANGSTROM CRYSTAL STRUCTURE OF BPI'''<br /> | ||
==Overview== | ==Overview== | ||
| - | We have extended the resolution of the crystal structure of human | + | We have extended the resolution of the crystal structure of human bactericidal/permeability-increasing protein (BPI) to 1.7 A. BPI has two domains with the same fold, but with little sequence similarity. To understand the similarity in structure of the two domains, we compare the corresponding residue positions in the two domains by the method of 3D-1D profiles. A 3D-1D profile is a string formed by assigning each position in the 3D structure to one of 18 environment classes. The environment classes are defined by the local secondary structure, the area of the residue which is buried from solvent, and the fraction of the area buried by polar atoms. A structural alignment between the two BPI domains was used to compare the 3D-1D environments of structurally equivalent positions. Greater than 31% of the aligned positions have conserved 3D-1D environments, but only 13% have conserved residue identities. Analysis of the 3D-1D environmentally conserved positions helps to identify pairs of residues likely to be important in conserving the fold, regardless of the residue similarity. We find examples of 3D-1D environmentally conserved positions with dissimilar residues which nevertheless play similar structural roles. To generalize our findings, we analyzed four other proteins with similar structures yet dissimilar sequences. Together, these examples show that aligned pairs of dissimilar residues often share similar structural roles, stabilizing dissimilar sequences in the same fold. |
==About this Structure== | ==About this Structure== | ||
| - | 1EWF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with PC1 as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1EWF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=PC1:'>PC1</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EWF OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Homo sapiens]] | [[Category: Homo sapiens]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Beamer, L | + | [[Category: Beamer, L J.]] |
[[Category: Eisenberg, D.]] | [[Category: Eisenberg, D.]] | ||
[[Category: Grothe, R.]] | [[Category: Grothe, R.]] | ||
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[[Category: permeability-increasing]] | [[Category: permeability-increasing]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:32:12 2008'' |
Revision as of 10:32, 21 February 2008
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THE 1.7 ANGSTROM CRYSTAL STRUCTURE OF BPI
Overview
We have extended the resolution of the crystal structure of human bactericidal/permeability-increasing protein (BPI) to 1.7 A. BPI has two domains with the same fold, but with little sequence similarity. To understand the similarity in structure of the two domains, we compare the corresponding residue positions in the two domains by the method of 3D-1D profiles. A 3D-1D profile is a string formed by assigning each position in the 3D structure to one of 18 environment classes. The environment classes are defined by the local secondary structure, the area of the residue which is buried from solvent, and the fraction of the area buried by polar atoms. A structural alignment between the two BPI domains was used to compare the 3D-1D environments of structurally equivalent positions. Greater than 31% of the aligned positions have conserved 3D-1D environments, but only 13% have conserved residue identities. Analysis of the 3D-1D environmentally conserved positions helps to identify pairs of residues likely to be important in conserving the fold, regardless of the residue similarity. We find examples of 3D-1D environmentally conserved positions with dissimilar residues which nevertheless play similar structural roles. To generalize our findings, we analyzed four other proteins with similar structures yet dissimilar sequences. Together, these examples show that aligned pairs of dissimilar residues often share similar structural roles, stabilizing dissimilar sequences in the same fold.
About this Structure
1EWF is a Single protein structure of sequence from Homo sapiens with as ligand. Full crystallographic information is available from OCA.
Reference
The 1.7 A crystal structure of BPI: a study of how two dissimilar amino acid sequences can adopt the same fold., Kleiger G, Beamer LJ, Grothe R, Mallick P, Eisenberg D, J Mol Biol. 2000 Jun 16;299(4):1019-34. PMID:10843855
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