1y7m
From Proteopedia
(New page: 200px<br /><applet load="1y7m" size="450" color="white" frame="true" align="right" spinBox="true" caption="1y7m, resolution 2.05Å" /> '''Crystal Structure of...) |
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| - | [[Image:1y7m.gif|left|200px]]<br /><applet load="1y7m" size=" | + | [[Image:1y7m.gif|left|200px]]<br /><applet load="1y7m" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1y7m, resolution 2.05Å" /> | caption="1y7m, resolution 2.05Å" /> | ||
'''Crystal Structure of the B. subtilis YkuD protein at 2 A resolution'''<br /> | '''Crystal Structure of the B. subtilis YkuD protein at 2 A resolution'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The crystal structure of the product of the Bacillus subtilis ykuD gene | + | The crystal structure of the product of the Bacillus subtilis ykuD gene was solved by the multiwavelength anomalous dispersion (MAD) method and refined using data to 2.0 A resolution. The ykuD protein is a representative of a distinctly prokaryotic and ubiquitous family found among both pathogenic and nonpathogenic Gram-positive and Gram-negative bacteria. The deduced amino acid sequence reveals the presence of an N-terminal LysM domain, which occurs among enzymes involved in cell wall metabolism, and a novel, putative catalytic domain with a highly conserved His/Cys-containing motif of hitherto unknown structure. As the wild-type protein did not crystallize, a double mutant was designed (Lys117Ala/Gln118Ala) to reduce excess surface conformational entropy. As expected, the structure of the LysM domain is similar to the NMR structure reported for an analogous domain from Escherichia coli murein transglycosylase MltD. The molecular model also shows that the 112-residue-long C-terminal domain has a novel tertiary fold consisting of a beta-sandwich with two mixed sheets, one containing five strands and the other, six strands. The two beta-sheets form a cradle capped by an alpha-helix. This domain contains a putative catalytic site with a tetrad of invariant His123, Gly124, Cys139, and Arg141. The stereochemistry of this active site shows similarities to peptidotransferases and sortases, and suggests that the enzymes of the ykuD family may play an important role in cell wall biology. |
==About this Structure== | ==About this Structure== | ||
| - | 1Y7M is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168] with CD and SO4 as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | + | 1Y7M is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168] with <scene name='pdbligand=CD:'>CD</scene> and <scene name='pdbligand=SO4:'>SO4</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y7M OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Bacillus subtilis subsp. subtilis str. 168]] | [[Category: Bacillus subtilis subsp. subtilis str. 168]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Bielnicki, J | + | [[Category: Bielnicki, J A.]] |
[[Category: Dauter, Z.]] | [[Category: Dauter, Z.]] | ||
[[Category: Derewenda, U.]] | [[Category: Derewenda, U.]] | ||
| - | [[Category: Derewenda, Z | + | [[Category: Derewenda, Z S.]] |
[[Category: Devedjiev, Y.]] | [[Category: Devedjiev, Y.]] | ||
[[Category: Joachimiak, A.]] | [[Category: Joachimiak, A.]] | ||
| - | [[Category: MCSG, Midwest | + | [[Category: MCSG, Midwest Center for Structural Genomics.]] |
[[Category: CD]] | [[Category: CD]] | ||
[[Category: SO4]] | [[Category: SO4]] | ||
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[[Category: surface mutagenesis]] | [[Category: surface mutagenesis]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:02:37 2008'' |
Revision as of 14:02, 21 February 2008
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Crystal Structure of the B. subtilis YkuD protein at 2 A resolution
Overview
The crystal structure of the product of the Bacillus subtilis ykuD gene was solved by the multiwavelength anomalous dispersion (MAD) method and refined using data to 2.0 A resolution. The ykuD protein is a representative of a distinctly prokaryotic and ubiquitous family found among both pathogenic and nonpathogenic Gram-positive and Gram-negative bacteria. The deduced amino acid sequence reveals the presence of an N-terminal LysM domain, which occurs among enzymes involved in cell wall metabolism, and a novel, putative catalytic domain with a highly conserved His/Cys-containing motif of hitherto unknown structure. As the wild-type protein did not crystallize, a double mutant was designed (Lys117Ala/Gln118Ala) to reduce excess surface conformational entropy. As expected, the structure of the LysM domain is similar to the NMR structure reported for an analogous domain from Escherichia coli murein transglycosylase MltD. The molecular model also shows that the 112-residue-long C-terminal domain has a novel tertiary fold consisting of a beta-sandwich with two mixed sheets, one containing five strands and the other, six strands. The two beta-sheets form a cradle capped by an alpha-helix. This domain contains a putative catalytic site with a tetrad of invariant His123, Gly124, Cys139, and Arg141. The stereochemistry of this active site shows similarities to peptidotransferases and sortases, and suggests that the enzymes of the ykuD family may play an important role in cell wall biology.
About this Structure
1Y7M is a Single protein structure of sequence from Bacillus subtilis subsp. subtilis str. 168 with and as ligands. Full crystallographic information is available from OCA.
Reference
B. subtilis ykuD protein at 2.0 A resolution: insights into the structure and function of a novel, ubiquitous family of bacterial enzymes., Bielnicki J, Devedjiev Y, Derewenda U, Dauter Z, Joachimiak A, Derewenda ZS, Proteins. 2006 Jan 1;62(1):144-51. PMID:16287140
Page seeded by OCA on Thu Feb 21 16:02:37 2008
Categories: Bacillus subtilis subsp. subtilis str. 168 | Single protein | Bielnicki, J A. | Dauter, Z. | Derewenda, U. | Derewenda, Z S. | Devedjiev, Y. | Joachimiak, A. | MCSG, Midwest Center for Structural Genomics. | CD | SO4 | Cell wall catabolism | Cysteine proteases | Mcsg | Midwest center for structural genomics | Protein structure initiative | Psi | Structural genomics | Surface mutagenesis
