1y7m
From Proteopedia
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|PDB= 1y7m |SIZE=350|CAPTION= <scene name='initialview01'>1y7m</scene>, resolution 2.05Å | |PDB= 1y7m |SIZE=350|CAPTION= <scene name='initialview01'>1y7m</scene>, resolution 2.05Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene> | + | |LIGAND= <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= ykud ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 Bacillus subtilis subsp. subtilis str. 168]) | |GENE= ykud ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 Bacillus subtilis subsp. subtilis str. 168]) | ||
| + | |DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam03734 ErfK_YbiS_YhnG], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd00118 LysM]</span> | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1y7m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y7m OCA], [http://www.ebi.ac.uk/pdbsum/1y7m PDBsum], [http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1kfv JenaLib], [http://www.rcsb.org/pdb/explore.do?structureId=1y7m RCSB]</span> | ||
}} | }} | ||
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[[Category: Joachimiak, A.]] | [[Category: Joachimiak, A.]] | ||
[[Category: MCSG, Midwest Center for Structural Genomics.]] | [[Category: MCSG, Midwest Center for Structural Genomics.]] | ||
| - | [[Category: CD]] | ||
| - | [[Category: SO4]] | ||
[[Category: cell wall catabolism]] | [[Category: cell wall catabolism]] | ||
[[Category: cysteine protease]] | [[Category: cysteine protease]] | ||
| Line 40: | Line 40: | ||
[[Category: surface mutagenesis]] | [[Category: surface mutagenesis]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 26 06:13:56 2008'' |
Revision as of 04:13, 26 March 2008
| |||||||
| , resolution 2.05Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Gene: | ykud (Bacillus subtilis subsp. subtilis str. 168) | ||||||
| Domains: | ErfK_YbiS_YhnG, LysM | ||||||
| Resources: | FirstGlance, OCA, PDBsum, JenaLib, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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. 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 Wed Mar 26 06:13:56 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. | Cell wall catabolism | Cysteine protease | Mcsg | Midwest center for structural genomic | Protein structure initiative | Psi | Structural genomic | Surface mutagenesis
