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| ==Crystal structure of MilB from Streptomyces rimofaciens== | | ==Crystal structure of MilB from Streptomyces rimofaciens== |
| <StructureSection load='4ohr' size='340' side='right' caption='[[4ohr]], [[Resolution|resolution]] 1.80Å' scene=''> | | <StructureSection load='4ohr' size='340' side='right'caption='[[4ohr]], [[Resolution|resolution]] 1.80Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[4ohr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/'streptomyces_rimofaciens' 'streptomyces rimofaciens']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OHR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OHR FirstGlance]. <br> | | <table><tr><td colspan='2'>[[4ohr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_rimofaciens Streptomyces rimofaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OHR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OHR FirstGlance]. <br> |
| </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ohb|4ohb]]</td></tr> | | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</td></tr> |
| <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MilB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=504097 'Streptomyces rimofaciens'])</td></tr>
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4ohr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ohr OCA], [https://pdbe.org/4ohr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ohr RCSB], [https://www.ebi.ac.uk/pdbsum/4ohr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ohr ProSAT]</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=4ohr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ohr OCA], [http://pdbe.org/4ohr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ohr RCSB], [http://www.ebi.ac.uk/pdbsum/4ohr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ohr ProSAT]</span></td></tr> | |
| </table> | | </table> |
| <div style="background-color:#fffaf0;">
| | == Function == |
| == Publication Abstract from PubMed == | | [https://www.uniprot.org/uniprot/B4Y381_9ACTN B4Y381_9ACTN] |
| 5-Hydroxymethylcytosine (5hmC) is present in T-even phage and mammalian DNA as well as some nucleoside antibiotics, including mildiomycin and bacimethrin, during whose synthesis 5hmC is produced by the hydrolysis of 5-hydroxymethyl cytidine 5'-monophosphate (hmCMP) by an N-glycosidase MilB. Recently, the MilB-CMP complex structure revealed its substrate specificity for CMP over dCMP. However, hmCMP instead of CMP is the preferred substrate for MilB as supported by that its KM for CMP is approximately 27-fold higher than that for hmCMP. Here, we determined the crystal structures of MilB and its catalytically inactive E103A mutant in complex with hmCMP. In the structure of the complex, Phe22 and Arg23 are positioned in a cage-like active site resembling the binding pocket for the flipped 5-methylcytosine (5mC) in eukaryotic 5mC-binding proteins. Van der Waals interaction between the benzene ring of Phe22 and the pyrimidine ring of hmCMP stabilizes its binding. Remarkably, upon hmCMP binding, the guanidinium group of Arg23 was bent approximately 65 degrees toward hmCMP to recognize its 5-hydroxymethyl group, inducing semi-closure of the cage-like pocket. Mutagenesis studies of Arg23 and bioinformatics analysis demonstrate that the positively charged Arg/Lys at this site is critical for the specific recognition of the 5-hydroxymethyl group of hmCMP.
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| Structure of the N-glycosidase MilB in complex with hydroxymethyl CMP reveals its Arg23 specifically recognizes the substrate and controls its entry.,Zhao G, Wu G, Zhang Y, Liu G, Han T, Deng Z, He X Nucleic Acids Res. 2014 Jun 11. pii: gku486. PMID:24920828<ref>PMID:24920828</ref>
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| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| </div>
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| <div class="pdbe-citations 4ohr" style="background-color:#fffaf0;"></div>
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| == References ==
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| <references/>
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| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] |
| [[Category: Streptomyces rimofaciens]] | | [[Category: Streptomyces rimofaciens]] |
| [[Category: He, X]] | | [[Category: He X]] |
| [[Category: Liu, G]] | | [[Category: Liu G]] |
| [[Category: Wu, G]] | | [[Category: Wu G]] |
| [[Category: Zhang, Y]] | | [[Category: Zhang Y]] |
| [[Category: Zhao, G]] | | [[Category: Zhao G]] |
| [[Category: Hydrolase]]
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