2ri1: Difference between revisions

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 ==Crystal Structure of glucosamine 6-phosphate deaminase (NagB) with GlcN6P from S. mutans==
-<StructureSection load='2ri1' size='340' side='right' caption='[[2ri1]], [[Resolution|resolution]] 2.03&Aring;' scene=''>
+<StructureSection load='2ri1' size='340' side='right'caption='[[2ri1]], [[Resolution|resolution]] 2.03&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2ri1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25175 Atcc 25175]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RI1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RI1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2ri1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_mutans Streptococcus mutans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RI1 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=GLP:GLUCOSAMINE+6-PHOSPHATE'>GLP</scene></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]] 2.03&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2ri0|2ri0]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=GLP:GLUCOSAMINE+6-PHOSPHATE'>GLP</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SMU.636 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1309 ATCC 25175])</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=2ri1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ri1 OCA], [https://pdbe.org/2ri1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ri1 RCSB], [https://www.ebi.ac.uk/pdbsum/2ri1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ri1 ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucosamine-6-phosphate_deaminase Glucosamine-6-phosphate deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.99.6 3.5.99.6] </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=2ri1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ri1 OCA], [http://pdbe.org/2ri1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ri1 RCSB], [http://www.ebi.ac.uk/pdbsum/2ri1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ri1 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NAGB_STRMU NAGB_STRMU]] Catalyzes the reversible isomerization-deamination of glucosamine 6-phosphate (GlcN6P) to form fructose 6-phosphate (Fru6P) and ammonium ion (By similarity).
+[https://www.uniprot.org/uniprot/NAGB_STRMU NAGB_STRMU] Catalyzes the reversible isomerization-deamination of glucosamine 6-phosphate (GlcN6P) to form fructose 6-phosphate (Fru6P) and ammonium ion (By similarity).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 22: / Line 20: @@
 </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ri1 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Glucosamine 6-phosphate deaminase (NagB) catalyzes the conversion of d-glucosamine 6-phosphate (GlcN6P) to d-fructose 6-phosphate and ammonia. This reaction is the final step of N-acetylglucosamine utilization and decides its metabolic fate. The enzyme from Streptococcus mutans belongs to the monomeric subfamily of NagB. The crystal structure of the native SmuNagB (NagB from S. mutans) presented here, compared with the structures of its homologs BsuNagB (NagB from Bacillus subtilis) and EcoNagB (NagB from E. coli), implies a conformational change of the 'lid' motif in the activation of the monomeric NagB enzyme. We have also captured the enzyme-substrate intermediate complex of the NagB family at low pH, where a remarkable loss of the catalytic activity of SmuNagB was detected. The enzyme-substrate intermediate presents the initial step of the GlcN6P deaminase reaction. The structural evidence (1) supports the alpha-anomer of GlcN6P as the specific natural substrate of NagB; (2) displays the substrate-binding pocket at the active site; and (3) together with the site-directed mutagenesis studies, demonstrates the ring-opening mechanism of an Asn-His-Glu triad that performs the proton transfer from O1 to O5 to open the sugar ring.
-Ring-opening mechanism revealed by crystal structures of NagB and its ES intermediate complex.,Liu C, Li D, Liang YH, Li LF, Su XD J Mol Biol. 2008 May 23;379(1):73-81. Epub 2008 Mar 26. PMID:18436239<ref>PMID:18436239</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2ri1" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Deaminase|Deaminase]]
+*[[Deaminase 3D structures|Deaminase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 25175]]
+[[Category: Large Structures]]
-[[Category: Glucosamine-6-phosphate deaminase]]
+[[Category: Streptococcus mutans]]
-[[Category: Li, D]]
+[[Category: Li D]]
-[[Category: Liu, C]]
+[[Category: Liu C]]
-[[Category: Su, X D]]
+[[Category: Su XD]]
-[[Category: Carbohydrate metabolism]]
-[[Category: Glucosamine 6-phosphate deaminase]]
-[[Category: Hydrolase]]