3vgl: Difference between revisions

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-[[Image:3vgl.jpg|left|200px]]
-<!--
+==Crystal structure of a ROK family glucokinase from Streptomyces griseus in complex with glucose and AMPPNP==
-The line below this paragraph, containing "STRUCTURE_3vgl", creates the "Structure Box" on the page.
+<StructureSection load='3vgl' size='340' side='right'caption='[[3vgl]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3vgl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_griseus_subsp._griseus_NBRC_13350 Streptomyces griseus subsp. griseus NBRC 13350]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VGL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VGL FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.55&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_3vgl|  PDB=3vgl  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vgl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vgl OCA], [https://pdbe.org/3vgl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vgl RCSB], [https://www.ebi.ac.uk/pdbsum/3vgl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vgl ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/B1VZT1_STRGG B1VZT1_STRGG]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Carbon catabolite repression (CCR) is a widespread phenomenon in many bacteria that is defined as the repression of catabolic enzyme activities for an unfavorable carbon source by the presence of a preferable carbon source. In Streptomyces, secondary metabolite production is often negatively affected by the carbon source, indicating the involvement of CCR in secondary metabolism. Although the CCR mechanism in Streptomyces is still unclear, glucokinase is presumably a central player in CCR. SgGlkA, a glucokinase from S. griseus, belongs to the ROK family glucokinases, which have two consensus sequence motifs (1 and 2). Here we report the crystal structures of apo-SgGlkA, SgGlkA in complex with glucose, and SgGlkA in complex with glucose and AMPPNP, which are the first structures of an ROK family glucokinase. SgGlkA is divided into a small alpha/beta domain and a large alpha+beta domain, and forms a dimer of dimer tetrameric configuration. SgGlkA binds a beta-anomer of glucose between the two domains, and His157 in the consensus sequence 1 plays an important role in the glucose-binding mechanism and anomer specificity of SgGlkA. In the structures of SgGlkA, His157 forms an HC3-type zinc-finger motif with three cysteine residues in the consensus sequence 2 to bind a zinc ion and forms two hydrogen bonds with the C1 and C2 hydroxyls of glucose. When the three structures are compared, the structure of SgGlkA is found to be modified by the binding of substrates. The substrate-dependent conformational changes of SgGlkA may be related to the CCR mechanism in Streptomyces.
-===Crystal structure of a ROK family glucokinase from Streptomyces griseus in complex with glucose and AMPPNP===
+Substrate recognition mechanism and substrate-dependent conformational changes of an ROK family glucokinase from Streptomyces griseus.,Miyazono KI, Tabei N, Morita S, Ohnishi Y, Horinouchi S, Tanokura M J Bacteriol. 2011 Nov 18. PMID:22101842<ref>PMID:22101842</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3vgl" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_22101842}}, adds the Publication Abstract to the page
+*[[Hexokinase 3D structures|Hexokinase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 22101842 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_22101842}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[3vgl]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_griseus Streptomyces griseus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VGL OCA].
+[[Category: Streptomyces griseus subsp. griseus NBRC 13350]]
+[[Category: Horinouchi S]]
-==Reference==
+[[Category: Miyazono K]]
-<ref group="xtra">PMID:022101842</ref><references group="xtra"/>
+[[Category: Morita S]]
-[[Category: Glucokinase]]
+[[Category: Ohnishi Y]]
-[[Category: Streptomyces griseus]]
+[[Category: Tabei N]]
-[[Category: Horinouchi, S.]]
+[[Category: Tanokura M]]
-[[Category: Miyazono, K.]]
-[[Category: Morita, S.]]
-[[Category: Ohnishi, Y.]]
-[[Category: Tabei, N.]]
-[[Category: Tanokura, M.]]
-[[Category: Glucokinase]]
-[[Category: Rok family]]
-[[Category: Transferase]]