2bmi: Difference between revisions

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-[[Image:2bmi.jpg|left|200px]]
- {{Structure
+==METALLO-BETA-LACTAMASE==
-|PDB= 2bmi |SIZE=350|CAPTION= <scene name='initialview01'>2bmi</scene>, resolution 2.00&Aring;
+<StructureSection load='2bmi' size='340' side='right'caption='[[2bmi]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
+<table><tr><td colspan='2'>[[2bmi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_fragilis Bacteroides fragilis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1bmi 1bmi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BMI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BMI FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span>
+</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&#8491;</td></tr>
-|GENE= CCRA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=817 Bacteroides fragilis])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bmi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bmi OCA], [https://pdbe.org/2bmi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bmi RCSB], [https://www.ebi.ac.uk/pdbsum/2bmi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bmi ProSAT]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2bmi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bmi OCA], [http://www.ebi.ac.uk/pdbsum/2bmi PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2bmi RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/BLAB_BACFG BLAB_BACFG] Can hydrolyze carbapenem compounds.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bm/2bmi_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=2bmi ConSurf].
+<div style="clear:both"></div>
-'''METALLO-BETA-LACTAMASE'''
+==See Also==
+*[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-beta-Lactamases are extracellular or periplasmic bacterial enzymes which confer resistance to beta-lactam antibiotics. On the basis of their catalytic mechanisms, they can be divided into two major groups: active-site serine enzymes (classes A, C and D) and the ZnII enzymes (class B). The first crystal structure of a class B enzyme, the metallo-beta-lactamase from Bacillus cereus, has been solved at 2.5 A resolution [Carfi, Pares, Duee, Galleni, Duez, Frere &amp; Dideberg (1995). EMBO J. 14, 4914-4921]. Recently, the crystal structure of the metallo-beta-lactamase from Bacteroides fragilis has been determined in a tetragonal space group [Concha, Rasmussen, Bush &amp; Herzberg (1996). Structure, 4, 823-836]. The structure of the metallo-beta-lactamase from B. fragilis in an orthorhombic crystal form at 2.0 A resolution is reported here. The final crystallographic R is 0.196 for all the 32501 observed reflections in the range 10-2.0 A. The refined model includes 458 residues, 437 water molecules, four zinc and two sodium ions. These structures are discussed with reference to Zn binding and activity. A catalytic mechanism is proposed which is coherent with metallo-beta-lactamases being active with either one Zn ion (as in Aeromonas hydrophila) or two Zn ions (as in B. fragilis) bound to the protein.
-==About this Structure==
-BMI is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacteroides_fragilis Bacteroides fragilis]. This structure supersedes the now removed PDB entry 1BMI. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BMI OCA].
-==Reference==
-X-ray structure of the ZnII beta-lactamase from Bacteroides fragilis in an orthorhombic crystal form., Carfi A, Duee E, Paul-Soto R, Galleni M, Frere JM, Dideberg O, Acta Crystallogr D Biol Crystallogr. 1998 Jan 1;54(Pt 1):45-57. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9761816 9761816]
 [[Category: Bacteroides fragilis]]
-[[Category: Beta-lactamase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Carfi A]]
-[[Category: Carfi, A.]]
+[[Category: Dideberg O]]
-[[Category: Dideberg, O.]]
+[[Category: Duee E]]
-[[Category: Duee, E.]]
-[[Category: beta-lactamase]]
-[[Category: metallo beta-lactamase]]
-[[Category: zinc]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:08:37 2008''