1tdg: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1tdg.jpg|left|200px]]
- {{Structure
+==Complex of S130G SHV-1 beta-lactamase with tazobactam==
-|PDB= 1tdg |SIZE=350|CAPTION= <scene name='initialview01'>1tdg</scene>, resolution 1.8&Aring;
+<StructureSection load='1tdg' size='340' side='right'caption='[[1tdg]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=MA4:CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE'>MA4</scene>, <scene name='pdbligand=MDD:MALONALDEHYDE'>MDD</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=TBE:TAZOBACTAM+INTERMEDIATE'>TBE</scene>
+<table><tr><td colspan='2'>[[1tdg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TDG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TDG 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]] 1.8&#8491;</td></tr>
-|GENE= bla ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=573 Klebsiella pneumoniae])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MA4:CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE'>MA4</scene>, <scene name='pdbligand=MDD:MALONALDEHYDE'>MDD</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=TBE:TAZOBACTAM+INTERMEDIATE'>TBE</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=1tdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tdg OCA], [https://pdbe.org/1tdg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tdg RCSB], [https://www.ebi.ac.uk/pdbsum/1tdg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tdg ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1shv|1SHV]], [[1g56|1G56]], [[1rcj|1RCJ]], [[1tdl|1TDL]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1tdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tdg OCA], [http://www.ebi.ac.uk/pdbsum/1tdg PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1tdg RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/BLA1_KLEPN BLA1_KLEPN]
+== 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/td/1tdg_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1tdg ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+A bacterial response to the clinical use of class A beta-lactamase inhibitors such as tazobactam and clavulanic acid is the expression of variant beta-lactamases with weaker binding affinities for these mechanism-based inhibitors. Some of these inhibitor-resistant variants contain a glycine mutation at Ser130, a conserved active site residue known to be adventitiously involved in the inhibition mechanism. The crystallographic structure of a complex of tazobactam with the Ser130Gly variant of the class A SHV-1 beta-lactamase has been determined to 1.8 A resolution. Two reaction intermediates are observed. The primary intermediate is an acyclic species bound to the reactive Ser70. It is poorly primed for catalytic hydrolysis because its ester carbonyl group is completely displaced from the enzyme's oxyanion hole. A smaller fraction of the enzyme contains a Ser70-bound aldehyde resulting from hydrolytic loss of the triazoyl-sulfinyl amino acid moiety from the primary species. This first structure of a class A beta-lactamase lacking Ser130, the side chain of which functions in beta-lactam binding and possibly in catalysis, gives crystallographic evidence that the acylation step of beta-lactam turnover can occur without Ser130. Unexpectedly, the crystal structure of the uncomplexed Ser130Gly enzyme, also determined to 1.8 A resolution, shows that a critical Glu166-activated water molecule is missing from the catalytic site. Comparison of this uncomplexed variant with the wild-type structure reveals that Ser130 is required for orienting the side chain of Ser70 and ensuring the hydrogen bonding of Ser70 to both Lys73 and the catalytic water molecule.
-'''Complex of S130G SHV-1 beta-lactamase with tazobactam'''
+Inhibitor-resistant class A beta-lactamases: consequences of the Ser130-to-Gly mutation seen in Apo and tazobactam structures of the SHV-1 variant.,Sun T, Bethel CR, Bonomo RA, Knox JR Biochemistry. 2004 Nov 9;43(44):14111-7. PMID:15518561<ref>PMID:15518561</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1tdg" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-A bacterial response to the clinical use of class A beta-lactamase inhibitors such as tazobactam and clavulanic acid is the expression of variant beta-lactamases with weaker binding affinities for these mechanism-based inhibitors. Some of these inhibitor-resistant variants contain a glycine mutation at Ser130, a conserved active site residue known to be adventitiously involved in the inhibition mechanism. The crystallographic structure of a complex of tazobactam with the Ser130Gly variant of the class A SHV-1 beta-lactamase has been determined to 1.8 A resolution. Two reaction intermediates are observed. The primary intermediate is an acyclic species bound to the reactive Ser70. It is poorly primed for catalytic hydrolysis because its ester carbonyl group is completely displaced from the enzyme's oxyanion hole. A smaller fraction of the enzyme contains a Ser70-bound aldehyde resulting from hydrolytic loss of the triazoyl-sulfinyl amino acid moiety from the primary species. This first structure of a class A beta-lactamase lacking Ser130, the side chain of which functions in beta-lactam binding and possibly in catalysis, gives crystallographic evidence that the acylation step of beta-lactam turnover can occur without Ser130. Unexpectedly, the crystal structure of the uncomplexed Ser130Gly enzyme, also determined to 1.8 A resolution, shows that a critical Glu166-activated water molecule is missing from the catalytic site. Comparison of this uncomplexed variant with the wild-type structure reveals that Ser130 is required for orienting the side chain of Ser70 and ensuring the hydrogen bonding of Ser70 to both Lys73 and the catalytic water molecule.
+*[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-TDG is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TDG OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Inhibitor-resistant class A beta-lactamases: consequences of the Ser130-to-Gly mutation seen in Apo and tazobactam structures of the SHV-1 variant., Sun T, Bethel CR, Bonomo RA, Knox JR, Biochemistry. 2004 Nov 9;43(44):14111-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15518561 15518561]
-[[Category: Beta-lactamase]]
 [[Category: Klebsiella pneumoniae]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Bethel, C R.]]
+[[Category: Bethel CR]]
-[[Category: Bonomo, R A.]]
+[[Category: Bonomo RA]]
-[[Category: Knox, J R.]]
+[[Category: Knox JR]]
-[[Category: Sun, T.]]
+[[Category: Sun T]]
-[[Category: aldehyde]]
-[[Category: beta-lactam hydrolase]]
-[[Category: cymal-6]]
-[[Category: detergent binding]]
-[[Category: inhibitor complex]]
-[[Category: penicillinase]]
-[[Category: s130g shv-1 class a beta-lactamase]]
-[[Category: tazobactam]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:54:41 2008''