1hfw: Difference between revisions

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-[[Image:1hfw.gif|left|200px]]
- {{Structure
+==X-ray structure of the complex between Erwinia chrysanthemi L-asparaginase and L-Glutamate==
-|PDB= 1hfw |SIZE=350|CAPTION= <scene name='initialview01'>1hfw</scene>, resolution 1.80&Aring;
+<StructureSection load='1hfw' size='340' side='right'caption='[[1hfw]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-|SITE= <scene name='pdbsite=AS1:Active+Site+Chain+A,+TYR-A29+Not+Visible+In+Electron+Density'>AS1</scene>, <scene name='pdbsite=AS2:Active+Site+Chain+B,+TYR-B29+Not+Visible+In+Electron+Density'>AS2</scene>, <scene name='pdbsite=AS3:Active+Site+Chain+C,+TYR-C29+Not+Visible+In+Electron+Density'>AS3</scene>, <scene name='pdbsite=AS4:Active+Site+Chain+D,+TYR-D29+Not+Visible+In+Electron+Density'>AS4</scene>, <scene name='pdbsite=LI1:GLU+Binding+Site+For+Chain+A'>LI1</scene>, <scene name='pdbsite=LI2:GLU+Binding+Site+For+Chain+B'>LI2</scene>, <scene name='pdbsite=LI3:GLU+Binding+Site+For+Chain+C'>LI3</scene> and <scene name='pdbsite=LI4:GLU+Binding+Site+For+Chain+D'>LI4</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=GLU:GLUTAMIC ACID'>GLU</scene>
+<table><tr><td colspan='2'>[[1hfw]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Dickeya_chrysanthemi Dickeya chrysanthemi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HFW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HFW FirstGlance]. <br>
-|ACTIVITY= [http://en.wikipedia.org/wiki/Asparaginase Asparaginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.1 3.5.1.1]
+</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=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene></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=1hfw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hfw OCA], [https://pdbe.org/1hfw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hfw RCSB], [https://www.ebi.ac.uk/pdbsum/1hfw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hfw ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ASPG_DICCH ASPG_DICCH]
+== 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/hf/1hfw_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=1hfw ConSurf].
+<div style="clear:both"></div>
-'''X-RAY STRUCTURE OF THE COMPLEX BETWEEN ERWINIA CHRYSANTHEMI L-ASPARAGINASE AND L-GLUTAMATE'''
+==See Also==
+*[[Asparaginase 3D structures|Asparaginase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-Bacterial L-asparaginases, enzymes that catalyze the hydrolysis of L-asparagine to aspartic acid, have been used for over 30 years as therapeutic agents in the treatment of acute childhood lymphoblastic leukemia. Other substrates of asparaginases include L-glutamine, D-asparagine, and succinic acid monoamide. In this report, we present high-resolution crystal structures of the complexes of Erwinia chrysanthemi L-asparaginase (ErA) with the products of such reactions that also can serve as substrates, namely L-glutamic acid (L-Glu), D-aspartic acid (D-Asp), and succinic acid (Suc). Comparison of the four independent active sites within each complex indicates unique and specific binding of the ligand molecules; the mode of binding is also similar between complexes. The lack of the alpha-NH3(+) group in Suc, compared to L-Asp, does not affect the binding mode. The side chain of L-Glu, larger than that of L-Asp, causes several structural distortions in the ErA active side. The active site flexible loop (residues 15-33) does not exhibit stable conformation, resulting in suboptimal orientation of the nucleophile, Thr15. Additionally, the delta-COO(-) plane of L-Glu is approximately perpendicular to the plane of gamma-COO(-) in L-Asp bound to the asparaginase active site. Binding of D-Asp to the ErA active site is very distinctive compared to the other ligands, suggesting that the low activity of ErA against D-Asp could be mainly attributed to the low k(cat) value. A comparison of the amino acid sequence and the crystal structure of ErA with those of other bacterial L-asparaginases shows that the presence of two active-site residues, Glu63(ErA) and Ser254(ErA), may correlate with significant glutaminase activity, while their substitution by Gln and Asn, respectively, may lead to minimal L-glutaminase activity.
+[[Category: Dickeya chrysanthemi]]
+[[Category: Large Structures]]
-==About this Structure==
+[[Category: Kolyani KA]]
-HFW is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Erwinia_chrysanthemi Erwinia chrysanthemi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HFW OCA].
+[[Category: Lubkowski J]]
+[[Category: Wlodawer A]]
-==Reference==
-Structural basis for the activity and substrate specificity of Erwinia chrysanthemi L-asparaginase., Aghaiypour K, Wlodawer A, Lubkowski J, Biochemistry. 2001 May 15;40(19):5655-64. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11341830 11341830]
-[[Category: Asparaginase]]
-[[Category: Erwinia chrysanthemi]]
-[[Category: Single protein]]
-[[Category: Kolyani, K A.]]
-[[Category: Lubkowski, J.]]
-[[Category: Wlodawer, A.]]
-[[Category: GLU]]
-[[Category: asparaginase]]
-[[Category: complex]]
-[[Category: d-aspartate]]
-[[Category: hydrolase]]
-[[Category: structure]]
-[[Category: x-ray]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 11:36:35 2008''