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1nq9

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[[Image:1nq9.jpg|left|200px]]<br /><applet load="1nq9" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1nq9, resolution 2.60&Aring;" />
 
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'''Crystal Structure of Antithrombin in the Pentasaccharide-Bound Intermediate State'''<br />
 
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==Overview==
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==Crystal Structure of Antithrombin in the Pentasaccharide-Bound Intermediate State==
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Antithrombin is activated as an inhibitor of the coagulation proteases, through its specific interaction with a heparin pentasaccharide. The, binding of heparin induces a global conformational change in antithrombin, which results in the freeing of its reactive center loop for interaction, with target proteases and a 1000-fold increase in heparin affinity. The, allosteric mechanism by which the properties of antithrombin are altered, by its interactions with the specific pentasaccharide sequence of heparin, is of great interest to the medical and protein biochemistry communities., Heparin binding has previously been characterized as a two-step, three-state mechanism where, after an initial weak interaction, antithrombin undergoes a conformational change to its high-affinity state., Although the native and heparin-activated states have been determined, through protein crystallography, the number and magnitude of, conformational changes render problematic the task of determining which, account for the improved heparin affinity and how the heparin binding, region is linked to the expulsion of the reactive center loop. Here we, present the structure of an intermediate pentasaccharide-bound, conformation of antithrombin which has undergone all of the conformational, changes associated with activation except loop expulsion and helix D, elongation. We conclude that the basis of the high-affinity state is not, improved interaction with the pentasaccharide but a lowering of the global, free energy due to conformational changes elsewhere in antithrombin. We, suggest a mechanism in which the role of helix D elongation is to lock, antithrombin in the five-stranded fully activated conformation.
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<StructureSection load='1nq9' size='340' side='right'caption='[[1nq9]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1nq9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NQ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NQ9 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GU1:2,3-DI-O-METHYL-BETA-D-GLUCOPYRANURONIC+ACID'>GU1</scene>, <scene name='pdbligand=GU6:2,3,6-TRI-O-SULFONATO-ALPHA-D-GLUCOPYRANOSE'>GU6</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PRD_900031:heparin+pentasaccharide'>PRD_900031</scene>, <scene name='pdbligand=Z9H:3,4-di-O-methyl-2,6-di-O-sulfo-alpha-D-glucopyranose'>Z9H</scene>, <scene name='pdbligand=Z9K:3-O-methyl-2-O-sulfo-alpha-L-idopyranuronic+acid'>Z9K</scene>, <scene name='pdbligand=Z9L:methyl+2,3,6-tri-O-sulfo-alpha-D-glucopyranoside'>Z9L</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nq9 OCA], [https://pdbe.org/1nq9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nq9 RCSB], [https://www.ebi.ac.uk/pdbsum/1nq9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nq9 ProSAT]</span></td></tr>
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</table>
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== Disease ==
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[https://www.uniprot.org/uniprot/ANT3_HUMAN ANT3_HUMAN] Defects in SERPINC1 are the cause of antithrombin III deficiency (AT3D) [MIM:[https://omim.org/entry/613118 613118]. AT3D is an important risk factor for hereditary thrombophilia, a hemostatic disorder characterized by a tendency to recurrent thrombosis. AT3D is classified into 4 types. Type I: characterized by a 50% decrease in antigenic and functional levels. Type II: has defects affecting the thrombin-binding domain. Type III: alteration of the heparin-binding domain. Plasma AT-III antigen levels are normal in type II and III. Type IV: consists of miscellaneous group of unclassifiable mutations.<ref>PMID:7734359</ref> [:]<ref>PMID:3191114</ref> <ref>PMID:9031473</ref> <ref>PMID:6582486</ref> <ref>PMID:3080419</ref> <ref>PMID:3805013</ref> <ref>PMID:3179438</ref> <ref>PMID:3162733</ref> <ref>PMID:2781509</ref> <ref>PMID:2365065</ref> <ref>PMID:2229057</ref> <ref>PMID:2013320</ref> <ref>PMID:1906811</ref> <ref>PMID:1555650</ref> <ref>PMID:1547341</ref> <ref>PMID:8443391</ref> <ref>PMID:8486379</ref> <ref>PMID:7981186</ref> <ref>PMID:7959685</ref> <ref>PMID:8274732</ref> <ref>PMID:7994035</ref> <ref>PMID:7989582</ref> [:]<ref>PMID:7878627</ref> <ref>PMID:7832187</ref> <ref>PMID:9157604</ref> <ref>PMID:9845533</ref> <ref>PMID:9759613</ref> <ref>PMID:10997988</ref> <ref>PMID:11794707</ref> <ref>PMID:11713457</ref> <ref>PMID:12353073</ref> <ref>PMID:12595305</ref> <ref>PMID:12894857</ref> <ref>PMID:15164384</ref> <ref>PMID:16908819</ref>
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== Function ==
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[https://www.uniprot.org/uniprot/ANT3_HUMAN ANT3_HUMAN] Most important serine protease inhibitor in plasma that regulates the blood coagulation cascade. AT-III inhibits thrombin, matriptase-3/TMPRSS7, as well as factors IXa, Xa and XIa. Its inhibitory activity is greatly enhanced in the presence of heparin.<ref>PMID:15853774</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nq/1nq9_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1nq9 ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1NQ9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=NAG:'>NAG</scene> and <scene name='pdbligand=NTP:'>NTP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NQ9 OCA].
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*[[Antithrombin 3D structures|Antithrombin 3D structures]]
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== References ==
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==Reference==
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<references/>
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Crystal structure of antithrombin in a heparin-bound intermediate state., Johnson DJ, Huntington JA, Biochemistry. 2003 Jul 29;42(29):8712-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12873131 12873131]
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__TOC__
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</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Huntington, J.A.]]
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[[Category: Huntington JA]]
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[[Category: Johnson, D.J.D.]]
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[[Category: Johnson DJD]]
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[[Category: NAG]]
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[[Category: NTP]]
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[[Category: thrombin; inhibition; heparin analogue; serine protease inhibitor]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Feb 15 16:30:21 2008''
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Current revision

Crystal Structure of Antithrombin in the Pentasaccharide-Bound Intermediate State

PDB ID 1nq9

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