3eyx: Difference between revisions
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< | ==Crystal structure of Carbonic Anhydrase Nce103 from Saccharomyces cerevisiae== | ||
<StructureSection load='3eyx' size='340' side='right'caption='[[3eyx]], [[Resolution|resolution]] 2.04Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3eyx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EYX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EYX FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.04Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=3eyx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eyx OCA], [https://pdbe.org/3eyx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3eyx RCSB], [https://www.ebi.ac.uk/pdbsum/3eyx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3eyx ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/CAN_YEAST CAN_YEAST] Catalyzes the reversible hydration of CO(2) to H(2)CO(3). The main role may be to provide inorganic carbon for the bicarbonate-dependent carboxylation reactions catalyzed by pyruvate carboxylase, acetyl-CoA carboxylase and carbamoyl-phosphate synthetase. Involved in protection against oxidative damage. Encodes a substrate for the non-classical protein export pathway for proteins that lack a cleavable signal sequence.<ref>PMID:10407265</ref> <ref>PMID:15096093</ref> <ref>PMID:15948716</ref> <ref>PMID:15813743</ref> <ref>PMID:18993072</ref> | |||
== 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/ey/3eyx_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=3eyx ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
BACKGROUND: The carbonic anhydrases (CAs) are involved in inorganic carbon utilization. They have been classified into six evolutionary and structural families: alpha-, beta-, gamma-, delta-, epsilon-, zeta- CAs, with beta-CAs present in higher plants, algae and prokaryotes. The yeast Saccharomyces cerevisiae encodes a single copy of beta-CA Nce103/YNL036W. RESULTS: We determined the crystal structure of Nce103 in complex with a substrate analog at 2.04 A resolution. It assembles as a homodimer, with the active site located at the interface between two monomers. At the bottom of the substrate pocket, a zinc ion is coordinated by the three highly conserved residues Cys57, His112 and Cys115 in addition to a water molecule. Residues Asp59, Arg61, Gly111, Leu102, Val80, Phe75 and Phe97 form a tunnel to the bottom of the active site which is occupied by a molecule of the substrate analog acetate. Activity assays of full length and two truncated versions of Nce103 indicated that the N-terminal arm is indispensable. CONCLUSION: The quaternary structure of Nce103 resembles the typical plant type beta-CAs of known structure, with an N-terminal arm indispensable for the enzymatic activity. Comparative structure analysis enables us to draw a possible tunnel for the substrate to access the active site which is located at the bottom of a funnel-shaped substrate pocket. | |||
Structural insights into the substrate tunnel of Saccharomyces cerevisiae carbonic anhydrase Nce103.,Teng YB, Jiang YL, He YX, He WW, Lian FM, Chen Y, Zhou CZ BMC Struct Biol. 2009 Oct 24;9:67. PMID:19852838<ref>PMID:19852838</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3eyx" style="background-color:#fffaf0;"></div> | |||
== | ==See Also== | ||
*[[Carbonic anhydrase 3D structures|Carbonic anhydrase 3D structures]] | |||
[[Category: | == References == | ||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Saccharomyces cerevisiae]] | [[Category: Saccharomyces cerevisiae]] | ||
[[Category: Chen | [[Category: Chen Y]] | ||
[[Category: Jiang | [[Category: Jiang YL]] | ||
[[Category: Teng | [[Category: Teng YB]] | ||
[[Category: Zhou | [[Category: Zhou CZ]] | ||
Latest revision as of 18:25, 1 November 2023
Crystal structure of Carbonic Anhydrase Nce103 from Saccharomyces cerevisiaeCrystal structure of Carbonic Anhydrase Nce103 from Saccharomyces cerevisiae
Structural highlights
FunctionCAN_YEAST Catalyzes the reversible hydration of CO(2) to H(2)CO(3). The main role may be to provide inorganic carbon for the bicarbonate-dependent carboxylation reactions catalyzed by pyruvate carboxylase, acetyl-CoA carboxylase and carbamoyl-phosphate synthetase. Involved in protection against oxidative damage. Encodes a substrate for the non-classical protein export pathway for proteins that lack a cleavable signal sequence.[1] [2] [3] [4] [5] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedBACKGROUND: The carbonic anhydrases (CAs) are involved in inorganic carbon utilization. They have been classified into six evolutionary and structural families: alpha-, beta-, gamma-, delta-, epsilon-, zeta- CAs, with beta-CAs present in higher plants, algae and prokaryotes. The yeast Saccharomyces cerevisiae encodes a single copy of beta-CA Nce103/YNL036W. RESULTS: We determined the crystal structure of Nce103 in complex with a substrate analog at 2.04 A resolution. It assembles as a homodimer, with the active site located at the interface between two monomers. At the bottom of the substrate pocket, a zinc ion is coordinated by the three highly conserved residues Cys57, His112 and Cys115 in addition to a water molecule. Residues Asp59, Arg61, Gly111, Leu102, Val80, Phe75 and Phe97 form a tunnel to the bottom of the active site which is occupied by a molecule of the substrate analog acetate. Activity assays of full length and two truncated versions of Nce103 indicated that the N-terminal arm is indispensable. CONCLUSION: The quaternary structure of Nce103 resembles the typical plant type beta-CAs of known structure, with an N-terminal arm indispensable for the enzymatic activity. Comparative structure analysis enables us to draw a possible tunnel for the substrate to access the active site which is located at the bottom of a funnel-shaped substrate pocket. Structural insights into the substrate tunnel of Saccharomyces cerevisiae carbonic anhydrase Nce103.,Teng YB, Jiang YL, He YX, He WW, Lian FM, Chen Y, Zhou CZ BMC Struct Biol. 2009 Oct 24;9:67. PMID:19852838[6] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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