3eyx

From Proteopedia

(Difference between revisions)

Revision as of 05:49, 7 February 2016

Crystal structure of Carbonic Anhydrase Nce103 from Saccharomyces cerevisiae

Structural highlights

3eyx is a 2 chain structure with sequence from Atcc 18824. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Gene:	NCE103 (ATCC 18824)
Activity:	Carbonate dehydratase, with EC number 4.2.1.1
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[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.^[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 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^[6]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Gotz R, Gnann A, Zimmermann FK. Deletion of the carbonic anhydrase-like gene NCE103 of the yeast Saccharomyces cerevisiae causes an oxygen-sensitive growth defect. Yeast. 1999 Jul;15(10A):855-64. PMID:10407265 doi:<855::AID-YEA425>3.0.CO;2-C http://dx.doi.org/10.1002/(SICI)1097-0061(199907)15:10A<855::AID-YEA425>3.0.CO;2-C
↑ Clark D, Rowlett RS, Coleman JR, Klessig DF. Complementation of the yeast deletion mutant DeltaNCE103 by members of the beta class of carbonic anhydrases is dependent on carbonic anhydrase activity rather than on antioxidant activity. Biochem J. 2004 May 1;379(Pt 3):609-15. PMID:15096093 doi:http://dx.doi.org/10.1042/BJ20031711
↑ Aguilera J, Van Dijken JP, De Winde JH, Pronk JT. Carbonic anhydrase (Nce103p): an essential biosynthetic enzyme for growth of Saccharomyces cerevisiae at atmospheric carbon dioxide pressure. Biochem J. 2005 Oct 15;391(Pt 2):311-6. PMID:15948716 doi:http://dx.doi.org/10.1042/BJ20050556
↑ Amoroso G, Morell-Avrahov L, Muller D, Klug K, Sultemeyer D. The gene NCE103 (YNL036w) from Saccharomyces cerevisiae encodes a functional carbonic anhydrase and its transcription is regulated by the concentration of inorganic carbon in the medium. Mol Microbiol. 2005 Apr;56(2):549-58. PMID:15813743 doi:http://dx.doi.org/MMI4560
↑ Isik S, Kockar F, Arslan O, Guler OO, Innocenti A, Supuran CT. Carbonic anhydrase inhibitors. Inhibition of the beta-class enzyme from the yeast Saccharomyces cerevisiae with anions. Bioorg Med Chem Lett. 2008 Dec 15;18(24):6327-31. doi:, 10.1016/j.bmcl.2008.10.100. Epub 2008 Oct 25. PMID:18993072 doi:http://dx.doi.org/10.1016/j.bmcl.2008.10.100
↑ Teng YB, Jiang YL, He YX, He WW, Lian FM, Chen Y, Zhou CZ. Structural insights into the substrate tunnel of Saccharomyces cerevisiae carbonic anhydrase Nce103. BMC Struct Biol. 2009 Oct 24;9:67. PMID:19852838 doi:10.1186/1472-6807-9-67

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3eyx"

@@ Line 2: / Line 2: @@
 <StructureSection load='3eyx' size='340' side='right' caption='[[3eyx]], [[Resolution|resolution]] 2.04&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3eyx]] is a 2 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EYX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3eyx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EYX FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NCE103 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NCE103 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carbonate_dehydratase Carbonate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.1 4.2.1.1] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3eyx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eyx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3eyx RCSB], [http://www.ebi.ac.uk/pdbsum/3eyx PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3eyx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eyx OCA], [http://pdbe.org/3eyx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3eyx RCSB], [http://www.ebi.ac.uk/pdbsum/3eyx PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 18: / Line 18: @@
     <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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;">
@@ Line 28: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3eyx" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 35: / Line 36: @@
 __TOC__
 </StructureSection>
+[[Category: Atcc 18824]]
 [[Category: Carbonate dehydratase]]
-[[Category: Saccharomyces cerevisiae]]
 [[Category: Chen, Y]]
 [[Category: Jiang, Y L]]

3eyx

From Proteopedia

Revision as of 05:49, 7 February 2016

Crystal structure of Carbonic Anhydrase Nce103 from Saccharomyces cerevisiae

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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