This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2b5d

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:42, 13 March 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2b5d.gif|left|200px]]<br /><applet load="2b5d" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2b5d, resolution 2.20&Aring;" />
 
-
'''Crystal structure of the novel alpha-amylase AmyC from Thermotoga maritima'''<br />
 
-
==Overview==
+
==Crystal structure of the novel alpha-amylase AmyC from Thermotoga maritima==
-
alpha-Amylases are essential enzymes in alpha-glucan metabolism and catalyse the hydrolysis of long sugar polymers such as amylose and starch. The crystal structure of a previously unidentified amylase (AmyC) from the hyperthermophilic organism Thermotoga maritima was determined at 2.2 Angstroms resolution by means of MAD. AmyC lacks sequence similarity to canonical alpha-amylases, which belong to glycosyl hydrolase families 13, 70 and 77, but exhibits significant similarity to a group of as yet uncharacterized proteins in COG1543 and is related to glycerol hydrolase family 57 (GH-57). AmyC reveals features that are characteristic of alpha-amylases, such as a distorted TIM-barrel structure formed by seven beta-strands and alpha-helices (domain A), and two additional but less well conserved domains. The latter are domain B, which contains three helices inserted in the TIM-barrel after beta-sheet 2, and domain C, a five-helix region at the C-terminus. Interestingly, despite moderate sequence homology, structure comparison revealed significant similarities to a member of GH-57 with known three-dimensional structure, Thermococcus litoralis 4-glucanotransferase, and an even higher similarity to a structure of an enzyme of unknown function from Thermus thermophilus.
+
<StructureSection load='2b5d' size='340' side='right'caption='[[2b5d]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[2b5d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B5D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B5D 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]] 2.2&#8491;</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=2b5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b5d OCA], [https://pdbe.org/2b5d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b5d RCSB], [https://www.ebi.ac.uk/pdbsum/2b5d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b5d ProSAT]</span></td></tr>
 +
</table>
 +
== 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/b5/2b5d_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=2b5d ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
2B5D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Active as [http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B5D OCA].
+
*[[Amylase 3D structures|Amylase 3D structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
Structure of the novel alpha-amylase AmyC from Thermotoga maritima., Dickmanns A, Ballschmiter M, Liebl W, Ficner R, Acta Crystallogr D Biol Crystallogr. 2006 Mar;62(Pt 3):262-70. Epub 2006, Feb 22. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16510973 16510973]
+
[[Category: Large Structures]]
-
[[Category: Alpha-amylase]]
+
[[Category: Thermotoga maritima MSB8]]
-
[[Category: Protein complex]]
+
[[Category: Ballschmiter M]]
-
[[Category: Thermotoga maritima]]
+
[[Category: Dickmanns A]]
-
[[Category: Ballschmiter, M.]]
+
[[Category: Ficner R]]
-
[[Category: Dickmanns, A.]]
+
[[Category: Liebl W]]
-
[[Category: Ficner, R.]]
+
-
[[Category: Liebl, W.]]
+
-
[[Category: (beta/alpha)7 barrel]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:34:20 2008''
+

Current revision

Crystal structure of the novel alpha-amylase AmyC from Thermotoga maritima

PDB ID 2b5d

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2b5d"
Personal tools