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.


3bc9

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px <!-- The line below this paragraph, containing "STRUCTURE_3bc9", creates the "Structure Box" on the page. You may change the PDB parameter (which sets the PD...)
Current revision (14:03, 13 March 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:3bc9.jpg|left|200px]]
 
-
<!--
+
==Alpha-amylase B in complex with acarbose==
-
The line below this paragraph, containing "STRUCTURE_3bc9", creates the "Structure Box" on the page.
+
<StructureSection load='3bc9' size='340' side='right'caption='[[3bc9]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[3bc9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halothermothrix_orenii_H_168 Halothermothrix orenii H 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BC9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BC9 FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.35&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AC1:6-METHYL-5-(4,5,6-TRIHYDROXY-3-HYDROXYMETHYL-CYCLOHEX-2-ENYLAMINO)-TETRAHYDRO-PYRAN-2,3,4-TRIOL'>AC1</scene>, <scene name='pdbligand=ACI:6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL'>ACI</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=G6D:6-DEOXY-ALPHA-D-GLUCOSE'>G6D</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GLD:4,6-DIDEOXYGLUCOSE'>GLD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PRD_900007:alpha-acarbose'>PRD_900007</scene></td></tr>
-
{{STRUCTURE_3bc9| PDB=3bc9 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bc9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bc9 OCA], [https://pdbe.org/3bc9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bc9 RCSB], [https://www.ebi.ac.uk/pdbsum/3bc9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bc9 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/B8CZ54_HALOH B8CZ54_HALOH]
 +
== 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/bc/3bc9_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=3bc9 ConSurf].
 +
<div style="clear:both"></div>
-
'''Alpha-amylase B in complex with acarbose'''
+
==See Also==
-
 
+
*[[Amylase 3D structures|Amylase 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
The gene for a membrane-bound, halophilic, and thermostable alpha-amylase, AmyB, from Halothermothrix orenii was cloned and sequenced. The crystal structure shows that, in addition to the typical domain organization of family 13 glycoside hydrolases, AmyB carries an additional N-terminal domain (N domain) that forms a large groove--the N-C groove--some 30 A away from the active site. The structure of AmyB with the inhibitor acarbose at 1.35 A resolution shows that a nonasaccharide has been synthesized through successive transglycosylation reactions of acarbose. Unexpectedly, in a complex of wild-type AmyB with alpha-cyclodextrin and maltoheptaose at 2.2 A resolution, a maltotetraose molecule is bound in subsites -1 to +3, spanning the cleavage point at -1/+1, with the -1 glucosyl residue present as a (2)S(o) skew boat. This wild-type AmyB complex was obtained in the presence of a large excess of substrate, a condition under which it is possible to capture Michaelis complexes, which may explain the observed binding across -1/+1 and ring distortion. We observe three methionine side chains that serve as "binding platforms" for glucosyl rings in AmyB, a seemingly rare occurrence in carbohydrate-binding proteins. The structures and results from the biochemical characterization of AmyB and AmyB lacking the N domain show that the N domain increases binding of the enzyme to raw starch. Furthermore, theoretical modeling suggests that the N-C groove can accommodate, spatially and chemically, large substrates such as A-starch.
+
[[Category: Halothermothrix orenii H 168]]
-
 
+
[[Category: Large Structures]]
-
==About this Structure==
+
[[Category: Divne C]]
-
3BC9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Halothermothrix_orenii Halothermothrix orenii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BC9 OCA].
+
[[Category: Mijts BN]]
-
 
+
[[Category: Patel BKC]]
-
==Reference==
+
[[Category: Swaminathan K]]
-
Crystal structure of the polyextremophilic alpha-amylase AmyB from Halothermothrix orenii: details of a productive enzyme-substrate complex and an N domain with a role in binding raw starch., Tan TC, Mijts BN, Swaminathan K, Patel BK, Divne C, J Mol Biol. 2008 May 9;378(4):850-68. Epub 2008 Feb 29. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18387632 18387632]
+
[[Category: Tan T-C]]
-
[[Category: Alpha-amylase]]
+
-
[[Category: Halothermothrix orenii]]
+
-
[[Category: Single protein]]
+
-
[[Category: Divne, C.]]
+
-
[[Category: Mijts, B N.]]
+
-
[[Category: Patel, B K.C.]]
+
-
[[Category: Swaminathan, K.]]
+
-
[[Category: Tan, T C.]]
+
-
[[Category: Acarbose]]
+
-
[[Category: Alpha-amylase]]
+
-
[[Category: Halophilic]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: N domain]]
+
-
[[Category: Raw starch binding]]
+
-
[[Category: Thermostable]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 24 09:48:10 2008''
+

Current revision

Alpha-amylase B in complex with acarbose

PDB ID 3bc9

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/3bc9"
Personal tools