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1ukq

From Proteopedia

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Current revision

Crystal structure of cyclodextrin glucanotransferase complexed with a pseudo-maltotetraose derived from acarbose

Structural highlights

1ukq is a 2 chain structure with sequence from Bacillus sp. 1011. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CDGT_BACS0

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

The stacking interaction between a tyrosine residue and the sugar ring at the catalytic subsite -1 is strictly conserved in the glycoside hydrolase family 13 enzymes. Replacing Tyr100 with leucine in cyclodextrin glycosyltransferase (CGTase) from Bacillus sp. 1011 to prevent stacking significantly decreased all CGTase activities. The adjacent stacking interaction with both Phe183 and Phe259 onto the sugar ring at subsite +2 is essentially conserved among CGTases. F183L/F259L mutant CGTase affects donor substrate binding and/or acceptor binding during transglycosylation [Nakamura et al. (1994) Biochemistry 33, 9929-9936]. To elucidate the precise role of carbohydrate/aromatic stacking interaction at subsites -1 and +2 on the substrate binding of CGTases, we analyzed the X-ray structures of wild-type (2.0 A resolution), and Y100L (2.2 A resolution) and F183L/F259L mutant (1.9 A resolution) CGTases complexed with the inhibitor, acarbose. The refined structures revealed that acarbose molecules bound to the Y100L mutant moved from the active center toward the side chain of Tyr195, and the hydrogen bonding and hydrophobic interaction between acarbose and subsites significantly diminished. The position of pseudo-tetrasaccharide binding in the F183L/F259L mutant was closer to the non-reducing end, and the torsion angles of glycosidic linkages at subsites -1 to +1 on molecule 1 and subsites -2 to -1 on molecule 2 significantly changed compared with that of each molecule of wild-type-acarbose complex to adopt the structural change of subsite +2. These structural and biochemical data suggest that substrate binding in the active site of CGTase is critically affected by the carbohydrate/aromatic stacking interaction with Tyr100 at the catalytic subsite -1 and that this effect is likely a result of cooperation between Tyr100 and Phe259 through stacking interaction with substrate at subsite +2.

Effects of essential carbohydrate/aromatic stacking interaction with Tyr100 and Phe259 on substrate binding of cyclodextrin glycosyltransferase from alkalophilic Bacillus sp. 1011.,Haga K, Kanai R, Sakamoto O, Aoyagi M, Harata K, Yamane K J Biochem. 2003 Dec;134(6):881-91. PMID:14769878^[1]

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

References

↑ Haga K, Kanai R, Sakamoto O, Aoyagi M, Harata K, Yamane K. Effects of essential carbohydrate/aromatic stacking interaction with Tyr100 and Phe259 on substrate binding of cyclodextrin glycosyltransferase from alkalophilic Bacillus sp. 1011. J Biochem. 2003 Dec;134(6):881-91. PMID:14769878

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/1ukq"

@@ Line 1: / Line 1: @@
 ==Crystal structure of cyclodextrin glucanotransferase complexed with a pseudo-maltotetraose derived from acarbose==
-<StructureSection load='1ukq' size='340' side='right' caption='[[1ukq]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='1ukq' size='340' side='right'caption='[[1ukq]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ukq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacs0 Bacs0]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UKQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ukq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._1011 Bacillus sp. 1011]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UKQ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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></td></tr>
+</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&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1pam|1pam]], [[1uks|1uks]], [[1ukt|1ukt]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cyclomaltodextrin_glucanotransferase Cyclomaltodextrin glucanotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.19 2.4.1.19] </span></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=1ukq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ukq OCA], [https://pdbe.org/1ukq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ukq RCSB], [https://www.ebi.ac.uk/pdbsum/1ukq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ukq ProSAT]</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=1ukq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ukq OCA], [http://pdbe.org/1ukq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ukq RCSB], [http://www.ebi.ac.uk/pdbsum/1ukq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ukq ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/CDGT_BACS0 CDGT_BACS0]
 == 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/uk/1ukq_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/uk/1ukq_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 28: / Line 29: @@
 </div>
 <div class="pdbe-citations 1ukq" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Glycosyltransferase 3D structures|Glycosyltransferase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacs0]]
+[[Category: Bacillus sp. 1011]]
-[[Category: Cyclomaltodextrin glucanotransferase]]
+[[Category: Large Structures]]
-[[Category: Haga, K]]
+[[Category: Haga K]]
-[[Category: Harata, K]]
+[[Category: Harata K]]
-[[Category: Kanai, R]]
+[[Category: Kanai R]]
-[[Category: Sakamoto, O]]
+[[Category: Sakamoto O]]
-[[Category: Yamane, K]]
+[[Category: Yamane K]]
-[[Category: Acarbose]]
-[[Category: Carbohydrate-protein complex]]
-[[Category: Cgtase]]
-[[Category: Transferase]]

1ukq

From Proteopedia

Current revision

Crystal structure of cyclodextrin glucanotransferase complexed with a pseudo-maltotetraose derived from acarbose

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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