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3b9g

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Current revision

Crystal structure of loop deletion mutant of Trypanosoma vivax nucleoside hydrolase (3GTvNH) in complex with ImmH

Structural highlights

3b9g is a 2 chain structure with sequence from Trypanosoma vivax. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.4Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q9GPQ4_TRYVI

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 nucleoside hydrolase of Trypanosoma vivax hydrolyzes the N-glycosidic bond of purine nucleosides. Structural and kinetic studies on this enzyme have suggested a catalytic role for a flexible loop in the vicinity of the active sites. Here we present the analysis of the role of this flexible loop via the combination of a proline scan of the loop, loop deletion mutagenesis, steady state and pre-steady state analysis, and x-ray crystallography. Our analysis reveals that this loop has an important role in leaving group activation and product release. The catalytic role involves the entire loop and could only be perturbed by deletion of the entire loop and not by single site mutagenesis. We present evidence that the loop closes over the active site during catalysis, thereby ordering a water channel that is involved in leaving group activation. Once chemistry has taken place, the loop dynamics determine the rate of product release.

A flexible loop as a functional element in the catalytic mechanism of nucleoside hydrolase from Trypanosoma vivax.,Vandemeulebroucke A, De Vos S, Van Holsbeke E, Steyaert J, Versees W J Biol Chem. 2008 Aug 8;283(32):22272-82. Epub 2008 Jun 2. PMID:18519562^[1]

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

References

↑ Vandemeulebroucke A, De Vos S, Van Holsbeke E, Steyaert J, Versees W. A flexible loop as a functional element in the catalytic mechanism of nucleoside hydrolase from Trypanosoma vivax. J Biol Chem. 2008 Aug 8;283(32):22272-82. Epub 2008 Jun 2. PMID:18519562 doi:10.1074/jbc.M803705200

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3b9g"

@@ Line 3: / Line 3: @@
 <StructureSection load='3b9g' size='340' side='right'caption='[[3b9g]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3b9g]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Duttonella_vivax Duttonella vivax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B9G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B9G FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3b9g]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_vivax Trypanosoma vivax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B9G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B9G FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=IMH:1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL'>IMH</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.4&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1hoz|1hoz]], [[1hpo|1hpo]], [[1kic|1kic]], [[1kie|1kie]], [[1r4f|1r4f]], [[2mas|2mas]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=IMH:1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL'>IMH</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Purine_nucleosidase Purine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.1 3.2.2.1] </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=3b9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b9g OCA], [https://pdbe.org/3b9g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b9g RCSB], [https://www.ebi.ac.uk/pdbsum/3b9g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b9g 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=3b9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b9g OCA], [http://pdbe.org/3b9g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3b9g RCSB], [http://www.ebi.ac.uk/pdbsum/3b9g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3b9g ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9GPQ4_TRYVI Q9GPQ4_TRYVI]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Duttonella vivax]]
 [[Category: Large Structures]]
-[[Category: Purine nucleosidase]]
+[[Category: Trypanosoma vivax]]
-[[Category: Holsbeke, E Van]]
+[[Category: De Vos S]]
-[[Category: Steyaert, J]]
+[[Category: Steyaert J]]
-[[Category: Vandemeulebroucke, A]]
+[[Category: Van Holsbeke E]]
-[[Category: Versees, W]]
+[[Category: Vandemeulebroucke A]]
-[[Category: Vos, S De]]
+[[Category: Versees W]]
-[[Category: Flexible loop deletion]]
-[[Category: Hydrolase]]
-[[Category: Rossmann fold]]
-[[Category: Transition state complex]]

3b9g

From Proteopedia

Current revision

Crystal structure of loop deletion mutant of Trypanosoma vivax nucleoside hydrolase (3GTvNH) in complex with ImmH

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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