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.


6ntj

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (14:49, 13 March 2024) (edit) (undo)
 
Line 3: Line 3:
<StructureSection load='6ntj' size='340' side='right'caption='[[6ntj]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='6ntj' size='340' side='right'caption='[[6ntj]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[6ntj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/9entr 9entr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NTJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NTJ FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[6ntj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterobacteriaceae Enterobacteriaceae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NTJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NTJ FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLL:(2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDROXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL'>LLL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Hybrid , Neutron Diffraction , X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aacC, aac3-VI, aac3-VI_1, NCTC13462_00209, pAPEC1990_61_126, pAR060302_0140, pAR060302_133, peH4H_0115, SAMEA3485113_05325 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=543 9ENTR])</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LLL:(2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDROXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL'>LLL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aminoglycoside_N(3')-acetyltransferase Aminoglycoside N(3')-acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.81 2.3.1.81] </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=6ntj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ntj OCA], [https://pdbe.org/6ntj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ntj RCSB], [https://www.ebi.ac.uk/pdbsum/6ntj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ntj 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=6ntj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ntj OCA], [http://pdbe.org/6ntj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ntj RCSB], [http://www.ebi.ac.uk/pdbsum/6ntj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ntj ProSAT]</span></td></tr>
+
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/C4NV15_ECOLX C4NV15_ECOLX]
-
The position, bonding and dynamics of hydrogen atoms in the catalytic centers of proteins are essential for catalysis. The role of short hydrogen bonds in catalysis has remained highly debated and led to establishment of several distinctive geometrical arrangements of hydrogen atoms vis-a-vis the heavier donor and acceptor counterparts, that is, low-barrier, single-well or short canonical hydrogen bonds. Here we demonstrate how the position of a hydrogen atom in the catalytic triad of an aminoglycoside inactivating enzyme leads to a thirty-fold increase in catalytic turnover. A low-barrier hydrogen bond is present in the enzyme active site for the substrates that are turned over the best, whereas a canonical hydrogen bond is found with the least preferred substrate. This is the first comparison of these hydrogen bonds involving an identical catalytic network, while directly demonstrating how active site electrostatics adapt to the electronic nature of substrates to tune catalysis.
+
-
 
+
-
Low-Barrier and Canonical Hydrogen Bonds Modulate Activity and Specificity of a Catalytic Triad.,Kumar P, Agarwal PK, Waddell MB, Mittag T, Serpersu EH, Cuneo MJ Angew Chem Int Ed Engl. 2019 Nov 4;58(45):16260-16266. doi:, 10.1002/anie.201908535. Epub 2019 Sep 24. PMID:31515870<ref>PMID:31515870</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 6ntj" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
 +
[[Category: Enterobacteriaceae]]
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Cuneo, M J]]
+
[[Category: Cuneo MJ]]
-
[[Category: Kumar, P]]
+
[[Category: Kumar P]]
-
[[Category: Acetyl transferase]]
+
-
[[Category: Neutron]]
+
-
[[Category: Transferase]]
+
-
[[Category: Transferase-antibiotic complex]]
+

Current revision

Neutron/X-ray crystal structure of AAC-VIa bound to gentamicin C1A

PDB ID 6ntj

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/6ntj"
Personal tools