View source for 3w21


==Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase in complex with alpha-KG from Burkholderia ambifaria AMMD==
<StructureSection load='3w21' size='340' side='right'caption='[[3w21]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3w21]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_ambifaria_AMMD Burkholderia ambifaria AMMD]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W21 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W21 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]] 1.98&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=3w21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w21 OCA], [https://pdbe.org/3w21 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w21 RCSB], [https://www.ebi.ac.uk/pdbsum/3w21 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w21 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q0B2N4_BURCM Q0B2N4_BURCM] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A novel dioxygenase from Burkholderia ambifaria AMMD (SadA) stereoselectively catalyzes the C3-hydroxylation of N-substituted branched-chain or aromatic L-amino acids, especially N-succinyl-L-leucine, coupled with the conversion of alpha-ketoglutarate to succinate and CO2. To elucidate the structural basis of the substrate specificity and stereoselective hydroxylation, we determined the crystal structures of the SadA.Zn(II) and SadA.Zn(II).alpha-KG complexes at 1.77 A and 1.98 A resolutions, respectively. SadA adopted a double-stranded beta-helix fold at the core of the structure. In addition, an HXD/EXnH motif in the active site coordinated a Zn(II) as a substitute for Fe(II). The alpha-KG molecule also coordinated Zn(II) in a bidentate manner via its 1-carboxylate and 2-oxo groups. Based on the SadA.Zn(II).alpha-KG structure and mutation analyses, we constructed substrate-binding models with N-succinyl-L-leucine and N-succinyl-L-phenylalanine, which provided new insight into the substrate specificity. The results will be useful for the rational design of SadA variants aimed at the recognition of various N-succinyl L-amino acids.

Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase from Burkholderia ambifaria AMMD.,Qin HM, Miyakawa T, Jia MZ, Nakamura A, Ohtsuka J, Xue YL, Kawashima T, Kasahara T, Hibi M, Ogawa J, Tanokura M PLoS One. 2013 May 28;8(5):e63996. doi: 10.1371/journal.pone.0063996. Print 2013. PMID:23724013<ref>PMID:23724013</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3w21" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Burkholderia ambifaria AMMD]]
[[Category: Large Structures]]
[[Category: Hibi M]]
[[Category: Jia MZ]]
[[Category: Kasahara T]]
[[Category: Kawashima T]]
[[Category: Miyakawa T]]
[[Category: Nakamura A]]
[[Category: Ogawa J]]
[[Category: Ohtsuka J]]
[[Category: Qin HM]]
[[Category: Tanokura M]]
[[Category: Xue YL]]