8j1c: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

~~The entry~~ 8j1c is ~~ON HOLD until Paper~~ Publication

==Structure of amino acid dehydrogenase in complex with NADP==

== Structural highlights ==

<table><tr><td colspan='2'>[[8j1c]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_veronii Pseudomonas veronii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8J1C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8J1C 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]] 2.2Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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=8j1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8j1c OCA], [https://pdbe.org/8j1c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8j1c RCSB], [https://www.ebi.ac.uk/pdbsum/8j1c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8j1c ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/A0A7Y0ZV07_PSEVE A0A7Y0ZV07_PSEVE]

== Publication Abstract from PubMed ==

Crystal structures of Pseudomonas veroniil-arginine dehydrogenase (l-ArgDH), belonging to the mu-crystallin/ornithine cyclodeaminase family, were determined for the enzyme in complex with l-lysine and NADP(+) and with l-arginine and NADPH. The main chain coordinates of the P. veroniil-ArgDH monomer showed notable similarity to those of Archaeoglobus fulgidusl-AlaDH, belonging to the same family, and pro-R specificity similar to l-AlaDH for hydride transfer to NADP(+) was postulated. However, the residues recognizing the alpha-amino group of the substrates differed between the two enzymes. Based on a substrate modeling study, it was proposed that in A. fulgidusl-AlaDH, the amino group of l-alanine interacts via a water molecule (W510) with the side chains of Lys41 and Arg52. By contrast, the alpha-amino group of l-arginine formed hydrogen bonds with the side chains of Thr224 and Asn225 in P. veroniil-ArgDH. Moreover, the guanidino group of l-arginine was fixed into the active site via hydrogen bonds with the side chain of Asp54. Site-directed mutagenesis suggested that Asp54 plays an important role in maintaining high reactivity against the substrate and that Tyr58 and Lys71 play critical roles in enzyme catalysis.

~~Authors: Sakuraba~~, H., Ohshima, T.

First crystal structure of an NADP(+)-dependent l-arginine dehydrogenase belonging to the mu-crystallin family.,Kawakami R, Takami N, Hayashi J, Yoneda K, Ohmori T, Ohshima T, Sakuraba H Int J Biol Macromol. 2023 Jul 29;249:126070. doi: 10.1016/j.ijbiomac.2023.126070. PMID:37524275<ref>PMID:37524275</ref>

~~Description~~: ~~Structure of amino acid dehydrogenase in complex with NADP~~

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

[[Category: ~~Unreleased~~ Structures]]

</div>

[[Category: ~~Sakuraba, H~~]]

[[Category: Ohshima, T]]

== References ==

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Pseudomonas veronii]]

[[Category: Ohshima T]]

[[Category: Sakuraba H]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8j1c is ON HOLD  until Paper Publication
+==Structure of amino acid dehydrogenase in complex with NADP==
+<StructureSection load='8j1c' size='340' side='right'caption='[[8j1c]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8j1c]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_veronii Pseudomonas veronii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8J1C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8J1C 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]] 2.2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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=8j1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8j1c OCA], [https://pdbe.org/8j1c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8j1c RCSB], [https://www.ebi.ac.uk/pdbsum/8j1c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8j1c ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A0A7Y0ZV07_PSEVE A0A7Y0ZV07_PSEVE]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Crystal structures of Pseudomonas veroniil-arginine dehydrogenase (l-ArgDH), belonging to the mu-crystallin/ornithine cyclodeaminase family, were determined for the enzyme in complex with l-lysine and NADP(+) and with l-arginine and NADPH. The main chain coordinates of the P. veroniil-ArgDH monomer showed notable similarity to those of Archaeoglobus fulgidusl-AlaDH, belonging to the same family, and pro-R specificity similar to l-AlaDH for hydride transfer to NADP(+) was postulated. However, the residues recognizing the alpha-amino group of the substrates differed between the two enzymes. Based on a substrate modeling study, it was proposed that in A. fulgidusl-AlaDH, the amino group of l-alanine interacts via a water molecule (W510) with the side chains of Lys41 and Arg52. By contrast, the alpha-amino group of l-arginine formed hydrogen bonds with the side chains of Thr224 and Asn225 in P. veroniil-ArgDH. Moreover, the guanidino group of l-arginine was fixed into the active site via hydrogen bonds with the side chain of Asp54. Site-directed mutagenesis suggested that Asp54 plays an important role in maintaining high reactivity against the substrate and that Tyr58 and Lys71 play critical roles in enzyme catalysis.
-Authors: Sakuraba, H., Ohshima, T.
+First crystal structure of an NADP(+)-dependent l-arginine dehydrogenase belonging to the mu-crystallin family.,Kawakami R, Takami N, Hayashi J, Yoneda K, Ohmori T, Ohshima T, Sakuraba H Int J Biol Macromol. 2023 Jul 29;249:126070. doi: 10.1016/j.ijbiomac.2023.126070. PMID:37524275<ref>PMID:37524275</ref>
-Description: Structure of amino acid dehydrogenase in complex with NADP
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Sakuraba, H]]
+<div class="pdbe-citations 8j1c" style="background-color:#fffaf0;"></div>
-[[Category: Ohshima, T]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Pseudomonas veronii]]
+[[Category: Ohshima T]]
+[[Category: Sakuraba H]]