2a5h: Difference between revisions

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-[[Image:2a5h.gif|left|200px]]
-<!--
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-{{STRUCTURE_2a5h|  PDB=2a5h  |  SCENE=  }}
-'''2.1 Angstrom X-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale SB4, with Michaelis analog (L-alpha-lysine external aldimine form of pyridoxal-5'-phosphate).'''
+==2.1 Angstrom X-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale SB4, with Michaelis analog (L-alpha-lysine external aldimine form of pyridoxal-5'-phosphate).==
+<StructureSection load='2a5h' size='340' side='right'caption='[[2a5h]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2a5h]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_subterminale Clostridium subterminale]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A5H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A5H 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]] 2.1&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2a5h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a5h OCA], [https://pdbe.org/2a5h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a5h RCSB], [https://www.ebi.ac.uk/pdbsum/2a5h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a5h ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/KAMA_CLOSU KAMA_CLOSU] Catalyzes the interconversion of L-alpha-lysine and L-beta-lysine.<ref>PMID:1329954</ref> <ref>PMID:1850415</ref> <ref>PMID:5438361</ref>
+== 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/a5/2a5h_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2a5h ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The x-ray crystal structure of the pyridoxal-5'-phosphate (PLP), S-adenosyl-L-methionine (SAM), and [4Fe-4S]-dependent lysine-2,3-aminomutase (LAM) of Clostridium subterminale has been solved to 2.1-A resolution by single-wavelength anomalous dispersion methods on a L-selenomethionine-substituted complex of LAM with [4Fe-4S]2+, PLP, SAM, and L-alpha-lysine, a very close analog of the active Michaelis complex. The unit cell contains a dimer of hydrogen-bonded, domain-swapped dimers, the subunits of which adopt a fold that contains all three cofactors in a central channel defined by six beta/alpha structural units. Zinc coordination links the domain-swapped dimers. In each subunit, the solvent face of the channel is occluded by an N-terminal helical domain, with the opposite end of the channel packed against the domain-swapped subunit. Hydrogen-bonded ionic contacts hold the external aldimine of PLP and L-alpha-lysine in position for abstraction of the 3-pro-R hydrogen of lysine by C5' of SAM. The structure of the SAM/[4Fe-4S] complex confirms and extends conclusions from spectroscopic studies of LAM and shows selenium in Se-adenosyl-L-selenomethionine poised to ligate the unique iron in the [4Fe-4S] cluster upon electron transfer and radical formation. The chain fold in the central domain is in part analogous to other radical-SAM enzymes.
-==Overview==
+The x-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale.,Lepore BW, Ruzicka FJ, Frey PA, Ringe D Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13819-24. Epub 2005 Sep 15. PMID:16166264<ref>PMID:16166264</ref>
-The x-ray crystal structure of the pyridoxal-5'-phosphate (PLP), S-adenosyl-L-methionine (SAM), and [4Fe-4S]-dependent lysine-2,3-aminomutase (LAM) of Clostridium subterminale has been solved to 2.1-A resolution by single-wavelength anomalous dispersion methods on a L-selenomethionine-substituted complex of LAM with [4Fe-4S]2+, PLP, SAM, and L-alpha-lysine, a very close analog of the active Michaelis complex. The unit cell contains a dimer of hydrogen-bonded, domain-swapped dimers, the subunits of which adopt a fold that contains all three cofactors in a central channel defined by six beta/alpha structural units. Zinc coordination links the domain-swapped dimers. In each subunit, the solvent face of the channel is occluded by an N-terminal helical domain, with the opposite end of the channel packed against the domain-swapped subunit. Hydrogen-bonded ionic contacts hold the external aldimine of PLP and L-alpha-lysine in position for abstraction of the 3-pro-R hydrogen of lysine by C5' of SAM. The structure of the SAM/[4Fe-4S] complex confirms and extends conclusions from spectroscopic studies of LAM and shows selenium in Se-adenosyl-L-selenomethionine poised to ligate the unique iron in the [4Fe-4S] cluster upon electron transfer and radical formation. The chain fold in the central domain is in part analogous to other radical-SAM enzymes.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-A5H is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Clostridium_subterminale Clostridium subterminale]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A5H OCA].
+</div>
+<div class="pdbe-citations 2a5h" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-The x-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale., Lepore BW, Ruzicka FJ, Frey PA, Ringe D, Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13819-24. Epub 2005 Sep 15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16166264 16166264]
+*[[Aminomutase 3D structures|Aminomutase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Clostridium subterminale]]
-[[Category: Lysine 2,3-aminomutase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Frey PA]]
-[[Category: Frey, P A.]]
+[[Category: Lepore BW]]
-[[Category: Lepore, B W.]]
+[[Category: Ringe D]]
-[[Category: Ringe, D.]]
+[[Category: Ruzicka FJ]]
-[[Category: Ruzicka, F J.]]
-[[Category: 4fe4]]
-[[Category: Alpha-beta channel]]
-[[Category: External aldimine]]
-[[Category: Four-iron-four-sulfur cluster]]
-[[Category: Fs4]]
-[[Category: Michaelis analog]]
-[[Category: Pyridoxal-5'-phosphate]]
-[[Category: Radical sam]]
-[[Category: S-adenosylmethionine]]
-[[Category: Sam]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 18:37:55 2008''