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| | <StructureSection load='2a5h' size='340' side='right'caption='[[2a5h]], [[Resolution|resolution]] 2.10Å' scene=''> | | <StructureSection load='2a5h' size='340' side='right'caption='[[2a5h]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2a5h]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_subterminalis"_hall_and_whitehead_1927 "bacillus subterminalis" hall and whitehead 1927]. 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> | + | <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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LYS:LYSINE'>LYS</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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">KamA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1550 "Bacillus subterminalis" Hall and Whitehead 1927])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Lysine_2,3-aminomutase Lysine 2,3-aminomutase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.3.2 5.4.3.2] </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=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> | | <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> | | </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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus subterminalis hall and whitehead 1927]] | + | [[Category: Clostridium subterminale]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Lysine 2,3-aminomutase]]
| + | [[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: Alpha-beta channel]]
| + | |
| - | [[Category: External aldimine]]
| + | |
| - | [[Category: Four-iron-four-sulfur cluster]]
| + | |
| - | [[Category: Fs4]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Michaelis analog]]
| + | |
| - | [[Category: Pyridoxal-5'-phosphate]]
| + | |
| - | [[Category: Radical sam]]
| + | |
| - | [[Category: S-adenosylmethionine]]
| + | |
| - | [[Category: Sam]]
| + | |
| Structural highlights
2a5h is a 4 chain structure with sequence from Clostridium subterminale. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.1Å |
| Ligands: | , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
KAMA_CLOSU Catalyzes the interconversion of L-alpha-lysine and L-beta-lysine.[1] [2] [3]
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 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.
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[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Petrovich RM, Ruzicka FJ, Reed GH, Frey PA. Characterization of iron-sulfur clusters in lysine 2,3-aminomutase by electron paramagnetic resonance spectroscopy. Biochemistry. 1992 Nov 10;31(44):10774-81. PMID:1329954 doi:10.1021/bi00159a019
- ↑ Petrovich RM, Ruzicka FJ, Reed GH, Frey PA. Metal cofactors of lysine-2,3-aminomutase. J Biol Chem. 1991 Apr 25;266(12):7656-60 PMID:1850415
- ↑ Chirpich TP, Zappia V, Costilow RN, Barker HA. Lysine 2,3-aminomutase. Purification and properties of a pyridoxal phosphate and S-adenosylmethionine-activated enzyme. J Biol Chem. 1970 Apr 10;245(7):1778-89 PMID:5438361
- ↑ Lepore BW, Ruzicka FJ, Frey PA, Ringe D. The x-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale. Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13819-24. Epub 2005 Sep 15. PMID:16166264 doi:0505726102
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