2a5h
From Proteopedia
(New page: 200px<br /><applet load="2a5h" size="450" color="white" frame="true" align="right" spinBox="true" caption="2a5h, resolution 2.10Å" /> '''2.1 Angstrom X-ray c...) |
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| - | [[Image:2a5h.gif|left|200px]]<br /><applet load="2a5h" size=" | + | [[Image:2a5h.gif|left|200px]]<br /><applet load="2a5h" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="2a5h, resolution 2.10Å" /> | caption="2a5h, resolution 2.10Å" /> | ||
'''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).'''<br /> | '''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).'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The x-ray crystal structure of the pyridoxal-5'-phosphate (PLP), S-adenosyl-L-methionine (SAM), and [4Fe-4S]-dependent | + | 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== | ==About this Structure== | ||
| - | 2A5H is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Clostridium_subterminale Clostridium subterminale] with ZN, SO4, SAM, LYS and SF4 as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Lysine_2,3-aminomutase Lysine 2,3-aminomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.3.2 5.4.3.2] Full crystallographic information is available from [http:// | + | 2A5H is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Clostridium_subterminale Clostridium subterminale] with <scene name='pdbligand=ZN:'>ZN</scene>, <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=SAM:'>SAM</scene>, <scene name='pdbligand=LYS:'>LYS</scene> and <scene name='pdbligand=SF4:'>SF4</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Lysine_2,3-aminomutase Lysine 2,3-aminomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.3.2 5.4.3.2] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A5H OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Lysine 2,3-aminomutase]] | [[Category: Lysine 2,3-aminomutase]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Frey, P | + | [[Category: Frey, P A.]] |
| - | [[Category: Lepore, B | + | [[Category: Lepore, B W.]] |
[[Category: Ringe, D.]] | [[Category: Ringe, D.]] | ||
| - | [[Category: Ruzicka, F | + | [[Category: Ruzicka, F J.]] |
[[Category: LYS]] | [[Category: LYS]] | ||
[[Category: SAM]] | [[Category: SAM]] | ||
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[[Category: sam]] | [[Category: sam]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:23:47 2008'' |
Revision as of 14:23, 21 February 2008
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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).
Overview
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
2A5H is a Single protein structure of sequence from Clostridium subterminale with , , , and as ligands. Active as Lysine 2,3-aminomutase, with EC number 5.4.3.2 Full crystallographic information is available from OCA.
Reference
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
Page seeded by OCA on Thu Feb 21 16:23:47 2008
Categories: Clostridium subterminale | Lysine 2,3-aminomutase | Single protein | Frey, P A. | Lepore, B W. | Ringe, D. | Ruzicka, F J. | LYS | SAM | SF4 | SO4 | ZN | 4fe4s | Alpha-beta channel | External aldimine | Four-iron-four-sulfur cluster | Fs4 | Michaelis analog | Pyridoxal-5'-phosphate | Radical sam | S-adenosylmethionine | Sam
