2a5h
From Proteopedia
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|PDB= 2a5h |SIZE=350|CAPTION= <scene name='initialview01'>2a5h</scene>, resolution 2.10Å | |PDB= 2a5h |SIZE=350|CAPTION= <scene name='initialview01'>2a5h</scene>, resolution 2.10Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <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> |
| - | |ACTIVITY= [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] | + | |ACTIVITY= <span class='plainlinks'>[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] </span> |
|GENE= KamA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1550 Clostridium subterminale]) | |GENE= KamA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1550 Clostridium subterminale]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2a5h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a5h OCA], [http://www.ebi.ac.uk/pdbsum/2a5h PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2a5h RCSB]</span> | ||
}} | }} | ||
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[[Category: Ringe, D.]] | [[Category: Ringe, D.]] | ||
[[Category: Ruzicka, F J.]] | [[Category: Ruzicka, F J.]] | ||
| - | [[Category: LYS]] | ||
| - | [[Category: SAM]] | ||
| - | [[Category: SF4]] | ||
| - | [[Category: SO4]] | ||
| - | [[Category: ZN]] | ||
[[Category: 4fe4]] | [[Category: 4fe4]] | ||
[[Category: alpha-beta channel]] | [[Category: alpha-beta channel]] | ||
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[[Category: sam]] | [[Category: sam]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:48:06 2008'' |
Revision as of 22:48, 30 March 2008
| |||||||
| , resolution 2.10Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , | ||||||
| Gene: | KamA (Clostridium subterminale) | ||||||
| Activity: | Lysine 2,3-aminomutase, with EC number 5.4.3.2 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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. 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 Mon Mar 31 01:48:06 2008
Categories: Clostridium subterminale | Lysine 2,3-aminomutase | Single protein | Frey, P A. | Lepore, B W. | Ringe, D. | Ruzicka, F J. | 4fe4 | Alpha-beta channel | External aldimine | Four-iron-four-sulfur cluster | Fs4 | Michaelis analog | Pyridoxal-5'-phosphate | Radical sam | S-adenosylmethionine | Sam
