This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
2a5h
From Proteopedia
| Line 4: | Line 4: | ||
|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> | ||
}} | }} | ||
| Line 27: | Line 30: | ||
[[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]] | ||
| Line 43: | Line 41: | ||
[[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
