Summary: D-Lysine 5,6-aminomutase alpha subunit
This is the Wikipedia entry entitled "D-lysine 5,6-aminomutase". More...
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D-lysine 5,6-aminomutase Edit Wikipedia article
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / EGO|
|D-Lysine 5,6-aminomutase alpha subunit|
crystal structure of lysine 5,6-aminomutase in complex with plp, cobalamin, and 5'-deoxyadenosine
- D-lysine 2,5-diaminohexanoate
This enzyme belongs to the family of isomerases, specifically those intramolecular transferases transferring amino groups. The systematic name of this enzyme class is D-2,6-diaminohexanoate 5,6-aminomutase. Other names in common use include D-alpha-lysine mutase, and adenosylcobalamin-dependent D-lysine 5,6-aminomutase. This enzyme participates in lysine degradation. It employs one cofactor, cobamide.
The structure of the alpha subunit is predominantly a PLP-binding TIM barrel domain, with several additional alpha-helices and beta-strands at the N and C termini. These helices and strands form an intertwined accessory clamp structure that wraps around the sides of the TIM barrel and extends up toward the Ado ligand of the Cbl cofactor, providing most of the interactions observed between the protein and the Ado ligand of the Cbl, suggesting that its role is mainly in stabilising AdoCbl in the precatalytic resting state.
- Berkovitch F, Behshad E, Tang KH, Enns EA, Frey PA, Drennan CL (2004). "A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase.". Proc Natl Acad Sci U S A 101 (45): 15870–5. doi:10.1073/pnas.0407074101. PMC 528771. PMID 15514022.
- Morley CG, Stadtman TC (1970). "Studies on the fermentation of D-alpha-lysine. Purification and properties of an adenosine triphosphate regulated B 12-coenzyme-dependent D-alpha-lysine mutase complex from Clostridium sticklandii". Biochemistry. 9 (25): 4890–900. doi:10.1021/bi00827a010. PMID 5480154.
- Stadtman TC, Tsai L (1967). "A cobamide coenzyme dependent migration of the epsilon-amino group of D-lysine". Biochem. Biophys. Res. Commun. 28 (6): 920–6. doi:10.1016/0006-291X(67)90067-8. PMID 4229021.
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D-Lysine 5,6-aminomutase alpha subunit Provide feedback
Members of his family are involved in the 1,2 rearrangement of the terminal amino group of DL-lysine and of L-beta-lysine, using adenosylcobalamin (AdoCbl) and pyridoxal-5'-phosphate as cofactors. The structure is predominantly a PLP-binding TIM barrel domain, with several additional alpha-helices and beta-strands at the N and C termini. These helices and strands form an intertwined accessory clamp structure that wraps around the sides of the TIM barrel and extends up toward the Ado ligand of the Cbl cofactor, providing most of the interactions observed between the protein and the Ado ligand of the Cbl, suggesting that its role is mainly in stabilising AdoCbl in the precatalytic resting state .
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR015130
This domain is found in proteins involved in the 1,2 rearrangement of the terminal amino group of DL-lysine and of L-beta-lysine, using adenosylcobalamin (AdoCbl) and pyridoxal-5'-phosphate as cofactors. The structure is predominantly a PLP-binding TIM barrel domain, with several additional alpha-helices and beta-strands at the N and C termini. These helices and strands form an intertwined accessory clamp structure that wraps around the sides of the TIM barrel and extends up toward the Ado ligand of the Cbl cofactor, providing most of the interactions observed between the protein and the Ado ligand of the Cbl, suggesting that its role is mainly in stabilising AdoCbl in the precatalytic resting state.
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This example describes an architecture with one
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Curation and family details
|Author:||Mistry J, Sammut SJ|
|Number in seed:||8|
|Number in full:||226|
|Average length of the domain:||435.60 aa|
|Average identity of full alignment:||50 %|
|Average coverage of the sequence by the domain:||68.49 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||6|
|Download:||download the raw HMM for this family|
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There are 2 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Lys-AminoMut_A domain has been found. There are 25 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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