2A5H | pdb_00002a5h

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).

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	e2a5hA1	A: DEATH domain	X: 6-phosphogluconate dehydrogenase C-terminal domain-like	H: 6-phosphogluconate dehydrogenase C-terminal domain-like	T: DUF4170	F:	ECOD (20:10:01)
C	e2a5hC1	A: Epidermal growth factor receptor transmembrane-juxtamembrane segment-like	X: Cytochrome c	H: Cytochrome c	T: Radical_SAM,LAM_C	F:	ECOD (20:10:01)
D	e2a5hD1	A: DEATH domain	X: 6-phosphogluconate dehydrogenase C-terminal domain-like	H: 6-phosphogluconate dehydrogenase C-terminal domain-like	T: DUF4170	F:	ECOD (20:10:01)
B	e2a5hB1	A: DEATH domain	X: 6-phosphogluconate dehydrogenase C-terminal domain-like	H: 6-phosphogluconate dehydrogenase C-terminal domain-like	T: DUF4170	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	6.10.140.1170	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	6.20.120.40	Special	Other non-globular	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
C	6.10.140.1170	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
C	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
C	6.20.120.40	Special	Other non-globular	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
D	6.10.140.1170	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
D	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
D	6.20.120.40	Special	Other non-globular	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
B	6.10.140.1170	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
B	6.20.120.40	Special	Other non-globular	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	L-lysine 2,3-aminomutase	L-lysine 2,3-aminomutase activity isomerase activity intramolecular aminotransferase activity catalytic activity intramolecular transferase activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	lysine metabolic process catabolic process oxoacid metabolic process energy derivation by oxidation of organic compounds short-chain fatty acid metabolic process L-lysine catabolic process amino acid metabolic process organic acid metabolic process organic acid catabolic process alpha-amino acid metabolic process fermentation carboxylic acid catabolic process small molecule metabolic process amino acid catabolic process lysine metabolic process catabolic process oxoacid metabolic process energy derivation by oxidation of organic compounds short-chain fatty acid metabolic process L-lysine catabolic process amino acid metabolic process organic acid metabolic process organic acid catabolic process alpha-amino acid metabolic process fermentation carboxylic acid catabolic process small molecule metabolic process amino acid catabolic process fatty acid metabolic process carboxylic acid metabolic process L-amino acid catabolic process primary metabolic process acetate metabolic process generation of precursor metabolites and energy L-lysine fermentation L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process amino acid fermentation metabolic process cellular process monocarboxylic acid metabolic process small molecule catabolic process butyrate metabolic process lipid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR007197	Radical SAM	Domain
A, B, C, D	IPR058240	Radical SAM superfamily	Homologous Superfamily
A, B, C, D	IPR022459	Lysine-2,3-aminomutase	Family
A, B, C, D	IPR003739	Lysine-2,3-aminomutase/glutamate 2,3-aminomutase	Family
A, B, C, D	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B, C, D	IPR025895	Lysine-2,3-aminomutase, C-terminal domain	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	lysine 2,3-aminomutase M-CSA #358	Lysine 2,3-aminomutase (LAM) is a member of the Radical SAM superfamily and is involved in the metabolism of lysine. The superfamily is characterised by the presence of a CxxxCxxC motif which binds a [4Fe-4S] cluster, leaving one of the iron ions unsatisfied. It is often found in anaerobic bacteria that utilise (S)-lysine for growth as a source of nitrogen and/or carbon. Biosynthetically, the (S)-beta-lysine produced is incorporated into antibiotics that contain beta-aminoacyl substituents. Whilst most LAM enzymes produce the (S)-beta-lysine, some produce the R form, such as the Escherichia coli gene yjeK which encodes for a variant of the classical LAM. Whilst zinc is required for enzyme activity,the Zn ion is structural, rather than a cofactor and is required for maintaining the oligomeric state of the biological unit.	Defined by 10 residues: ARG:A-112TYR:A-113ARG:A-116CYS:A-125CYS:A-129CYS:A-132ARG:A-134ASP:A-293ASP:A-330LYS:A-337 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 5.4.3.2 (PDB Primary Data) Search M-CSA Motif + EC 5.4.3.2

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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