1XRS

Crystal structure of Lysine 5,6-Aminomutase in complex with PLP, cobalamin, and 5'-deoxyadenosine

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1xrsa_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Cobalamin (vitamin B12)-dependent enzymes	D-lysine 5,6-aminomutase alpha subunit, KamD	D-lysine 5,6-aminomutase alpha subunit, KamD	(Acetoanaerobium sticklandii ) [TaxId: 1511 ],	SCOPe (2.08)
B	d1xrsb1	Alpha and beta proteins (a/b)	Flavodoxin-like	Cobalamin (vitamin B12)-binding domain	Cobalamin (vitamin B12)-binding domain	D-lysine 5,6-aminomutase beta subunit KamE, C-terminal domain	(Acetoanaerobium sticklandii ) [TaxId: 1511 ],	SCOPe (2.08)
B	d1xrsb2	Alpha and beta proteins (a+b)	Dodecin subunit-like	D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain	D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain	D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain	(Acetoanaerobium sticklandii ) [TaxId: 1511 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	D-lysine 5 6-aminomutase alpha subunit KamD	8031763	4003317	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cobalamin (vitamin B12)-dependent enzymes	8044141	3000609	SCOP2 (2022-06-29)
B	SCOP2 Family	Cobalamin (vitamin B12)-binding domain	8031764	4003680	SCOP2 (2022-06-29)
B	SCOP2 Family	D-lysine 5 6-aminomutase beta subunit KamE N-terminal domain	8031765	4003630	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Cobalamin (vitamin B12)-binding domain	8044142	3001260	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	D-lysine 5 6-aminomutase beta subunit KamE N-terminal domain	8044143	3001150	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF09043	e1xrsA3	A: alpha arrays	X: D-ornithine aminomutase S component-related (From Topology)	H: D-ornithine aminomutase S component-related (From Topology)	T: D-ornithine aminomutase S component-related	F: PF09043	ECOD (1.6)
A	PF09043	e1xrsA2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF09043	ECOD (1.6)
B	PF16554	e1xrsB1	A: a+b two layers	X: Dodecin subunit-like	H: D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain (From Topology)	T: D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain	F: PF16554	ECOD (1.6)
B	PF02310	e1xrsB2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: PF02310	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.440	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	D-Lysine 5,6-aminomutase alpha subunit	CATH (4.3.0)
B	3.30.30.60	Alpha Beta	2-Layer Sandwich	Defensin A-like	D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain	CATH (4.3.0)
B	3.40.50.280	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Cobalamin-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF09043	D-Lysine 5,6-aminomutase TIM-barrel domain of alpha subunit (Lys-AminoMut_A)	D-Lysine 5,6-aminomutase TIM-barrel domain of alpha subunit	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 co-factors. The structure is predominantly a PLP-binding TIM ba ...	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 co-factors. 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 co-factor, 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 [1]. This is a TIM-barrel domain.	Domain
B	PF02310	B12 binding domain (B12-binding)	B12 binding domain	This domain binds to B12 (adenosylcobamide)[1-3], it is found in several enzymes, such as glutamate mutase Swiss:Q05488, methionine synthase Swiss:Q99707 and methylmalonyl-CoA mutase Swiss:P22033. It contains a conserved DxHxxGx(41)SxVx(26)GG motif, ...	This domain binds to B12 (adenosylcobamide)[1-3], it is found in several enzymes, such as glutamate mutase Swiss:Q05488, methionine synthase Swiss:Q99707 and methylmalonyl-CoA mutase Swiss:P22033. It contains a conserved DxHxxGx(41)SxVx(26)GG motif, which is important for B12 binding [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	D-lysine 5,6-aminomutase alpha subunit	isomerase activity intramolecular aminotransferase activity catalytic activity lysine 5,6-aminomutase activity intramolecular transferase activity vitamin binding binding cobalamin binding organic cyclic compound binding tetrapyrrole binding heterocyclic compound binding small molecule binding	-	-
B	D-lysine 5,6-aminomutase beta subunit	isomerase activity intramolecular aminotransferase activity catalytic activity lysine 5,6-aminomutase activity intramolecular transferase activity vitamin binding binding cobalamin binding organic cyclic compound binding tetrapyrrole binding heterocyclic compound binding small molecule binding protein binding protein dimerization activity isomerase activity intramolecular aminotransferase activity catalytic activity lysine 5,6-aminomutase activity intramolecular transferase activity vitamin binding binding cobalamin binding organic cyclic compound binding tetrapyrrole binding heterocyclic compound binding small molecule binding protein binding protein dimerization activity cation binding ion binding metal ion binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR015130	D-Lysine 5,6-aminomutase alpha subunit	Domain
A	IPR037086	D-Lysine 5,6-aminomutase alpha subunit superfamily	Homologous Superfamily
A	IPR016176	Cobalamin (vitamin B12)-dependent enzyme, catalytic	Homologous Superfamily
B	IPR036724	Cobalamin-binding domain superfamily	Homologous Superfamily
B	IPR006158	Cobalamin (vitamin B12)-binding domain	Domain
B	IPR028991	D-lysine 5,6-aminomutase beta subunit KamE, N-terminal	Domain
B	IPR036843	D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain superfamily	Homologous Superfamily

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

Chains	Enzyme Name	Description	Catalytic Residues
A, B	beta-lysine 5,6-aminomutase M-CSA #737	Lysine 5,6-aminomutase (5,6-LAM) is sourced from Clostridium sticklandii. It catalyses the reversible transformations of D-lysine into 2,5-diaminohexanoate and of L-beta-lysine into 3,5-diaminohexanoate. The activity of 5,6-LAM is dependent on pyridoxal-5'-phosphate (PLP) and adenosylcobalamin.	Defined by 4 residues: TYR:A-263ASP:A-298LYS:A-370LYS:B-144 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 5.4.3.3 (PDB Primary Data) Search M-CSA Motif + EC 5.4.3.3

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 R01GM133198.