1XRS
Crystal structure of Lysine 5,6-Aminomutase in complex with PLP, cobalamin, and 5'-deoxyadenosine
External Resource: 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 |
---|---|---|---|---|---|
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 ... | Domain | |
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, ... | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR015130 | D-Lysine 5,6-aminomutase alpha subunit | Domain | |
IPR037086 | D-Lysine 5,6-aminomutase alpha subunit superfamily | Homologous Superfamily | |
IPR016176 | Cobalamin (vitamin B12)-dependent enzyme, catalytic | Homologous Superfamily | |
IPR036724 | Cobalamin-binding domain superfamily | Homologous Superfamily | |
IPR006158 | Cobalamin (vitamin B12)-binding domain | Domain | |
IPR028991 | D-lysine 5,6-aminomutase beta subunit KamE, N-terminal | Domain | |
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 |
---|---|---|---|
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. | EC: 5.4.3.3 (PDB Primary Data) |