3KOY | pdb_00003koy

Crystal Structure of ornithine 4,5 aminomutase in complex with ornithine (Aerobic)

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
F [auth G]SCOP2B SuperfamilyOraS globular domain-like 8092026 3002551 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyOraS globular domain-like 8092026 3002551 SCOP2B (2022-06-29)
D [auth F]SCOP2B SuperfamilyOraS globular domain-like 8092026 3002551 SCOP2B (2022-06-29)
B [auth E]SCOP2B SuperfamilyOraS globular domain-like 8092026 3002551 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
F [auth G]Trypsine3koyG1 A: alpha bundlesX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: TrypsinECOD (develop294)
HTrypsine3koyH1 A: alpha bundlesX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: TrypsinECOD (develop294)
D [auth F]Trypsine3koyF1 A: alpha bundlesX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: TrypsinECOD (develop294)
B [auth E]Trypsine3koyE1 A: alpha bundlesX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: TrypsinECOD (develop294)
Ae3koyA3 A: alpha bundlesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF:ECOD (develop294)
AAlpha-amylasee3koyA5 A: alpha bundlesX: DEATH domainH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: Alpha-amylaseECOD (develop294)
AAcetyltransf_9e3koyA1 A: alpha bundlesX: RuvA-CH: post-HMGL domain-likeT: post-HMGL domain-likeF: Acetyltransf_9ECOD (develop294)
C [auth B]e3koyB3 A: alpha bundlesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF:ECOD (develop294)
C [auth B]Alpha-amylasee3koyB5 A: alpha bundlesX: DEATH domainH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: Alpha-amylaseECOD (develop294)
C [auth B]Acetyltransf_9e3koyB1 A: alpha bundlesX: RuvA-CH: post-HMGL domain-likeT: post-HMGL domain-likeF: Acetyltransf_9ECOD (develop294)
E [auth C]e3koyC3 A: alpha bundlesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF:ECOD (develop294)
E [auth C]Alpha-amylasee3koyC5 A: alpha bundlesX: DEATH domainH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: Alpha-amylaseECOD (develop294)
E [auth C]Acetyltransf_9e3koyC1 A: alpha bundlesX: RuvA-CH: post-HMGL domain-likeT: post-HMGL domain-likeF: Acetyltransf_9ECOD (develop294)
G [auth D]e3koyD3 A: alpha bundlesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF:ECOD (develop294)
G [auth D]Alpha-amylasee3koyD5 A: alpha bundlesX: DEATH domainH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: Alpha-amylaseECOD (develop294)
G [auth D]Acetyltransf_9e3koyD1 A: alpha bundlesX: RuvA-CH: post-HMGL domain-likeT: post-HMGL domain-likeF: Acetyltransf_9ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
F [auth G]6.10.250.2220 Special Helix non-globular Single alpha-helices involved in coiled-coils or other helix-helix interfaces CATH (4.3.0)
F [auth G]1.10.8.1000 Mainly Alpha Orthogonal Bundle Helicase, Ruva Protein domain 3CATH (4.3.0)
H6.10.250.2220 Special Helix non-globular Single alpha-helices involved in coiled-coils or other helix-helix interfaces CATH (4.3.0)
H1.10.8.1000 Mainly Alpha Orthogonal Bundle Helicase, Ruva Protein domain 3CATH (4.3.0)
D [auth F]6.10.250.2220 Special Helix non-globular Single alpha-helices involved in coiled-coils or other helix-helix interfaces CATH (4.3.0)
D [auth F]1.10.8.1000 Mainly Alpha Orthogonal Bundle Helicase, Ruva Protein domain 3CATH (4.3.0)
B [auth E]6.10.250.2220 Special Helix non-globular Single alpha-helices involved in coiled-coils or other helix-helix interfaces CATH (4.3.0)
B [auth E]1.10.8.1000 Mainly Alpha Orthogonal Bundle Helicase, Ruva Protein domain 3CATH (4.3.0)
A3.20.20.440 Alpha Beta Alpha-Beta Barrel TIM Barrel D-Lysine 5,6-aminomutase alpha subunitCATH (4.3.0)
A3.30.30.60 Alpha Beta 2-Layer Sandwich Defensin A-like D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domainCATH (4.3.0)
A3.40.50.280 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Cobalamin-binding domainCATH (4.3.0)
C [auth B]3.20.20.440 Alpha Beta Alpha-Beta Barrel TIM Barrel D-Lysine 5,6-aminomutase alpha subunitCATH (4.3.0)
C [auth B]3.30.30.60 Alpha Beta 2-Layer Sandwich Defensin A-like D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domainCATH (4.3.0)
C [auth B]3.40.50.280 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Cobalamin-binding domainCATH (4.3.0)
E [auth C]3.20.20.440 Alpha Beta Alpha-Beta Barrel TIM Barrel D-Lysine 5,6-aminomutase alpha subunitCATH (4.3.0)
E [auth C]3.30.30.60 Alpha Beta 2-Layer Sandwich Defensin A-like D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domainCATH (4.3.0)
E [auth C]3.40.50.280 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Cobalamin-binding domainCATH (4.3.0)
G [auth D]3.20.20.440 Alpha Beta Alpha-Beta Barrel TIM Barrel D-Lysine 5,6-aminomutase alpha subunitCATH (4.3.0)
G [auth D]3.30.30.60 Alpha Beta 2-Layer Sandwich Defensin A-like D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domainCATH (4.3.0)
G [auth D]3.40.50.280 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Cobalamin-binding domainCATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A,
C [auth B],
E [auth C],
G [auth D]		PF09043D-Lysine 5,6-aminomutase TIM-barrel domain of alpha subunit (Lys-AminoMut_A)D-Lysine 5,6-aminomutase TIM-barrel domain of alpha subunitMembers 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
A,
C [auth B],
E [auth C],
G [auth D]		PF16554Dimerisation domain of d-ornithine 4,5-aminomutase (OAM_dimer)Dimerisation domain of d-ornithine 4,5-aminomutaseThis family is the short dimerisation domain of the enzyme D-ornithine 4,5-aminomutase. It sits between the TIM-barrel Pfam:PF09043 and Pfam:PF02310. The enzyme is an alpha2-beta2-heterodimer that converts D-ornithine to 2,4-diaminopentanoic acid by ...This family is the short dimerisation domain of the enzyme D-ornithine 4,5-aminomutase. It sits between the TIM-barrel Pfam:PF09043 and Pfam:PF02310. The enzyme is an alpha2-beta2-heterodimer that converts D-ornithine to 2,4-diaminopentanoic acid by way of radical propagation from an adenosylcobalamin to a pyridoxal 5'-phosphate cofactor [1].
Domain
A,
C [auth B],
E [auth C],
G [auth D]		PF02310B12 binding domain (B12-binding)B12 binding domainThis 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

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
B [auth E],
D [auth F],
F [auth G],
H		D-ornithine aminomutase S component - -
A,
C [auth B],
E [auth C],
G [auth D]		D-ornithine aminomutase E component - -

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
B [auth E],
D [auth F],
F [auth G],
H		IPR015130D-Lysine 5,6-aminomutase alpha subunitDomain
B [auth E],
D [auth F],
F [auth G],
H		IPR016176Cobalamin (vitamin B12)-dependent enzyme, catalyticHomologous Superfamily
A,
C [auth B],
E [auth C],
G [auth D]		IPR036724Cobalamin-binding domain superfamilyHomologous Superfamily
A,
C [auth B],
E [auth C],
G [auth D]		IPR049834D-ornithine 4,5-aminomutase subunit beta-likeFamily
A,
C [auth B],
E [auth C],
G [auth D]		IPR015130D-Lysine 5,6-aminomutase alpha subunitDomain
A,
C [auth B],
E [auth C],
G [auth D]		IPR006158Cobalamin (vitamin B12)-binding domainDomain
A,
C [auth B],
E [auth C],
G [auth D]		IPR028991D-lysine 5,6-aminomutase beta subunit KamE, N-terminalDomain
A,
C [auth B],
E [auth C],
G [auth D]		IPR037086D-Lysine 5,6-aminomutase alpha subunit superfamilyHomologous Superfamily
A,
C [auth B],
E [auth C],
G [auth D]		IPR036843D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain superfamilyHomologous Superfamily
A,
C [auth B],
E [auth C],
G [auth D]		IPR016176Cobalamin (vitamin B12)-dependent enzyme, catalyticHomologous Superfamily