1ORD | pdb_00001ord

CRYSTALLOGRAPHIC STRUCTURE OF A PLP-DEPENDENT ORNITHINE DECARBOXYLASE FROM LACTOBACILLUS 30A TO 3.1 ANGSTROMS RESOLUTION

External Resource: Annotation


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

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Bd1ordb1 Alpha and beta proteins (a/b) Flavodoxin-like CheY-like Ornithine decarboxylase N-terminal 'wing' domain Ornithine decarboxylase N-terminal 'wing' domain (Lactobacillus sp. 30A ) [TaxId: 1593 ], SCOPe (2.08)
Bd1ordb2 Alpha and beta proteins (a/b) PLP-dependent transferase-like PLP-dependent transferases Ornithine decarboxylase major domain Ornithine decarboxylase major domain (Lactobacillus sp. 30A ) [TaxId: 1593 ], SCOPe (2.08)
Bd1ordb3 Alpha and beta proteins (a+b) Ornithine decarboxylase C-terminal domain Ornithine decarboxylase C-terminal domain Ornithine decarboxylase C-terminal domain Ornithine decarboxylase C-terminal domain (Lactobacillus sp. 30A ) [TaxId: 1593 ], SCOPe (2.08)
Ad1orda1 Alpha and beta proteins (a/b) Flavodoxin-like CheY-like Ornithine decarboxylase N-terminal 'wing' domain Ornithine decarboxylase N-terminal 'wing' domain (Lactobacillus sp. 30A ) [TaxId: 1593 ], SCOPe (2.08)
Ad1orda2 Alpha and beta proteins (a/b) PLP-dependent transferase-like PLP-dependent transferases Ornithine decarboxylase major domain Ornithine decarboxylase major domain (Lactobacillus sp. 30A ) [TaxId: 1593 ], SCOPe (2.08)
Ad1orda3 Alpha and beta proteins (a+b) Ornithine decarboxylase C-terminal domain Ornithine decarboxylase C-terminal domain Ornithine decarboxylase C-terminal domain Ornithine decarboxylase C-terminal domain (Lactobacillus sp. 30A ) [TaxId: 1593 ], SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
BSCOP2B SuperfamilyPLP-dependent transferases 8032410 3000954 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyCheY-like 8044105 3001156 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyOrnithine decarboxylase C-terminal domain 8036224 3000629 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyOrnithine decarboxylase C-terminal domain 8036224 3000629 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyPLP-dependent transferases 8032410 3000954 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyCheY-like 8044105 3001156 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
BOKR_DC_1_Ce1ordB1 A: a/b three-layered sandwichesX: ETN0001 domain-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: OKR_DC_1_CECOD (v294.1)
BT2SSMe1ordB2 A: a/b three-layered sandwichesX: ETN0001 domain-likeH: General secretion pathway protein M (EpsM) periplasmic domain-relatedT: General secretion pathway protein M (EpsM) periplasmic domain-relatedF: T2SSMECOD (v294.1)
BB12-bindinge1ordB3 A: a/b three-layered sandwichesX: HTHH: HTHT: winged helix domainF: B12-bindingECOD (v294.1)
BEsterasee1ordB4 A: a/b three-layered sandwichesX: HTHH: HTHT: winged helix domainF: EsteraseECOD (v294.1)
AOKR_DC_1_Ce1ordA1 A: a/b three-layered sandwichesX: ETN0001 domain-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: OKR_DC_1_CECOD (v294.1)
AT2SSMe1ordA2 A: a/b three-layered sandwichesX: ETN0001 domain-likeH: General secretion pathway protein M (EpsM) periplasmic domain-relatedT: General secretion pathway protein M (EpsM) periplasmic domain-relatedF: T2SSMECOD (v294.1)
AB12-bindinge1ordA3 A: a/b three-layered sandwichesX: HTHH: HTHT: winged helix domainF: B12-bindingECOD (v294.1)
AEsterasee1ordA4 A: a/b three-layered sandwichesX: HTHH: HTHT: winged helix domainF: EsteraseECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
B3.40.50.220 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold CATH (4.3.0)
B3.40.640.10 Alpha Beta 3-Layer(aba) Sandwich Aspartate Aminotransferase domain 2CATH (4.3.0)
B3.90.1150.10 Alpha Beta Alpha-Beta Complex Aspartate Aminotransferase, domain 1 Aspartate Aminotransferase, domain 1CATH (4.3.0)
B3.90.100.10 Alpha Beta Alpha-Beta Complex Ornithine Decarboxylase Chain A, domain 4CATH (4.3.0)
A3.40.50.220 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold CATH (4.3.0)
A3.40.640.10 Alpha Beta 3-Layer(aba) Sandwich Aspartate Aminotransferase domain 2CATH (4.3.0)
A3.90.1150.10 Alpha Beta Alpha-Beta Complex Aspartate Aminotransferase, domain 1 Aspartate Aminotransferase, domain 1CATH (4.3.0)
A3.90.100.10 Alpha Beta Alpha-Beta Complex Ornithine Decarboxylase Chain A, domain 4CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B
ORNITHINE DECARBOXYLASE

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, B
IPR011006CheY-like superfamilyHomologous Superfamily
A, B
IPR027464Ornithine decarboxylase, N-terminalHomologous Superfamily
A, B
IPR015421Pyridoxal phosphate-dependent transferase, major domainHomologous Superfamily
A, B
IPR015422Pyridoxal phosphate-dependent transferase, small domainHomologous Superfamily
A, B
IPR011193Ornithine/lysine/arginine decarboxylaseFamily
A, B
IPR008286Orn/Lys/Arg decarboxylase, C-terminalDomain
A, B
IPR005308Orn/Lys/Arg decarboxylase, N-terminalDomain
A, B
IPR036633Orn/Lys/Arg decarboxylase, C-terminal domain superfamilyHomologous Superfamily
A, B
IPR015424Pyridoxal phosphate-dependent transferaseHomologous Superfamily
A, B
IPR000310Orn/Lys/Arg decarboxylase, major domainDomain

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

ChainsEnzyme NameDescriptionCatalytic Residues
ornithine decarboxylase  M-CSA #860

Catalyses the decarboxylation of ornithine to form putrescine. It belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase domain superfamily (fold I)

Defined by 3 residues: HIS:A-223ASP:A-316LYS:A-355
 | 
 
Explore in 3D: M-CSA Motif Definition
Search M-CSA Motif
EC: 4.1.1.17 (PDB Primary Data)