6L07

Crystal structure of Escherichia coli phosphatidylserine decarboxylase (PE-bound form)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: mpstruc
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth B]	SCOP2B Superfamily	Duplicated hybrid motif	8092958	3001927	SCOP2B (2022-06-29)
G [auth D]	SCOP2B Superfamily	Duplicated hybrid motif	8092958	3001927	SCOP2B (2022-06-29)
I [auth E]	SCOP2B Superfamily	Duplicated hybrid motif	8092958	3001927	SCOP2B (2022-06-29)
K [auth F]	SCOP2B Superfamily	Duplicated hybrid motif	8092958	3001927	SCOP2B (2022-06-29)
M [auth G]	SCOP2B Superfamily	Duplicated hybrid motif	8092958	3001927	SCOP2B (2022-06-29)
O [auth H]	SCOP2B Superfamily	Duplicated hybrid motif	8092958	3001927	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Duplicated hybrid motif	8092958	3001927	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Duplicated hybrid motif	8092958	3001927	SCOP2B (2022-06-29)
B [auth I]	SCOP2B Superfamily	Duplicated hybrid motif	8092958	3001927	SCOP2B (2022-06-29)
D [auth J]	SCOP2B Superfamily	Duplicated hybrid motif	8092958	3001927	SCOP2B (2022-06-29)
F [auth K]	SCOP2B Superfamily	Duplicated hybrid motif	8092958	3001927	SCOP2B (2022-06-29)
J [auth L]	SCOP2B Superfamily	Duplicated hybrid motif	8092958	3001927	SCOP2B (2022-06-29)
N [auth M]	SCOP2B Superfamily	Duplicated hybrid motif	8092958	3001927	SCOP2B (2022-06-29)
H [auth N]	SCOP2B Superfamily	Duplicated hybrid motif	8092958	3001927	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	Duplicated hybrid motif	8092958	3001927	SCOP2B (2022-06-29)
L [auth O]	SCOP2B Superfamily	Duplicated hybrid motif	8092958	3001927	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F], M [auth G], O [auth H]	PF02666	Phosphatidylserine decarboxylase (PS_Dcarbxylase)	Phosphatidylserine decarboxylase	-	Family
B [auth I], D [auth J], F [auth K], J [auth L], N [auth M]	PF02666	Phosphatidylserine decarboxylase (PS_Dcarbxylase)	Phosphatidylserine decarboxylase	-	Family
H [auth N], L [auth O], P	PF02666	Phosphatidylserine decarboxylase (PS_Dcarbxylase)	Phosphatidylserine decarboxylase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F], M [auth G], O [auth H]	Phosphatidylserine decarboxylase beta chain	phosphatidylserine decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity	cellular biosynthetic process glycerophospholipid metabolic process lipid biosynthetic process phospholipid metabolic process organic substance metabolic process organic substance biosynthetic process phosphate-containing compound metabolic process phosphorus metabolic process glycerophospholipid biosynthetic process cellular metabolic process phosphatidylethanolamine metabolic process primary metabolic process phospholipid biosynthetic process phosphatidylethanolamine biosynthetic process cellular biosynthetic process glycerophospholipid metabolic process lipid biosynthetic process phospholipid metabolic process organic substance metabolic process organic substance biosynthetic process phosphate-containing compound metabolic process phosphorus metabolic process glycerophospholipid biosynthetic process cellular metabolic process phosphatidylethanolamine metabolic process primary metabolic process phospholipid biosynthetic process phosphatidylethanolamine biosynthetic process biosynthetic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process cellular lipid metabolic process metabolic process cellular process glycerolipid metabolic process lipid metabolic process organonitrogen compound metabolic process gene expression macromolecule biosynthetic process protein maturation protein autoprocessing proteolysis protein processing protein metabolic process macromolecule metabolic process zymogen activation	cell periphery plasma membrane membrane cellular anatomical entity
B [auth I], D [auth J], F [auth K], J [auth L], N [auth M]	Phosphatidylserine decarboxylase alpha chain	phosphatidylserine decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity	cellular biosynthetic process glycerophospholipid metabolic process lipid biosynthetic process phospholipid metabolic process organic substance metabolic process organic substance biosynthetic process phosphate-containing compound metabolic process phosphorus metabolic process glycerophospholipid biosynthetic process cellular metabolic process phosphatidylethanolamine metabolic process primary metabolic process phospholipid biosynthetic process phosphatidylethanolamine biosynthetic process cellular biosynthetic process glycerophospholipid metabolic process lipid biosynthetic process phospholipid metabolic process organic substance metabolic process organic substance biosynthetic process phosphate-containing compound metabolic process phosphorus metabolic process glycerophospholipid biosynthetic process cellular metabolic process phosphatidylethanolamine metabolic process primary metabolic process phospholipid biosynthetic process phosphatidylethanolamine biosynthetic process biosynthetic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process cellular lipid metabolic process metabolic process cellular process glycerolipid metabolic process lipid metabolic process organonitrogen compound metabolic process gene expression macromolecule biosynthetic process protein maturation protein autoprocessing proteolysis protein processing protein metabolic process macromolecule metabolic process zymogen activation	cell periphery plasma membrane membrane cellular anatomical entity
H [auth N], L [auth O], P	Phosphatidylserine decarboxylase alpha chain	phosphatidylserine decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity	cellular biosynthetic process glycerophospholipid metabolic process lipid biosynthetic process phospholipid metabolic process organic substance metabolic process organic substance biosynthetic process phosphate-containing compound metabolic process phosphorus metabolic process glycerophospholipid biosynthetic process cellular metabolic process phosphatidylethanolamine metabolic process primary metabolic process phospholipid biosynthetic process phosphatidylethanolamine biosynthetic process cellular biosynthetic process glycerophospholipid metabolic process lipid biosynthetic process phospholipid metabolic process organic substance metabolic process organic substance biosynthetic process phosphate-containing compound metabolic process phosphorus metabolic process glycerophospholipid biosynthetic process cellular metabolic process phosphatidylethanolamine metabolic process primary metabolic process phospholipid biosynthetic process phosphatidylethanolamine biosynthetic process biosynthetic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process cellular lipid metabolic process metabolic process cellular process glycerolipid metabolic process lipid metabolic process organonitrogen compound metabolic process gene expression macromolecule biosynthetic process protein maturation protein autoprocessing proteolysis protein processing protein metabolic process macromolecule metabolic process zymogen activation	cell periphery plasma membrane membrane cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F], M [auth G], O [auth H]	IPR003817	Phosphatidylserine decarboxylase-related	Family
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F], M [auth G], O [auth H]	IPR033178	Phosphatidylserine decarboxylase, prokaryotic type 1	Family
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F], M [auth G], O [auth H]	IPR033177	Phosphatidylserine decarboxylase, bacterial/eukaryotic	Family
B [auth I], D [auth J], F [auth K], J [auth L], N [auth M]	IPR003817	Phosphatidylserine decarboxylase-related	Family
B [auth I], D [auth J], F [auth K], J [auth L], N [auth M]	IPR033178	Phosphatidylserine decarboxylase, prokaryotic type 1	Family
B [auth I], D [auth J], F [auth K], J [auth L], N [auth M]	IPR033177	Phosphatidylserine decarboxylase, bacterial/eukaryotic	Family
H [auth N], L [auth O], P	IPR003817	Phosphatidylserine decarboxylase-related	Family
H [auth N], L [auth O], P	IPR033178	Phosphatidylserine decarboxylase, prokaryotic type 1	Family
H [auth N], L [auth O], P	IPR033177	Phosphatidylserine decarboxylase, bacterial/eukaryotic	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B [auth I], C [auth B], D [auth J], E [auth C] A, B [auth I], C [auth B], D [auth J], E [auth C], F [auth K], G [auth D], H [auth N], I [auth E], J [auth L], K [auth F], L [auth O], M [auth G], N [auth M], O [auth H], P	OPM				Phosphatidylserine decarboxylase

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B [auth I], C [auth B], D [auth J], E [auth C] A, B [auth I], C [auth B], D [auth J], E [auth C], F [auth K], G [auth D], H [auth N], I [auth E], J [auth L], K [auth F], L [auth O], M [auth G], N [auth M], O [auth H], P	mpstruc	MONOTOPIC MEMBRANE PROTEINS	Decarboxylases (Monotopic)	phosphatidylserine decarboxylase (PSD), apo-form

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth I], D [auth J], F [auth K], J [auth L], N [auth M]	PPI
H [auth N], L [auth O], P	PYR	RESID: AA0127 PSI-MOD : pyruvic acid (Cys) MOD:00136 , pyruvic acid (Ser) MOD:00807 , pyruvic acid MOD:01154 , pyruvic acid (Tyr) MOD:01661

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.