3MC6 | pdb_00003mc6

Crystal structure of ScDPL1

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth C]	Chorismate_bind	e3mc6C2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Chorismate_bind	ECOD (v294.1)
A		e3mc6A2	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: RIFT-related	T: double psi	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth C]	6.10.250.3090	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B [auth C]	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
B [auth C]	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
A	6.10.250.3090	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
A	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
A	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth C]	PF00282	Pyridoxal-dependent decarboxylase conserved domain (Pyridoxal_deC)	Pyridoxal-dependent decarboxylase conserved domain		Domain
A	PF00282	Pyridoxal-dependent decarboxylase conserved domain (Pyridoxal_deC)	Pyridoxal-dependent decarboxylase conserved domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth C]	Sphingosine-1-phosphate lyase	vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding sphinganine-1-phosphate aldolase activity lyase activity catalytic activity carbon-carbon lyase activity aldehyde-lyase activity identical protein binding vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding sphinganine-1-phosphate aldolase activity lyase activity catalytic activity carbon-carbon lyase activity aldehyde-lyase activity identical protein binding protein binding	cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress cellular process response to starvation cellular response to starvation sphingolipid metabolic process primary metabolic process metabolic process lipid metabolic process sphingolipid catabolic process cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress cellular process response to starvation cellular response to starvation sphingolipid metabolic process primary metabolic process metabolic process lipid metabolic process sphingolipid catabolic process lipid catabolic process catabolic process oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process organic acid metabolic process regulation of biological process regulation of cellular process signaling biological regulation intracellular signal transduction cell communication calcium-mediated signaling intracellular signaling cassette signal transduction	membrane-bounded organelle cell cortex intracellular anatomical structure cortical endoplasmic reticulum organelle subcompartment intracellular membrane-bounded organelle endomembrane system cell periphery endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure organelle endoplasmic reticulum cytoplasm membrane-bounded organelle cell cortex intracellular anatomical structure cortical endoplasmic reticulum organelle subcompartment intracellular membrane-bounded organelle endomembrane system cell periphery endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure organelle endoplasmic reticulum cytoplasm endoplasmic reticulum tubular network peroxisome microbody perinuclear endoplasmic reticulum perinuclear region of cytoplasm membrane nuclear outer membrane-endoplasmic reticulum membrane network organelle membrane endoplasmic reticulum membrane
A	Sphingosine-1-phosphate lyase	vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding sphinganine-1-phosphate aldolase activity lyase activity catalytic activity carbon-carbon lyase activity aldehyde-lyase activity identical protein binding vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding sphinganine-1-phosphate aldolase activity lyase activity catalytic activity carbon-carbon lyase activity aldehyde-lyase activity identical protein binding protein binding	cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress cellular process response to starvation cellular response to starvation sphingolipid metabolic process primary metabolic process metabolic process lipid metabolic process sphingolipid catabolic process cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress cellular process response to starvation cellular response to starvation sphingolipid metabolic process primary metabolic process metabolic process lipid metabolic process sphingolipid catabolic process lipid catabolic process catabolic process oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process organic acid metabolic process regulation of biological process regulation of cellular process signaling biological regulation intracellular signal transduction cell communication calcium-mediated signaling intracellular signaling cassette signal transduction	membrane-bounded organelle cell cortex intracellular anatomical structure cortical endoplasmic reticulum organelle subcompartment intracellular membrane-bounded organelle endomembrane system cell periphery endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure organelle endoplasmic reticulum cytoplasm membrane-bounded organelle cell cortex intracellular anatomical structure cortical endoplasmic reticulum organelle subcompartment intracellular membrane-bounded organelle endomembrane system cell periphery endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure organelle endoplasmic reticulum cytoplasm endoplasmic reticulum tubular network peroxisome microbody perinuclear endoplasmic reticulum perinuclear region of cytoplasm membrane nuclear outer membrane-endoplasmic reticulum membrane network organelle membrane endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C]	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
B [auth C]	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
B [auth C]	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
B [auth C]	IPR002129	Pyridoxal phosphate-dependent decarboxylase, major domain	Domain
B [auth C]	IPR050477	Group II Amino Acid Decarboxylases	Family
A	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A	IPR002129	Pyridoxal phosphate-dependent decarboxylase, major domain	Domain
A	IPR050477	Group II Amino Acid Decarboxylases	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	LLP	Parent Component: LYS RESID: AA0119 PSI-MOD : N6-pyridoxal phosphate-L-lysine MOD:00128

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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.