1LC3 | pdb_00001lc3

Crystal Structure of a Biliverdin Reductase Enzyme-Cofactor Complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1lc3a1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Biliverdin reductase	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d1lc3a2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Biliverdin reductase	Biliverdin reductase	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	GAPDH-like	8000942	3000043	SCOP2B (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		e1lc3A1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: NTP_transf_2, PAP_NTPase	F:	ECOD (20:10:01)
A		e1lc3A2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: FAD_binding_3	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01408	Oxidoreductase family, NAD-binding Rossmann fold (GFO_IDH_MocA)	Oxidoreductase family, NAD-binding Rossmann fold	This entry represents the N-terminal domain of a group of enzymes that utilise NADP or NAD, known as the GFO/IDH/MOCA family, which includes enzymes that catalyse different chemical reactions such as oxidation and reduction of carbohydrates, oxidatio ...	This entry represents the N-terminal domain of a group of enzymes that utilise NADP or NAD, known as the GFO/IDH/MOCA family, which includes enzymes that catalyse different chemical reactions such as oxidation and reduction of carbohydrates, oxidation of trans-dihydrodiols, reduction of biliverdin and hydrolysation of glycosidic bonds. This domain adopts a a typical Rossmann fold.	Domain
A	PF09166	Biliverdin reductase, catalytic (Biliv-reduc_cat)	Biliverdin reductase, catalytic	Members of this family adopt a structure consisting of four alpha helices and six beta sheets, in an alpha-beta-alpha-alpha-alpha-beta-beta-beta-beta-beta arrangement. They contain a catalytic active site, capable of reducing the gamma-methene bridge ...	Members of this family adopt a structure consisting of four alpha helices and six beta sheets, in an alpha-beta-alpha-alpha-alpha-beta-beta-beta-beta-beta arrangement. They contain a catalytic active site, capable of reducing the gamma-methene bridge of the open tetrapyrrole, biliverdin IX alpha, to bilirubin with the concomitant oxidation of a NADH or NADPH cofactor [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Biliverdin Reductase A	biliverdin reductase [NAD(P)H] activity oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on the CH-CH group of donors catalytic activity biliverdin reductase (NADPH) activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding DNA binding sequence-specific DNA binding double-stranded DNA binding biliverdin reductase [NAD(P)H] activity oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on the CH-CH group of donors catalytic activity biliverdin reductase (NADPH) activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding biliberdin reductase (NADH) activity protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups cation binding transition metal ion binding zinc ion binding ion binding metal ion binding	cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation canonical NF-kappaB signal transduction intracellular signal transduction cell communication intracellular signaling cassette cellular process signal transduction response to cyclosporin A response to chemical cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation canonical NF-kappaB signal transduction intracellular signal transduction cell communication intracellular signaling cassette cellular process signal transduction response to cyclosporin A response to chemical response to oxygen-containing compound response to nitrogen compound developmental process ear development sensory organ development animal organ development anatomical structure development immune response immune system process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process insulin metabolic process phosphatidylinositol 3-kinase/protein kinase B signal transduction negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death lipid metabolic process pigment metabolic process multicellular organismal process system process sensory perception nervous system process sensory perception of itch MAPK cascade chemotaxis taxis response to external stimulus locomotion fatty acid metabolic process oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process monocarboxylic acid metabolic process organic acid metabolic process biosynthetic process gene expression macromolecule biosynthetic process cellular response to nitrogen compound response to peptide hormone insulin receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway cellular response to endogenous stimulus response to hormone enzyme-linked receptor protein signaling pathway cellular response to hormone stimulus cell surface receptor signaling pathway response to endogenous stimulus cellular response to peptide hormone stimulus cellular response to oxygen-containing compound cellular response to chemical stimulus response to insulin cellular response to insulin stimulus immune response-regulating cell surface receptor signaling pathway complement receptor mediated signaling pathway positive regulation of biological process positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process positive regulation of immune system process immune response-activating cell surface receptor signaling pathway regulation of response to stimulus complement component C5a signaling pathway regulation of immune response G protein-coupled receptor signaling pathway activation of immune response pigment catabolic process heme metabolic process catabolic process tetrapyrrole metabolic process heme catabolic process porphyrin-containing compound catabolic process porphyrin-containing compound metabolic process tetrapyrrole catabolic process cellular component disassembly DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process cellular component organization execution phase of apoptosis apoptotic DNA fragmentation cellular component disassembly involved in execution phase of apoptosis DNA catabolic process nucleic acid catabolic process apoptotic nuclear changes cellular component organization or biogenesis neutral lipid metabolic process triglyceride metabolic process glycerolipid metabolic process acylglycerol metabolic process defense response response to stress inflammatory response response to oxidative stress biological process involved in interspecies interaction between organisms response to lipid response to other organism response to lipopolysaccharide response to biotic stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin chemical homeostasis homeostatic process glucose homeostasis carbohydrate homeostasis lipid modification lipid oxidation response to nutrient levels response to food carbohydrate metabolic process energy derivation by oxidation of organic compounds glycogen metabolic process generation of precursor metabolites and energy glucan metabolic process polysaccharide metabolic process energy reserve metabolic process reactive oxygen species biosynthetic process reactive oxygen species metabolic process	cell surface cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR017094	Biliverdin reductase A	Family
A	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A	IPR015249	Biliverdin reductase, catalytic	Domain
A	IPR051450	Gfo/Idh/MocA Oxidoreductases	Family
A	IPR000683	Gfo/Idh/MocA-like oxidoreductase, N-terminal	Domain

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.