1PV8 | pdb_00001pv8

Crystal structure of a low activity F12L mutant of human porphobilinogen synthase

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1pv8b_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)	5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1pv8a_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)	5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Aldolase	8039147	3000445	SCOP2B (2022-06-29)
A	SCOP2 Family	5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)	8026768	4003237	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Aldolase	8039147	3000445	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B		e1pv8B1	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: PF27526	F:	ECOD (20:10:01)
A		e1pv8A1	A: HTH	X: HTH	H: winged helix domain	T: Plexin_RBD	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00490	Delta-aminolevulinic acid dehydratase (ALAD)	Delta-aminolevulinic acid dehydratase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Delta-aminolevulinic acid dehydratase	protein-containing complex binding proteasome core complex binding binding catalytic activity hydro-lyase activity lyase activity porphobilinogen synthase activity carbon-oxygen lyase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding protein-containing complex binding proteasome core complex binding binding catalytic activity hydro-lyase activity lyase activity porphobilinogen synthase activity carbon-oxygen lyase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding identical protein binding protein binding	response to acid chemical response to stimulus response to chemical response to amino acid response to xenobiotic stimulus response to mercury ion response to metal ion response to selenium ion heme A biosynthetic process heme metabolic process pigment metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole metabolic process heme biosynthetic process response to acid chemical response to stimulus response to chemical response to amino acid response to xenobiotic stimulus response to mercury ion response to metal ion response to selenium ion heme A biosynthetic process heme metabolic process pigment metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole metabolic process heme biosynthetic process pigment biosynthetic process tetrapyrrole biosynthetic process biosynthetic process metabolic process cellular process porphyrin-containing compound metabolic process response to platinum ion response to methylmercury response to interleukin-4 response to peptide response to cytokine cellular response to cytokine stimulus cellular response to interleukin-4 response to activity response to iron ion response to corticosteroid response to lipid response to hormone response to steroid hormone response to endogenous stimulus response to glucocorticoid response to alcohol response to oxygen-containing compound response to ethanol response to zinc ion response to ionizing radiation response to radiation response to abiotic stimulus response to nutrient levels response to vitamin B1 response to nutrient response to nitrogen compound response to vitamin regulation of cellular process catabolic process negative regulation of biological process macromolecule catabolic process regulation of primary metabolic process negative regulation of protein catabolic process negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of catabolic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process biological regulation primary metabolic process proteasomal protein catabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process negative regulation of proteasomal protein catabolic process regulation of proteasomal protein catabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process response to stress response to herbicide response to toxic substance response to decreased oxygen levels response to hypoxia response to oxygen levels protoporphyrinogen IX metabolic process protoporphyrinogen IX biosynthetic process response to fatty acid response to vitamin E heme B biosynthetic process response to cadmium ion response to oxidative stress cellular response to stimulus cellular response to metal ion cellular response to chemical stimulus cellular response to lead ion response to lead ion cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis response to cobalt ion response to aluminum ion response to arsenic-containing substance biological process involved in interspecies interaction between organisms response to other organism response to external stimulus response to lipopolysaccharide response to biotic stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol membrane-enclosed lumen extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol membrane-enclosed lumen intracellular vesicle ficolin-1-rich granule intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen intracellular organelle organelle lumen cytoplasmic vesicle ficolin-1-rich granule lumen secretory granule secretory vesicle vesicle lumen cytoplasmic vesicle lumen secretory granule lumen nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001731	Delta-aminolevulinic acid dehydratase	Family
A, B	IPR030656	Delta-aminolevulinic acid dehydratase, active site	Active Site
A, B	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P13716	meningioma inherited porphyria secretory meningioma porphyria due to ALA dehydratase deficiency renal cell carcinoma hepatic porphyria fibrous meningioma microcystic meningioma visual epilepsy hypertensive disorder adult acute respiratory distress syndrome prostate cancer intraventricular meningioma cerebral convexity meningioma kidney disease meningioma inherited porphyria secretory meningioma porphyria due to ALA dehydratase deficiency renal cell carcinoma hepatic porphyria fibrous meningioma microcystic meningioma visual epilepsy hypertensive disorder adult acute respiratory distress syndrome prostate cancer intraventricular meningioma cerebral convexity meningioma kidney disease clear cell meningioma Lead Poisoning, Nervous System olfactory groove meningioma hematologic disease papillary renal cell carcinoma chromophobe renal cell carcinoma spinal meningioma meningothelial meningioma transitional meningioma parasagittal meningioma angiomatous meningioma intraorbital meningioma psammomatous meningioma benign meningioma sarcomatoid renal cell carcinoma cirrhosis of liver lead poisoning collecting duct carcinoma liver disease Sjogren syndrome tuberculosis osteosarcoma papillary meningioma renal carcinoma malignant mesothelioma gastric carcinoma ulcerative colitis ovarian cancer adenoma inborn errors of metabolism atypical teratoid rhabdoid tumor invasive ductal breast carcinoma large cell medulloblastoma clear cell renal carcinoma lymphoplasmacyte-rich meningioma cutaneous lupus erythematosus medulloblastoma pancreatic ductal adenocarcinoma adrenal cortex carcinoma inherited disease susceptibility

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.