6BH8 | pdb_00006bh8

Crystal structure of ZMPSTE24 in complex with phosphoramidon

External Resource: Annotation

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
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8049050	3001975	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8049050	3001975	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)
B	PK_Tyr_Ser-Thr	e6bh8B1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: ADP-ribosylation	T: ADP-ribosylation	F: PK_Tyr_Ser-Thr	ECOD (v294.1)
A	PK_Tyr_Ser-Thr	e6bh8A1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: ADP-ribosylation	T: ADP-ribosylation	F: PK_Tyr_Ser-Thr	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.2010.10	Alpha Beta	2-Layer Sandwich	Zincin-like	Metalloproteases ("zincins"), catalytic domain	CATH (4.3.0)
A	3.30.2010.10	Alpha Beta	2-Layer Sandwich	Zincin-like	Metalloproteases ("zincins"), catalytic domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF16491	CAAX prenyl protease N-terminal, five membrane helices (Peptidase_M48_N)	CAAX prenyl protease N-terminal, five membrane helices	The five N-terminal five transmembrane alpha-helices of peptidase_M48 family proteins including the CAAX prenyl proteases reside completely within the membrane of the endoplasmic reticulum.	Domain
A, B	PF01435	Peptidase family M48 (Peptidase_M48)	Peptidase family M48	Peptidase_M48 is the largely extracellular catalytic region of CAAX prenyl protease homologues such as Human FACE-1 protease. These are metallopeptidases, with the characteristic HExxH motif giving the two histidine-zinc-ligands and an adjacent gluta ...	Peptidase_M48 is the largely extracellular catalytic region of CAAX prenyl protease homologues such as Human FACE-1 protease. These are metallopeptidases, with the characteristic HExxH motif giving the two histidine-zinc-ligands and an adjacent glutamate on the next helix being the third. The whole molecule folds to form a deep groove/cleft into which the substrate can fit [1,2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	CAAX prenyl protease 1 homolog	peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity endopeptidase activity cation binding ion binding binding metal ion binding small molecule binding metalloendopeptidase activity metallopeptidase activity DNA binding double-stranded DNA binding peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity endopeptidase activity cation binding ion binding binding metal ion binding small molecule binding metalloendopeptidase activity metallopeptidase activity DNA binding double-stranded DNA binding nucleic acid binding exopeptidase activity metalloexopeptidase activity	multicellular organismal process connective tissue development developmental growth endochondral bone morphogenesis organ growth multicellular organism development skeletal system development growth plate cartilage development anatomical structure development endochondral bone growth animal organ morphogenesis bone development system development developmental process multicellular organismal process connective tissue development developmental growth endochondral bone morphogenesis organ growth multicellular organism development skeletal system development growth plate cartilage development anatomical structure development endochondral bone growth animal organ morphogenesis bone development system development developmental process growth animal organ development tissue development anatomical structure morphogenesis bone growth skeletal system morphogenesis cartilage development involved in endochondral bone morphogenesis bone morphogenesis cartilage development cellular response to stimulus regulation of biological process regulation of cellular process regulation of cellular senescence cellular response to stress response to stimulus response to stress biological regulation cellular process cellular senescence ossification bone mineralization biomineral tissue development chromosome organization primary metabolic process DNA metabolic process maintenance of DNA repeat elements nucleic acid metabolic process cellular component organization nucleobase-containing compound metabolic process maintenance of rDNA organelle organization metabolic process cellular component organization or biogenesis macromolecule metabolic process cellular response to biotic stimulus cellular response to endogenous stimulus response to DNA integrity checkpoint signaling response to DNA damage checkpoint signaling response to endogenous stimulus response to cell cycle checkpoint signaling response to biotic stimulus cardiac muscle cell membrane repolarization membrane repolarization regulation of membrane repolarization ventricular cardiac muscle cell membrane repolarization regulation of cardiac muscle cell membrane repolarization regulation of biological quality regulation of ventricular cardiac muscle cell membrane repolarization regulation of membrane potential heart development cardiac muscle tissue development striated muscle tissue development circulatory system development ventricular cardiac muscle tissue development muscle tissue development system process nervous system process neuromuscular process positive regulation of biological process RNA metabolic process positive regulation of gene expression via chromosomal CpG island demethylation positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic RNA biosynthetic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process positive regulation of cellular process transcription initiation at RNA polymerase II promoter regulation of biosynthetic process epigenetic regulation of gene expression regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process DNA-templated transcription initiation regulation of gene expression biosynthetic process positive regulation of gene expression transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process regulation of metabolic process regulation of multicellular organism growth regulation of growth regulation of developmental growth regulation of developmental process multicellular organism growth regulation of multicellular organismal process heart morphogenesis regulation of multicellular organismal development regulation of biomineral tissue development regulation of bone mineralization regulation of ossification CAAX-box protein processing protein maturation proteolysis CAAX-box protein maturation protein processing protein metabolic process inflammatory cell apoptotic process apoptotic process cell death programmed cell death heart process regulation of heart contraction regulation of system process circulatory system process regulation of blood circulation cardiac conduction heart contraction blood circulation DNA damage response DNA repair regulation of cellular component organization protein-containing complex disassembly DNA-templated transcription termination regulation of protein-containing complex disassembly regulation of primary metabolic process regulation of RNA metabolic process transcription by RNA polymerase I regulation of nucleobase-containing compound metabolic process termination of RNA polymerase I transcription regulation of RNA biosynthetic process cellular component disassembly regulation of transcription by RNA polymerase I regulation of termination of RNA polymerase I transcription protein-containing complex organization regulation of termination of DNA-templated transcription regulation of DNA-templated transcription adult walking behavior adult locomotory behavior behavior adult behavior locomotory behavior walking behavior negative regulation of biological process post-transcriptional regulation of gene expression RNA processing negative regulation of metabolic process regulation of miRNA processing miRNA-mediated post-transcriptional gene silencing negative regulation of gene expression negative regulation of macromolecule biosynthetic process negative regulation of miRNA-mediated gene silencing post-transcriptional gene silencing miRNA processing negative regulation of post-transcriptional gene silencing regulation of miRNA-mediated gene silencing negative regulation of post-transcriptional gene silencing by regulatory ncRNA regulation of regulatory ncRNA processing regulation of gene silencing by regulatory ncRNA negative regulation of cellular process regulation of post-transcriptional gene silencing by regulatory ncRNA negative regulation of miRNA processing negative regulation of macromolecule metabolic process negative regulation of gene silencing by regulatory ncRNA regulatory ncRNA-mediated post-transcriptional gene silencing regulatory ncRNA processing regulatory ncRNA-mediated gene silencing regulation of post-transcriptional gene silencing negative regulation of biosynthetic process hepaticobiliary system development gland development liver development regulation of lipid metabolic process lipid metabolic process immune system development hematopoietic or lymphoid organ development thymus development immune system process membrane organization nucleus organization nuclear envelope organization endomembrane system organization regulation of hormone metabolic process regulation of hormone levels hormone metabolic process cellular response to ionizing radiation cellular response to radiation cellular response to environmental stimulus response to ionizing radiation cellular response to gamma radiation response to radiation response to abiotic stimulus cellular response to abiotic stimulus response to gamma radiation epithelium development epidermis development molting cycle process hair cycle skin development skin epidermis development hair follicle development molting cycle hair cycle process signaling intracellular signal transduction cell communication calcium-mediated signaling intracellular signaling cassette signal transduction CAMKK-AMPK signaling cascade regulation of cellular response to stress regulation of signal transduction DNA damage response, signal transduction by p53 class mediator regulation of intracellular signal transduction regulation of response to stress regulation of signal transduction by p53 class mediator regulation of DNA damage response, signal transduction by p53 class mediator regulation of signaling signal transduction by p53 class mediator regulation of response to stimulus regulation of cell communication signal transduction in response to DNA damage fibroblast proliferation cell population proliferation regulation of cell population proliferation regulation of fibroblast proliferation cardiac chamber development cardiac ventricle development regulation of cell shape cell morphogenesis regulation of cell morphogenesis regulation of anatomical structure morphogenesis regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus defense response response to other organism response to external stimulus regulation of defense response to virus defense response to virus response to external biotic stimulus response to virus determination of adult lifespan catabolic process protein catabolic process macromolecule catabolic process prenylated protein catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process cardiac muscle cell development cellular developmental process cell development muscle cell differentiation muscle structure development striated muscle cell development muscle cell development cell differentiation cardiac cell development cardiac muscle cell differentiation cardiocyte differentiation striated muscle cell differentiation cellular localization transport sarcoplasmic reticulum calcium ion transport intracellular transport establishment of localization calcium ion transport metal ion transport localization establishment of localization in cell monoatomic ion transport monoatomic cation transport calcium ion import into sarcoplasmic reticulum mitotic DNA replication nuclear DNA replication cell cycle DNA replication mitotic cell cycle regulation of mitotic cell cycle cell cycle regulation of cell cycle cell cycle process DNA-templated DNA replication regulation of mitotic cell cycle DNA replication regulation of nuclear cell cycle DNA replication regulation of cell cycle process DNA replication mitotic cell cycle process regulation of DNA-templated DNA replication regulation of DNA replication regulation of DNA metabolic process autophagy regulation of catabolic process regulation of autophagy process utilizing autophagic mechanism TOR signaling regulation of TOR signaling renal system development kidney morphogenesis kidney development monosaccharide metabolic process carbohydrate metabolic process hexose metabolic process regulation of small molecule metabolic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process glucose metabolic process regulation of stress-activated protein kinase signaling cascade stress-activated protein kinase signaling cascade	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle endosome membrane intracellular anatomical structure endosome cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle endosome membrane intracellular anatomical structure endosome intracellular vesicle late endosome membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane late endosome cytoplasm organelle membrane organelle inner membrane nuclear membrane nucleus organelle envelope nuclear inner membrane nuclear envelope protein-containing complex organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane early endosome early endosome membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001915	Peptidase M48	Domain
A, B	IPR027057	CAAX prenyl protease 1	Family
A, B	IPR032456	CAAX prenyl protease 1, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: O75844	Hutchinson-Gilford progeria syndrome lipodystrophy mandibuloacral dysplasia with type B lipodystrophy lethal restrictive dermopathy Craniofacial Abnormalities focal segmental glomerulosclerosis intellectual disability lymphoplasmacytic lymphoma pancreatic intraductal papillary-mucinous neoplasm acroosteolysis dominant type malignant ependymoma osteogenesis imperfecta plasma cell myeloma arthrogryposis ovarian cancer

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Intramembrane Proteases	CAAX protease ZMPSTE24 with bound phosphoramidon

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.

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