1JKY | pdb_00001jky

Crystal Structure of the Anthrax Lethal Factor (LF): Wild-type LF Complexed with the N-terminal Sequence of MAPKK2

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)
A	d1jkya1	Alpha and beta proteins (a+b)	Zincin-like	Metalloproteases ('zincins'), catalytic domain	Anthrax toxin lethal factor, N- and C-terminal domains	Anthrax toxin lethal factor, N- and C-terminal domains	(Bacillus anthracis ) [TaxId: 1392 ],	SCOPe (2.08)
A	d1jkya3	Alpha and beta proteins (a+b)	ADP-ribosylation	ADP-ribosylation	ADP-ribosylating toxins	Anthrax toxin lethal factor, middle domain	(Bacillus anthracis ) [TaxId: 1392 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	ADP-ribosylation	8036792	3001208	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8036789	3001975	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8036791	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)
A	Met_synt_B12	e1jkyA1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Met_synt_B12	ECOD (develop294)
A	Glyco_hydro_20b	e1jkyA2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Glyco_hydro_20b	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.390.10	Alpha Beta	3-Layer(aba) Sandwich	Collagenase (Catalytic Domain)	Collagenase (Catalytic Domain)	CATH (4.3.0)
A	3.90.176.10	Alpha Beta	Alpha-Beta Complex	Toxin ADP-ribosyltransferase	Chain A, domain 1	CATH (4.3.0)
A	1.10.2030.10	Mainly Alpha	Orthogonal Bundle	Anthrax toxin lethal factor, domain 3, chain A	Anthrax toxin lethal factor, domain 3, chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF09156	Anthrax toxin lethal factor, middle domain (Anthrax-tox_M)	Anthrax toxin lethal factor, middle domain	Members of this family, which are predominantly found in anthrax toxin lethal factor, adopt a structure consisting of a core of antiparallel beta sheets and alpha helices. They form a long deep groove within the protein that anchors the 16-residue N- ...	Members of this family, which are predominantly found in anthrax toxin lethal factor, adopt a structure consisting of a core of antiparallel beta sheets and alpha helices. They form a long deep groove within the protein that anchors the 16-residue N-terminal tail of MAPKK-2 before cleavage. It has been noted that this domain resembles the ADP-ribosylating toxin from Bacillus cereus, but the active site has been modified to augment substrate recognition [1].	Domain
A	PF07737	Anthrax toxin lethal factor, N- and C-terminal domain (ATLF)	Anthrax toxin lethal factor, N- and C-terminal domain	The C-terminal domain is the catalytically active domain whereas the N-terminal domain is likely to be inactive.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	mitogen-activated protein kinase kinase 2	protein tyrosine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding protein tyrosine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding MAP kinase kinase activity protein serine/threonine/tyrosine kinase activity MAP-kinase scaffold activity protein-macromolecule adaptor activity molecular adaptor activity signaling adaptor activity enzyme regulator activity protein serine/threonine kinase activator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity cation binding metal ion binding protein binding PDZ domain binding protein domain specific binding scaffold protein binding protein serine kinase activity protein serine/threonine kinase activity	developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process positive regulation of nervous system development axonogenesis cell projection organization regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development positive regulation of developmental process cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation positive regulation of cell projection organization regulation of cell projection organization positive regulation of cell development nervous system development generation of neurons positive regulation of multicellular organismal process regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis cell development cell morphogenesis cellular component organization regulation of nervous system development neurogenesis positive regulation of cell differentiation regulation of axonogenesis positive regulation of neurogenesis regulation of multicellular organismal process cellular component organization or biogenesis positive regulation of axonogenesis regulation of anatomical structure morphogenesis regulation of multicellular organismal development plasma membrane bounded cell projection organization axon development cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis neuron development regulation of plasma membrane bounded cell projection organization cellular response to stimulus cell surface receptor signaling pathway response to stimulus signaling insulin-like growth factor receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway cell communication signal transduction enzyme-linked receptor protein signaling pathway Golgi inheritance organelle inheritance regulation of organelle organization regulation of Golgi organization organelle organization regulation of Golgi inheritance Golgi organization endomembrane system organization intracellular signal transduction intracellular signaling cassette MAPK cascade ERBB2 signaling pathway ERBB2-ERBB3 signaling pathway ERBB signaling pathway ERBB3 signaling pathway regulation of protein modification process positive regulation of phosphorylation regulation of catalytic activity regulation of protein phosphorylation positive regulation of protein metabolic process regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of protein serine/threonine kinase activity positive regulation of molecular function positive regulation of protein modification process phosphate-containing compound metabolic process protein metabolic process positive regulation of protein kinase activity phosphorus metabolic process protein modification process positive regulation of protein phosphorylation protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process positive regulation of catalytic activity primary metabolic process regulation of protein kinase activity regulation of molecular function positive regulation of kinase activity regulation of kinase activity macromolecule modification regulation of protein serine/threonine kinase activity regulation of phosphorylation regulation of phosphorus metabolic process positive regulation of locomotion regulation of cell motility regulation of locomotion positive regulation of cell motility cell motility locomotion head development face development immune system development gland development hematopoietic or lymphoid organ development thymus development immune system process thyroid gland development endocrine system development ERK1 and ERK2 cascade peripheral nervous system development glial cell development Schwann cell development gliogenesis glial cell differentiation Schwann cell differentiation regulation of cellular response to stress regulation of signal transduction stress-activated MAPK cascade cellular response to stress regulation of intracellular signal transduction response to stress regulation of response to stress regulation of signaling regulation of stress-activated protein kinase signaling cascade regulation of MAPK cascade regulation of stress-activated MAPK cascade stress-activated protein kinase signaling cascade regulation of response to stimulus regulation of cell communication trachea morphogenesis trachea formation trachea development anatomical structure formation involved in morphogenesis respiratory system development animal organ formation animal organ morphogenesis regulation of localization cellular localization transport regulation of transport intracellular transport regulation of vesicle-mediated transport establishment of localization vesicle-mediated transport endosomal transport vesicle-mediated transport between endosomal compartments regulation of early endosome to late endosome transport localization early endosome to late endosome transport regulation of cellular localization establishment of localization in cell regulation of intracellular transport positive regulation of DNA-templated transcription RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription protein autophosphorylation peptidyl-serine modification peptidyl-serine phosphorylation peptidyl-amino acid modification peptidyl-serine autophosphorylation myelination axon ensheathment ensheathment of neurons regulation of response to external stimulus regeneration response to axon injury neuron projection regeneration regulation of response to wounding axon regeneration response to wounding regulation of axon regeneration response to external stimulus regulation of neuron projection regeneration epithelium development cell population proliferation tube development respiratory tube development lung epithelium development tissue development epithelial cell proliferation involved in lung morphogenesis lung development lung morphogenesis epithelial cell proliferation	cell-cell junction cellular anatomical structure anchoring junction cell junction intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle cell projection sperm principal piece organelle cilium 9+2 motile cilium sperm flagellum cell-cell junction cellular anatomical structure anchoring junction cell junction intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle cell projection sperm principal piece organelle cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection sperm midpiece intracellular organelle Golgi apparatus intracellular membrane-bounded organelle endomembrane system perinuclear region of cytoplasm membrane peroxisome microbody membrane bounding membrane of organelle peroxisomal membrane microbody organelle membrane polymeric cytoskeletal fiber intracellular membraneless organelle cytoskeleton membraneless organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton mitochondrion focal adhesion cell-substrate junction sperm end piece early endosome endosome intracellular vesicle cytoplasmic vesicle vesicle extracellular region late endosome cell periphery cytoplasmic side of plasma membrane cytoplasmic side of membrane plasma membrane side of membrane nucleus endoplasmic reticulum
A	Lethal Factor	peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding metalloendopeptidase activity endopeptidase activity peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding metalloendopeptidase activity endopeptidase activity toxin activity	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure extracellular region host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region host cell cytosol other organism part host cell cytoplasm part

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR000719	Protein kinase domain	Domain
B	IPR050915	MAP kinase kinase	Family
B	IPR017441	Protein kinase, ATP binding site	Binding Site
B	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
B	IPR008271	Serine/threonine-protein kinase, active site	Active Site
A	IPR024079	Metallopeptidase, catalytic domain superfamily	Homologous Superfamily
A	IPR047568	Anthrax toxin lethal factor-like domain	Domain
A	IPR003541	Anthrax toxin, lethal/endema factor	Family
A	IPR014781	Anthrax toxin, lethal/endema factor, N-/C-terminal	Domain
A	IPR015239	Anthrax toxin lethal factor, central domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P36507	cardiofaciocutaneous syndrome Costello syndrome Noonan syndrome melanoma cardiofaciocutaneous syndrome 4 neurofibromatosis-Noonan syndrome salivary gland adenoid cystic carcinoma adenoid cystic carcinoma cardiomyopathy intellectual disability cutaneous melanoma Noonan syndrome with multiple lentigines plasma cell myeloma Cafe-au-lait macules with pulmonary stenosis chronic obstructive pulmonary disease cardiofaciocutaneous syndrome Costello syndrome Noonan syndrome melanoma cardiofaciocutaneous syndrome 4 neurofibromatosis-Noonan syndrome salivary gland adenoid cystic carcinoma adenoid cystic carcinoma cardiomyopathy intellectual disability cutaneous melanoma Noonan syndrome with multiple lentigines plasma cell myeloma Cafe-au-lait macules with pulmonary stenosis chronic obstructive pulmonary disease hypertrophic cardiomyopathy non-small cell lung carcinoma osteosarcoma psoriasis B-cell chronic lymphocytic leukemia neurofibromatosis type 1 ovarian cancer cardiofaciocutaneous syndrome 1 Charcot-Marie-Tooth disease hydrops fetalis juvenile dermatomyositis

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.