8TVT

Structure of human Cysteine desulfurase Nfs1 with L-propargylglycine bound to active site PLP in complex with ISD11, Acp1 and ISCU2

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PLP-dependent transferases	8074674	3000954	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF05347	Complex 1 protein (LYR family) (Complex1_LYR)	Complex 1 protein (LYR family)	-	Family
D	PF01592	NifU-like N terminal domain (NifU_N)	NifU-like N terminal domain	-	Family
A	PF00266	Aminotransferase class-V (Aminotran_5)	Aminotransferase class-V	This domain is found in amino transferases, and other enzymes including cysteine desulphurase EC:4.4.1.-.	Domain
C	PF00550	Phosphopantetheine attachment site (PP-binding)	Phosphopantetheine attachment site	A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes memb ...	A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes members not included in Prosite. The inclusion of these members is supported by sequence analysis and functional evidence. The related domain of Swiss:P19828 has the attachment serine replaced by an alanine.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	LYR motif-containing protein 4	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity	cellular component biogenesis cellular component organization metallo-sulfur cluster assembly cellular component assembly iron-sulfur cluster assembly cellular process cellular component organization or biogenesis [2Fe-2S] cluster assembly [4Fe-4S] cluster assembly	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle protein-containing complex cytosol iron-sulfur cluster assembly complex mitochondrial protein-containing complex catalytic complex sulfurtransferase complex membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle protein-containing complex cytosol iron-sulfur cluster assembly complex mitochondrial protein-containing complex catalytic complex sulfurtransferase complex transferase complex L-cysteine desulfurase complex mitochondrial [2Fe-2S] assembly complex nucleus membrane-enclosed lumen intracellular organelle lumen nuclear body nucleoplasm organelle lumen nuclear lumen mitochondrial matrix
D	Iron-sulfur cluster assembly enzyme ISCU	cation binding transition metal ion binding iron ion binding ion binding binding ferrous iron binding metal ion binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding cation binding transition metal ion binding iron ion binding ion binding binding ferrous iron binding metal ion binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding metal cluster binding molecular adaptor activity zinc ion binding	intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis regulation of lyase activity regulation of molecular function positive regulation of molecular function regulation of catalytic activity intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis regulation of lyase activity regulation of molecular function positive regulation of molecular function regulation of catalytic activity biological regulation positive regulation of catalytic activity positive regulation of aconitate hydratase activity regulation of aconitate hydratase activity positive regulation of lyase activity regulation of localization regulation of cellular process iron import into cell negative regulation of biological process negative regulation of iron ion transmembrane transport negative regulation of transport localization establishment of localization in cell negative regulation of cation transmembrane transport monoatomic cation transport regulation of biological process import across plasma membrane regulation of monoatomic ion transport iron ion transport iron ion transmembrane transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport negative regulation of iron ion import across plasma membrane transmembrane transport regulation of transmembrane transport import into cell cellular localization transport monoatomic ion transmembrane transport negative regulation of monoatomic ion transport regulation of monoatomic ion transmembrane transport metal ion transport negative regulation of transmembrane transport monoatomic cation transmembrane transport regulation of iron ion transmembrane transport negative regulation of monoatomic ion transmembrane transport negative regulation of cellular process monoatomic ion transport regulation of metal ion transport regulation of iron ion import across plasma membrane iron ion import across plasma membrane negative regulation of iron ion transport regulation of transport regulation of iron ion transport inorganic cation import across plasma membrane regulation of cellular localization inorganic ion import across plasma membrane transition metal ion transport cellular process regulation of monoatomic cation transmembrane transport cellular component biogenesis cellular component organization metallo-sulfur cluster assembly cellular component assembly iron-sulfur cluster assembly cellular component organization or biogenesis aerobic respiration cellular respiration aerobic electron transport chain oxidative phosphorylation energy derivation by oxidation of organic compounds ATP synthesis coupled electron transport positive regulation of biological process electron transport chain regulation of generation of precursor metabolites and energy positive regulation of cellular metabolic process regulation of cellular respiration positive regulation of cellular respiration positive regulation of metabolic process respiratory electron transport chain positive regulation of cellular process cellular metabolic process regulation of cellular metabolic process generation of precursor metabolites and energy mitochondrial electron transport, NADH to ubiquinone regulation of aerobic respiration regulation of mitochondrial electron transport, NADH to ubiquinone positive regulation of mitochondrial electron transport, NADH to ubiquinone metabolic process regulation of metabolic process mitochondrial ATP synthesis coupled electron transport [2Fe-2S] cluster assembly [4Fe-4S] cluster assembly	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle protein-containing complex cytosol iron-sulfur cluster assembly complex mitochondrial protein-containing complex catalytic complex sulfurtransferase complex membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle protein-containing complex cytosol iron-sulfur cluster assembly complex mitochondrial protein-containing complex catalytic complex sulfurtransferase complex transferase complex L-cysteine desulfurase complex mitochondrial [2Fe-2S] assembly complex membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen nucleus
A	Cysteine desulfurase	cysteine desulfurase activity sulfurtransferase activity transferase activity, transferring sulphur-containing groups transferase activity catalytic activity iron-sulfur cluster binding binding metal cluster binding small molecule binding vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding organic cyclic compound binding cysteine desulfurase activity sulfurtransferase activity transferase activity, transferring sulphur-containing groups transferase activity catalytic activity iron-sulfur cluster binding binding metal cluster binding small molecule binding vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding organic cyclic compound binding anion binding heterocyclic compound binding identical protein binding protein binding protein homodimerization activity protein dimerization activity cation binding metal ion binding	cellular component biogenesis cellular component organization metallo-sulfur cluster assembly cellular component assembly iron-sulfur cluster assembly cellular process cellular component organization or biogenesis cellular metabolic process primary metabolic process prosthetic group metabolic process organophosphate metabolic process molybdopterin cofactor metabolic process phosphate-containing compound metabolic process metabolic process cellular component biogenesis cellular component organization metallo-sulfur cluster assembly cellular component assembly iron-sulfur cluster assembly cellular process cellular component organization or biogenesis cellular metabolic process primary metabolic process prosthetic group metabolic process organophosphate metabolic process molybdopterin cofactor metabolic process phosphate-containing compound metabolic process metabolic process protein metabolic process macromolecule metabolic process phosphorus metabolic process [4Fe-4S] cluster assembly iron incorporation into metallo-sulfur cluster metal incorporation into metallo-sulfur cluster macromolecule modification protein modification process Mo-molybdopterin cofactor biosynthetic process Mo-molybdopterin cofactor metabolic process molybdopterin cofactor biosynthetic process biosynthetic process organophosphate biosynthetic process [2Fe-2S] cluster assembly	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle protein-containing complex cytosol iron-sulfur cluster assembly complex mitochondrial protein-containing complex catalytic complex sulfurtransferase complex membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle protein-containing complex cytosol iron-sulfur cluster assembly complex mitochondrial protein-containing complex catalytic complex sulfurtransferase complex transferase complex L-cysteine desulfurase complex mitochondrial [2Fe-2S] assembly complex centrosome microtubule organizing center cytoskeleton intracellular non-membrane-bounded organelle microtubule cytoskeleton non-membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen mitochondrial matrix
C	Acyl carrier protein	phosphopantetheine-dependent carrier activity prosthetic group binding binding acyl carrier activity molecular carrier activity ACP phosphopantetheine attachment site binding acyl binding small molecule binding	glycolipid metabolic process cellular biosynthetic process lipid A biosynthetic process carbohydrate derivative metabolic process lipid biosynthetic process phospholipid metabolic process phosphate-containing compound metabolic process lipooligosaccharide biosynthetic process phosphorus metabolic process carbohydrate derivative biosynthetic process membrane lipid metabolic process lipooligosaccharide metabolic process cellular metabolic process liposaccharide metabolic process glycolipid metabolic process cellular biosynthetic process lipid A biosynthetic process carbohydrate derivative metabolic process lipid biosynthetic process phospholipid metabolic process phosphate-containing compound metabolic process lipooligosaccharide biosynthetic process phosphorus metabolic process carbohydrate derivative biosynthetic process membrane lipid metabolic process lipooligosaccharide metabolic process cellular metabolic process liposaccharide metabolic process primary metabolic process glycolipid biosynthetic process phospholipid biosynthetic process lipid A metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process cellular lipid metabolic process metabolic process cellular process membrane lipid biosynthetic process lipid metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR051522	Iron-sulfur cluster assembly LYR protein	Family
B	IPR008011	Complex 1 LYR protein domain	Domain
B	IPR045297	LYRM4, LYR domain	Domain
D	IPR011339	Iron-sulfur cluster assembly scaffold protein IscU	Family
D	IPR002871	NIF system FeS cluster assembly, NifU, N-terminal	Domain
A	IPR020578	Aminotransferase class-V, pyridoxal-phosphate binding site	Binding Site
A	IPR000192	Aminotransferase class V domain	Domain
A	IPR010240	Cysteine desulfurase IscS	Family
A	IPR016454	Cysteine desulfurase	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
C	IPR006162	Phosphopantetheine attachment site	PTM
C	IPR009081	Phosphopantetheine binding ACP domain	Domain
C	IPR036736	ACP-like superfamily	Homologous Superfamily
C	IPR003231	Acyl carrier protein	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: Q9HD34	combined oxidative phosphorylation deficiency 19 breast cancer Friedreich ataxia Mitochondrial Diseases pancreatic intraductal papillary-mucinous neoplasm squamous cell carcinoma combined oxidative phosphorylation deficiency lung cancer osteosarcoma schizophrenia medulloblastoma ovarian cancer skin basal cell carcinoma
D	Pharos: Q9H1K1	hereditary myopathy with lactic acidosis due to ISCU deficiency arthrogryposis Friedreich ataxia Mitochondrial Diseases astrocytic tumor ovarian cancer large cell medulloblastoma rhabdomyolysis
A	Pharos: Q9Y697	Friedreich ataxia Mitochondrial Diseases skin carcinoma large cell medulloblastoma osteosarcoma medulloblastoma ovarian cancer

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.