5YAA | pdb_00005yaa

Crystal structure of Marf1 NYN domain from Mus musculus

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	IMS_HHH_1	e5yaaA1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: ADP-ribosylation	T: ADP-ribosylation	F: IMS_HHH_1	ECOD (v294.1)
D	Chlorophyllase2	e5yaaD1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
C	Chlorophyllase2	e5yaaC1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
B	Chlorophyllase2	e5yaaB1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01936	NYN domain (NYN)	NYN domain	These domains are found in the eukaryotic proteins typified by the Nedd4-binding protein 1 and the bacterial YacP-like proteins (Nedd4-BP1, YacP nucleases; NYN domains). The NYN domain shares a common protein fold with two other previously characteri ...	These domains are found in the eukaryotic proteins typified by the Nedd4-binding protein 1 and the bacterial YacP-like proteins (Nedd4-BP1, YacP nucleases; NYN domains). The NYN domain shares a common protein fold with two other previously characterized groups of nucleases, namely the PIN (PilT N-terminal) and FLAP/5' --> 3' exonuclease superfamilies. These proteins share a common set of 4 acidic conserved residues that are predicted to constitute their active site. Based on the conservation of the acidic residues and structural elements Aravind and colleagues suggest that PIN and NYN domains are likely to bind only a single metal ion, unlike the FLAP/5' --> 3' exonuclease superfamily, which binds two metal ions. Based on conserved gene neighborhoods Aravind and colleagues infer that the bacterial members are likely to be components of the processome/degradsome that process tRNAs or ribosomal RNAs.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Meiosis regulator and mRNA stability factor 1	nuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity RNA binding binding nucleic acid binding protein-containing complex binding CCR4-NOT complex binding	developmental process sexual reproduction cellular developmental process reproductive process oogenesis multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction female gamete generation gamete generation cell differentiation anatomical structure development germ cell development developmental process sexual reproduction cellular developmental process reproductive process oogenesis multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction female gamete generation gamete generation cell differentiation anatomical structure development germ cell development cellular process regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process organelle fission meiotic cell cycle meiotic cell cycle process cellular component organization nuclear division organelle organization female meiotic nuclear division meiotic nuclear division cellular component organization or biogenesis cell cycle cell cycle process cellular response to stimulus double-strand break repair response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress DNA repair	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system peroxisome microbody

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR021139	NYN domain	Domain
A, B, C, D	IPR000504	RNA recognition motif domain	Domain
A, B, C, D	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A, B, C, D	IPR025605	OST-HTH/LOTUS domain	Domain
A, B, C, D	IPR034189	MARF1, RNA recognition motif 1	Domain
A, B, C, D	IPR034191	MARF1, RNA recognition motif 2	Domain
A, B, C, D	IPR045602	MARF1, first and second LOTUS domain	Domain
A, B, C, D	IPR024768	Meiosis regulator and mRNA stability factor 1	Family
A, B, C, D	IPR041966	LOTUS-like domain	Homologous Superfamily
A, B, C, D	IPR035979	RNA-binding domain superfamily	Homologous Superfamily

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.