4REB | pdb_00004reb

Structural Insights into 5' Flap DNA Unwinding and Incision by the Human FAN1 Dimer

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E [auth H]	RNA_pol_Rpb1_2	e4rebH3	A: a/b three-layered sandwiches	X: Inserted helical domain in fatty acid synthase subunit beta	H: Voltage-gated ion channels	T: Voltage-gated ion channels	F: RNA_pol_Rpb1_2	ECOD (v294.1)
E [auth H]	MoCoBD_2	e4rebH4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: MoCoBD_2	ECOD (v294.1)
D [auth A]	FAN1_HTH	e4rebA3	A: a/b three-layered sandwiches	X: Inserted helical domain in fatty acid synthase subunit beta	H: Voltage-gated ion channels	T: Voltage-gated ion channels	F: FAN1_HTH	ECOD (v294.1)
D [auth A]	RNA_pol_Rpb1_2	e4rebA6	A: a/b three-layered sandwiches	X: Inserted helical domain in fatty acid synthase subunit beta	H: Voltage-gated ion channels	T: Voltage-gated ion channels	F: RNA_pol_Rpb1_2	ECOD (v294.1)
D [auth A]	MoCoBD_2	e4rebA4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: MoCoBD_2	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth A], E [auth H]	PF08774	VRR-NUC domain (VRR_NUC)	VRR-NUC domain	This is the VRR-NUC domain, a member of the PD-(D/E)XK nuclease superfamily found in FAN1 and type III restriction modification enzymes [1]. FAN1 is a a structure-selective DNA repair nuclease with 5' flap endonuclease activity, involved in the repai ...	This is the VRR-NUC domain, a member of the PD-(D/E)XK nuclease superfamily found in FAN1 and type III restriction modification enzymes [1]. FAN1 is a a structure-selective DNA repair nuclease with 5' flap endonuclease activity, involved in the repair of interstrand DNA crosslinks [2,3]. FAN1 is the only eukaryotic protein with a VRR-NUC domain. This domain is also found in TseVs antibacterial effectors secreted by the type VI secretion system (T6SS). TseVs are evolutionary related to Holliday junction resolvases and enzymes involved in DNA interstrand crosslink repair [4].	Domain
D [auth A], E [auth H]	PF21169	Fanconi-associated nuclease 1, SAP subdomain (Fan1_SAP)	Fanconi-associated nuclease 1, SAP subdomain	This domain is found in Fanconi-associated nuclease 1 from humans (Fan1) and similar proteins from chordates. Fan1 is involved in the processing of DNA interstrand crosslinks (ICLs) and therefore in the maintenance of genomic stability and prevention ...	This domain is found in Fanconi-associated nuclease 1 from humans (Fan1) and similar proteins from chordates. Fan1 is involved in the processing of DNA interstrand crosslinks (ICLs) and therefore in the maintenance of genomic stability and prevention of tissue decline in multiple organs. FAN1 consists of an SAP-containing N-terminal domain, a middle tetratricopeptide repeat domain (TPR) and a C-terminal viral replication and repair nuclease domain (VRR_nuc domain, Pfam:PF08774). This entry represents the SAP subdomain, part of the N-terminal domain. It consists of four alpha-helices [1-3].	Domain
D [auth A], E [auth H]	PF21170	Fanconi-associated nuclease 1, TPR domain (FAN1_TPR)	Fanconi-associated nuclease 1, TPR domain	-	Repeat
D [auth A], E [auth H]	PF21315	FAN1, HTH domain (FAN1_HTH)	FAN1, HTH domain	FAN1 is a DNA structure-specific nuclease involved in the processing of DNA interstrand crosslinks (ICLs). It maintains genomic stability and prevents tissue decline in several organs. This protein possesses preferential endonuclease activity toward ...	FAN1 is a DNA structure-specific nuclease involved in the processing of DNA interstrand crosslinks (ICLs). It maintains genomic stability and prevents tissue decline in several organs. This protein possesses preferential endonuclease activity toward 5' flap structures [1-5]. FAN1 is present in most eukaryotes and some bacterial sequences. It consists of four characterised domains: UBZ, SAP, TPR and VRR nuclease (Pfam:PF08774). However, monocellular eukaryote and bacterial homologues lack the UBZ domain [1]. The N-terminal helical domain of FAN1 can be subdivided in a winged-helix (WH) DNA-binding domain, represented in this entry, and a SAP domain (bacterial Pfam:PF18081 and eukaryotic Pfam:PF21169) [1-5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth A], E [auth H]	Fanconi-associated nuclease 1	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding flap-structured DNA binding nucleic acid binding ubiquitin-modified protein reader activity protein-macromolecule adaptor activity ubiquitin-like protein reader activity molecular adaptor activity 5'-flap endonuclease activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding flap-structured DNA binding nucleic acid binding ubiquitin-modified protein reader activity protein-macromolecule adaptor activity ubiquitin-like protein reader activity molecular adaptor activity 5'-flap endonuclease activity endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity DNA nuclease activity DNA endonuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity flap endonuclease activity DNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity 5'-3' exonuclease activity exonuclease activity transition metal ion binding zinc ion binding phosphoric ester hydrolase activity phosphodiesterase I activity phosphoric diester hydrolase activity	cellular response to stimulus double-strand break repair response to stimulus DNA recombination 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 recombinational repair metabolic process cellular process cellular response to stimulus double-strand break repair response to stimulus DNA recombination 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 recombinational repair metabolic process cellular process macromolecule metabolic process double-strand break repair via homologous recombination DNA repair nucleotide-excision repair interstrand cross-link repair	membrane-bounded organelle cell projection cellular anatomical structure organelle cilium plasma membrane bounded cell projection intercellular bridge intracellular anatomical structure cytoplasm cytosol nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen membrane-bounded organelle cell projection cellular anatomical structure organelle cilium plasma membrane bounded cell projection intercellular bridge intracellular anatomical structure cytoplasm cytosol nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen
C [auth F]	DNA (5'-D(PGPCPTPCPGPCPCPAPCPG)-3')	-	-	-
B [auth E]	DNA (5'-D(PCPGPTPGPGPCPGPAPGPCPGPCPTPCPGPCPCPAPCPG)-3')	-	-	-
A [auth D]	DNA (5'-D(PGPTPGPGPCPGPAPGP*C)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth A], E [auth H]	IPR049125	Fanconi-associated nuclease 1-like, winged-helix domain	Domain
D [auth A], E [auth H]	IPR033315	Fanconi-associated nuclease 1-like	Family
D [auth A], E [auth H]	IPR014883	VRR-NUC domain	Domain
D [auth A], E [auth H]	IPR049132	Fanconi-associated nuclease 1-like, eukaryotes	Family
D [auth A], E [auth H]	IPR049126	Fanconi-associated nuclease 1-like, TPR domain	Domain
D [auth A], E [auth H]	IPR049138	Fanconi-associated nuclease 1, SAP subdomain, metazoa	Domain
D [auth A], E [auth H]	IPR011856	tRNA endonuclease-like domain superfamily	Homologous Superfamily
D [auth A], E [auth H]	IPR006642	Rad18, zinc finger UBZ4-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D [auth A], E [auth H]	Pharos: Q9Y2M0	karyomegalic interstitial nephritis Megalocytic interstitial nephritis chromosome 15q13.3 microdeletion syndrome osteosarcoma Lynch syndrome 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.