4R8A | pdb_00004r8a

Crystal structure of paFAN1 - 5' flap DNA complex

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)
E [auth F]	TibC_1st	e4r8aF1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: TibC_1st	ECOD (v294.1)
A	FAN1_HTH	e4r8aA1	A: a/b three-layered sandwiches	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: FAN1_HTH	ECOD (v294.1)
A	VRR_NUC	e4r8aA2	A: a/b three-layered sandwiches	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: VRR_NUC	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, E [auth F]	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
A, E [auth F]	PF18081	Fanconi anemia-associated nuclease SAP domain (FANC_SAP)	Fanconi anemia-associated nuclease SAP domain	This domain is found in Fanconi-anemia-associated nuclease 1 (FAN1) present in Pseudomonas aeruginosa. FAN1 is a nuclease associated with Fanconi anemia (FA), an autosomal recessive genetic disorder caused by defects in FA genes responsible for proce ...	This domain is found in Fanconi-anemia-associated nuclease 1 (FAN1) present in Pseudomonas aeruginosa. FAN1 is a nuclease associated with Fanconi anemia (FA), an autosomal recessive genetic disorder caused by defects in FA genes responsible for processing DNA inter-strand cross-links (ICLs). The domain, known as the SAP domain, helps to augment the overall protein DNA interaction by interacting with the 3' and 5' ends of the template strand. Support of the pre-nick segment binding is crucial as multiple mutations in this domain resulted in hypersensitivity to a cross-linking agent in the SAP domain of Caenorhabditis elegans' FAN1. The helix-hairpin-helix of the SAP recognize three consecutive phosphate groups (C19, A20 and A21) at the 3' end of the template via the basic residues K116, K135 and K117 [1].	Domain
A, E [auth F]	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, H [auth I]	DNA (5'-D(PGPAPAPTPGPTPGPTPGPTPCPTPCPAPAPTPCPCPCPAP*A)-3')	-	-	-
C, G [auth H]	DNA (5'-D(PGPTPTPGPGPGPAPTPTPG)-3')	-	-	-
B, F [auth G]	DNA (5'-D(PAPCPCPAPGPAPCPAPCPAPCPAPTPTP*C)-3')	-	-	-
A, E [auth F]	Uncharacterized protein	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding manganese ion binding transition metal ion binding hydrolase activity, acting on ester bonds nuclease activity 5'-3' exonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity exonuclease activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding manganese ion binding transition metal ion binding hydrolase activity, acting on ester bonds nuclease activity 5'-3' exonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity exonuclease activity catalytic activity DNA binding flap-structured DNA binding nucleic acid binding phosphoric ester hydrolase activity phosphodiesterase I activity phosphoric diester hydrolase activity 5'-flap endonuclease activity endonuclease activity DNA nuclease activity DNA endonuclease activity catalytic activity, acting on DNA flap endonuclease activity DNA endonuclease activity, producing 5'-phosphomonoesters	cellular response to stimulus 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 metabolic process cellular process interstrand cross-link repair macromolecule metabolic process DNA repair	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, E [auth F]	IPR040603	Fanconi-associated nuclease 1, SAP domain, bacteria	Domain
A, E [auth F]	IPR049125	Fanconi-associated nuclease 1-like, winged-helix domain	Domain
A, E [auth F]	IPR011856	tRNA endonuclease-like domain superfamily	Homologous Superfamily
A, E [auth F]	IPR033315	Fanconi-associated nuclease 1-like	Family
A, E [auth F]	IPR014883	VRR-NUC domain	Domain

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.