6KCS | pdb_00006kcs

Crystal structure of HIRAN domain of HLTF in complex with duplex DNA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD 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	Nucleic acid-binding proteins	8094211	3000135	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	Ion_trans	e6kcsA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Ion_trans	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF08797	HIRAN domain (HIRAN)	HIRAN domain	The HIRAN domain (HIP116, Rad5p N-terminal) is found in the N-terminal regions of the SWI2/SNF2 proteins typified by HIP116 and Rad5p. The HIRAN domain is found as a standalone protein in several bacteria and prophages, or fused to other catalytic do ...	The HIRAN domain (HIP116, Rad5p N-terminal) is found in the N-terminal regions of the SWI2/SNF2 proteins typified by HIP116 and Rad5p. The HIRAN domain is found as a standalone protein in several bacteria and prophages, or fused to other catalytic domains, such as a nuclease of the restriction endonuclease fold and TDP1-like DNA phosphoesterases, in the eukaryotes [1]. It has been predicted that this domain functions as a DNA-binding domain that probably recognises features associated with damaged DNA or stalled replication forks [1]	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	DNA (5'-D(APCPTPGPTPAPCPGPTPAPCPAPGPT)-3')	-	-	-
A	Helicase-like transcription factor	nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid helicase activity macromolecular conformation isomerase activity catalytic activity ATP-dependent activity histone H3K9me2/3 reader activity histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity G-quadruplex unwinding activity nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid helicase activity macromolecular conformation isomerase activity catalytic activity ATP-dependent activity histone H3K9me2/3 reader activity histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity G-quadruplex unwinding activity ATP-dependent activity, acting on DNA catalytic activity, acting on DNA RNA binding binding nucleic acid binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity ubiquitin-protein transferase activity ATP-dependent chromatin remodeler activity 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 DNA translocase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding cation binding transition metal ion binding zinc ion binding metal ion binding histone H3K23 ubiquitin ligase activity histone ubiquitin ligase activity histone H3 ubiquitin ligase activity histone modifying activity DNA binding single-stranded DNA binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process multicellular organismal process regulation of multicellular organismal development regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process multicellular organismal process regulation of multicellular organismal development regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation cell development regulation of neurogenesis regulation of cell differentiation nervous system development regulation of cell development regulation of nervous system development multicellular organism development neurogenesis cell differentiation anatomical structure development regulation of multicellular organismal process system development localization protein localization to chromatin protein localization to chromosome protein localization to organelle macromolecule localization intracellular protein localization DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity primary metabolic process DNA metabolic process nucleic acid metabolic process replication fork reversal nucleobase-containing compound metabolic process DNA replication metabolic process macromolecule metabolic process replication fork processing protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal protein polyubiquitination protein K63-linked ubiquitination cellular component organization chromatin organization cellular component organization or biogenesis chromosomal DNA methylation maintenance following DNA replication DNA repair mRNA transcription by RNA polymerase II RNA metabolic process nucleobase-containing compound biosynthetic process gene expression mRNA transcription mRNA metabolic process macromolecule biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix intracellular membraneless organelle nucleolus membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix intracellular membraneless organelle nucleolus membraneless organelle membrane RNA polymerase II transcription regulator complex protein-containing complex nuclear protein-containing complex transcription regulator complex cell periphery plasma membrane cytoplasm nucleoplasm chromatin chromosome nuclear replication fork nuclear chromosome replication fork

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR049730	SNF2/RAD5-like, C-terminal helicase domain	Domain
A	IPR014905	HIRAN domain	Domain
A	IPR038718	SNF2-like, N-terminal domain superfamily	Homologous Superfamily
A	IPR000330	SNF2, N-terminal domain	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
A	IPR050628	SNF2_RAD54_helicase_TF	Unknown
A	IPR001650	Helicase, C-terminal domain-like	Domain
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A	IPR001841	Zinc finger, RING-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q14527	breast cancer kidney neoplasm lung carcinoma non-small cell lung carcinoma psoriasis IgA glomerulonephritis lung adenocarcinoma Malignant neoplasm of kidney ovarian cancer kidney cancer lung cancer medulloblastoma progressive supranuclear palsy

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.