MultifacetedProtDB - Bologna Biocomputing Group

EC number	EC number description
3.2.2.-	Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds;
4.2.99.18	Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases; DNA-(apurinic or apyrimidinic site) lyase

Structure

PDB	Resolution (Å)	PDB name
1TDH	2.1	Crystal structure of human endonuclease VIII-like 1 (NEIL1)
4NRV	2.601	Crystal Structure of non-edited human NEIL1
5ITQ	1.48	Crystal Structure of Human NEIL1, Free Protein
5ITR	2.46	Crystal Structure of Human NEIL1(P2G) bound to duplex DNA containing THF
5ITT	2.53	Crystal Structure of Human NEIL1 bound to duplex DNA containing THF
5ITU	2.41	Crystal Structure of Human NEIL1(242K) bound to duplex DNA containing THF
5ITX	2.65	Crystal Structure of Human NEIL1(P2G R242K) bound to duplex DNA containing Thymine Glycol
5ITY	2.48	Crystal Structure of Human NEIL1(P2G) bound to duplex DNA containing Thymine Glycol
6LWA	2.76	Crystal structure of human NEIL1(P2G, E3Q, K242) bound to duplex DNA containing 5-hydroxyuracil (5-OHU)
6LWB	2.55	Crystal structure of human NEIL1(P2G, E3Q, R242) bound to duplex DNA containing 5-hydroxyuracil (5-OHU)
6LWC	2.91	Crystal structure of human NEIL1(P2G, E3Q, K242) bound to duplex DNA containing spiroiminodihydantoin (Sp)
6LWD	2.41	Crystal structure of human NEIL1(P2G, E3Q, R242) bound to duplex DNA containing spiroiminodihydantoin (Sp)
6LWF	2.79	Crystal structure of human NEIL1(P2G, E3Q, K242) bound to duplex DNA containing guanidinohydantoin (Gh)
6LWG	2.53	Crystal structure of human NEIL1(P2G, E3Q, R242) bound to duplex DNA containing guanidinohydantoin (Gh)
6LWH	2.78	Crystal structure of human NEIL1(P2G, E3Q, K242) bound to duplex DNA containing dihydrothymine (DHT)
6LWI	2.72	Crystal structure of human NEIL1(P2G, E3Q, R242) bound to duplex DNA containing dihydrothymine (DHT)
6LWJ	2.83	Crystal structure of human NEIL1(P2G, E3Q, K242) bound to duplex DNA containing dihydrouracil (DHU)
6LWK	2.88	Crystal structure of human NEIL1(P2G, E3Q, R242) bound to duplex DNA containing dihydrouracil (DHU)
6LWL	2.55	Crystal structure of human NEIL1(R242) bound to duplex DNA containing 2'-fluoro-2'-deoxy-5,6-dihydrouridine
6LWM	2.67	Crystal structure of human NEIL1(K242) bound to duplex DNA containing 2'-fluoro-2'-deoxy-5,6-dihydrouridine
6LWN	2.74	Crystal structure of human NEIL1(R242, G249P) bound to duplex DNA containing 2'-fluoro-2'-deoxy-5,6-dihydrouridine
6LWO	2.51	Crystal structure of human NEIL1(R242, Y244H) bound to duplex DNA containing 2'-fluoro-2'-deoxy-5,6-dihydrouridine
6LWP	2.64	Crystal structure of human NEIL1(R242, Y244R) bound to duplex DNA containing 2'-fluoro-2'-deoxy-5,6-dihydrouridine
6LWQ	2.89	Crystal structure of human NEIL1(R242) bound to duplex DNA containing a C:T mismatch
6LWR	2.9	Crystal structure of human NEIL1(K242) bound to duplex DNA containing a cleaved C:T mismatch

GO term

GO ontology	GO term	GO description
Biological Process	GO:0006284	base-excision repair
Biological Process	GO:0006287	base-excision repair, gap-filling
Biological Process	GO:0045008	depyrimidination
Biological Process	GO:0032074	negative regulation of nuclease activity
Biological Process	GO:0006979	response to oxidative stress
Molecular Function	GO:0019104	DNA N-glycosylase activity
Molecular Function	GO:0003906	DNA-(apurinic or apyrimidinic site) endonuclease activity
Molecular Function	GO:0140078	class I DNA-(apurinic or apyrimidinic site) endonuclease activity
Molecular Function	GO:0003684	damaged DNA binding
Molecular Function	GO:0016798	hydrolase activity, acting on glycosyl bonds
Molecular Function	GO:0008270	zinc ion binding
Cellular Component	GO:0005694	chromosome
Cellular Component	GO:0005737	cytoplasm
Cellular Component	GO:0005829	cytosol
Cellular Component	GO:0005815	microtubule organizing center
Cellular Component	GO:0005654	nucleoplasm
Cellular Component	GO:0005634	nucleus

InterPro / Pfam

InterPro	InterPro name
IPR010979	Ribosomal protein S13-like, H2TH
IPR012319	Formamidopyrimidine-DNA glycosylase, catalytic domain
IPR015371	Endonuclease VIII-like 1, DNA binding
IPR015886	DNA glycosylase/AP lyase, H2TH DNA-binding
IPR035937	MutM-like, N-terminal

Pfam	Pfam name
PF01149	Formamidopyrimidine-DNA glycosylase N-terminal domain
PF09292	Endonuclease VIII-like 1, DNA bind

Reactome

Reactome	Reactome Name	Node type	Reactome Root	Reactome Root Name
R-HSA-110328	Recognition and association of DNA glycosylase with site containing an affected pyrimidine	Leaf	R-HSA-73894	DNA Repair
R-HSA-110329	Cleavage of the damaged pyrimidine	Leaf	R-HSA-73894	DNA Repair
R-HSA-5649702	APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway	Leaf	R-HSA-73894	DNA Repair
R-HSA-9616334	Defective Base Excision Repair Associated with NEIL1	Leaf	R-HSA-1643685	Disease

Subcellular location

Location	ECO term	Pubmed
Chromosome	ECO:0000269	PubMed:17556049
Cytoplasm, cytoskeleton, microtubule organizing center, centrosome	ECO:0000269	PubMed:17556049
Nucleus	ECO:0000269	PubMed:17556049

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Tissue	Cell type	Expression level	Reliability
adrenal gland	glandular cells	Medium	Approved
appendix	glandular cells	Medium	Approved
appendix	lymphoid tissue	High	Approved
bone marrow	hematopoietic cells	High	Approved
breast	glandular cells	Medium	Approved
breast	myoepithelial cells	Medium	Approved
bronchus	respiratory epithelial cells	Medium	Approved
caudate	glial cells	Medium	Approved
caudate	neuronal cells	Low	Approved
cerebellum	Purkinje cells	High	Approved
cerebellum	cells in granular layer	Medium	Approved
cerebellum	cells in molecular layer	Medium	Approved
cerebral cortex	endothelial cells	Low	Approved
cerebral cortex	glial cells	Medium	Approved
cerebral cortex	neuronal cells	Medium	Approved
cerebral cortex	neuropil	Low	Approved
cervix	glandular cells	Medium	Approved
cervix	squamous epithelial cells	Medium	Approved
colon	endothelial cells	Low	Approved
colon	glandular cells	Medium	Approved
duodenum	glandular cells	Medium	Approved
endometrium 1	glandular cells	Medium	Approved
endometrium 2	cells in endometrial stroma	Low	Approved
endometrium 2	glandular cells	Medium	Approved
epididymis	glandular cells	Medium	Approved
esophagus	squamous epithelial cells	Medium	Approved
fallopian tube	glandular cells	Medium	Approved
gallbladder	glandular cells	Medium	Approved
heart muscle	cardiomyocytes	Medium	Approved
hippocampus	glial cells	Low	Approved
hippocampus	neuronal cells	Medium	Approved
kidney	cells in glomeruli	Medium	Approved
kidney	cells in tubules	High	Approved
liver	cholangiocytes	Medium	Approved
liver	hepatocytes	High	Approved
lung	alveolar cells	Medium	Approved
lung	macrophages	Medium	Approved
lymph node	germinal center cells	High	Approved
lymph node	non-germinal center cells	Low	Approved
nasopharynx	respiratory epithelial cells	Medium	Approved
oral mucosa	squamous epithelial cells	Medium	Approved
pancreas	exocrine glandular cells	Medium	Approved
parathyroid gland	glandular cells	Medium	Approved
placenta	decidual cells	Low	Approved
prostate	glandular cells	Low	Approved
rectum	glandular cells	Medium	Approved
salivary gland	glandular cells	Medium	Approved
seminal vesicle	glandular cells	Medium	Approved
skeletal muscle	myocytes	Medium	Approved
skin 1	Langerhans	Medium	Approved
skin 1	fibroblasts	Low	Approved
skin 1	keratinocytes	Medium	Approved
skin 1	melanocytes	Medium	Approved
skin 2	epidermal cells	Medium	Approved
small intestine	glandular cells	Medium	Approved
smooth muscle	smooth muscle cells	Low	Approved
soft tissue 1	chondrocytes	Low	Approved
soft tissue 1	fibroblasts	Medium	Approved
spleen	cells in red pulp	Low	Approved
spleen	cells in white pulp	Medium	Approved
stomach 1	glandular cells	Medium	Approved
testis	Leydig cells	Medium	Approved
testis	cells in seminiferous ducts	Medium	Approved
thyroid gland	glandular cells	Medium	Approved
tonsil	germinal center cells	High	Approved
tonsil	non-germinal center cells	Medium	Approved
tonsil	squamous epithelial cells	Medium	Approved
urinary bladder	urothelial cells	Medium	Approved
vagina	squamous epithelial cells	Medium	Approved

Summary of Q96FI4

Gene: NEIL1
Protein: Endonuclease 8-like 1

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Summary of Q96FI4

Gene: NEIL1 Protein: Endonuclease 8-like 1

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Gene: NEIL1
Protein: Endonuclease 8-like 1