1DE8 | PD0093 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE-1 (APE1) BOUND TO ABASIC DNA

Authors :   C. D. Mol, T. Izumi, S. Mitra, J. A. Tainer

Date :   13 Nov 99 (Deposition) - 02 Feb 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.95

Chains :   Asym. Unit : A,B,U,V,X,Y
Biol. Unit 1: A,U,V  (1x)
Biol. Unit 2: B,X,Y  (1x)

Keywords :   Enzyme:Dna Complex, Dna Repair, Abasic Site, Lyase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. D. Mol, T. Izumi, S. Mitra, J. A. Tainer
Dna-Bound Structures And Mutants Reveal Abasic Dna Binding By Ape1 And Dna Repair Coordination [Corrected
Nature V. 403 451 2000
PubMed-ID: 10667800 | Reference-DOI: 10.1038/35000249
(for further references see the PDB file header)

*Molecule 1 - DNA (5'-D(GPCPTPAPCP(3DR)PGPAPTPCPG)- 3')**
	Chains	:	X, U
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - DNA (5'-D(CPGPAPTPCPGPGPTPAPGPC)-3')**
	Chains	:	Y, V
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - MAJOR APURINIC/APYRIMIDINIC ENDONUCLEASE
	Chains	:	B, A
	EC Number	:	4.2.99.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	APE1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	APE1

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	U	V	X	Y
Biological Unit 1 (1x)	:	A		U	V
Biological Unit 2 (1x)	:		B			X	Y

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	3DR	2	Mod. Nucleotide	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	3DR	1	Mod. Nucleotide	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	3DR	1	Mod. Nucleotide	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE

(no "Site" information available for 1DE8)

(no "SS Bond" information available for 1DE8)

Asymmetric Unit

No.	Residues
1	Val B:247	-	Pro B:248
2	Val A:247	-	Pro A:248

Asymmetric Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_013455	Q	51	H	APEX1_HUMAN	Polymorphism	1048945	A/B	H	51	H
2	UniProt	VAR_014823	I	64	V	APEX1_HUMAN	Polymorphism	2307486	A/B	I	64	V
3	UniProt	VAR_019790	D	148	E	APEX1_HUMAN	Polymorphism	1130409	A/B	D	148	E

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_013455	Q	51	H	APEX1_HUMAN	Polymorphism	1048945	A	H	51	H
2	UniProt	VAR_014823	I	64	V	APEX1_HUMAN	Polymorphism	2307486	A	I	64	V
3	UniProt	VAR_019790	D	148	E	APEX1_HUMAN	Polymorphism	1130409	A	D	148	E

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_013455	Q	51	H	APEX1_HUMAN	Polymorphism	1048945	B	H	51	H
2	UniProt	VAR_014823	I	64	V	APEX1_HUMAN	Polymorphism	2307486	B	I	64	V
3	UniProt	VAR_019790	D	148	E	APEX1_HUMAN	Polymorphism	1130409	B	D	148	E

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (4, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AP_NUCLEASE_F1_4	PS51435	AP endonucleases family 1 profile.	APEX1_HUMAN	62-318	2	A:62-318 B:62-318
2	AP_NUCLEASE_F1_1	PS00726	AP endonucleases family 1 signature 1.	APEX1_HUMAN	89-98	2	A:89-98 B:89-98
3	AP_NUCLEASE_F1_2	PS00727	AP endonucleases family 1 signature 2.	APEX1_HUMAN	251-267	2	A:251-267 B:251-267
4	AP_NUCLEASE_F1_3	PS00728	AP endonucleases family 1 signature 3.	APEX1_HUMAN	277-288	2	A:277-288 B:277-288

Biological Unit 1 (4, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AP_NUCLEASE_F1_4	PS51435	AP endonucleases family 1 profile.	APEX1_HUMAN	62-318	1	A:62-318 -
2	AP_NUCLEASE_F1_1	PS00726	AP endonucleases family 1 signature 1.	APEX1_HUMAN	89-98	1	A:89-98 -
3	AP_NUCLEASE_F1_2	PS00727	AP endonucleases family 1 signature 2.	APEX1_HUMAN	251-267	1	A:251-267 -
4	AP_NUCLEASE_F1_3	PS00728	AP endonucleases family 1 signature 3.	APEX1_HUMAN	277-288	1	A:277-288 -

Biological Unit 2 (4, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AP_NUCLEASE_F1_4	PS51435	AP endonucleases family 1 profile.	APEX1_HUMAN	62-318	1	- B:62-318
2	AP_NUCLEASE_F1_1	PS00726	AP endonucleases family 1 signature 1.	APEX1_HUMAN	89-98	1	- B:89-98
3	AP_NUCLEASE_F1_2	PS00727	AP endonucleases family 1 signature 2.	APEX1_HUMAN	251-267	1	- B:251-267
4	AP_NUCLEASE_F1_3	PS00728	AP endonucleases family 1 signature 3.	APEX1_HUMAN	277-288	1	- B:277-288

Asymmetric Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1c	ENST00000398030	1c	ENSE00001531237	chr14:20923400-20923497	98	APEX1_HUMAN	-	0	0	-	-
1.2	ENST00000398030	2	ENSE00000889014	chr14:20923737-20923862	126	APEX1_HUMAN	1-20	20	0	-	-
1.3a	ENST00000398030	3a	ENSE00000652723	chr14:20924073-20924260	188	APEX1_HUMAN	20-82	63	2	A:43-82 B:43-82	40 40
1.4	ENST00000398030	4	ENSE00000652726	chr14:20924827-20925019	193	APEX1_HUMAN	83-147	65	2	A:83-147 B:83-147	65 65
1.5a	ENST00000398030	5a	ENSE00001842242	chr14:20925150-20925895	746	APEX1_HUMAN	147-318	172	2	A:147-318 B:147-318	172 172

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:276
 aligned with APEX1_HUMAN | P27695 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:276
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312      
          APEX1_HUMAN    43 ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL 318
               SCOP domains d1de8a_ A: DNA repair endonuclease Hap1                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1de8A00 A:43-318  [code=3.60.10.10, no name defined]                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....................eeeeee..hhhhhhhhhhhhhhhhhh..eeeee.........hhhhh.hhhhheeeee..........eeeee.....eeee...hhhhhh...eeeee....eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.....hhhh...hhhhh.....hhhhhhhhhhhhhhh..eehhhhhh..............hhhhhh.....eeeee.hhhh..eeeeee...........eeeee.. Sec.struct. author
                 SAPs(SNPs) --------H------------V-----------------------------------------------------------------------------------E-------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------AP_NUCLEASE_F1_4  PDB: A:62-318 UniProt: 62-318                                                                                                                                                                                                                   PROSITE (1)
                PROSITE (2) ----------------------------------------------AP_NUCLEAS--------------------------------------------------------------------------------------------------------------------------------------------------------AP_NUCLEASE_F1_2 ---------AP_NUCLEASE_------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.3a  PDB: A:43-82 UniProt: 20-82  Exon 1.4  PDB: A:83-147 UniProt: 83-147                          --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------Exon 1.5a  PDB: A:147-318 UniProt: 147-318                                                                                                                                   Transcript 1 (2)
                 1de8 A  43 ALYEDPPDHKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL 318
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312

Chain B from PDB  Type:PROTEIN  Length:276
 aligned with APEX1_HUMAN | P27695 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:276
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312      
          APEX1_HUMAN    43 ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL 318
               SCOP domains d1de8b_ B: DNA repair endonuclease Hap1                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1de8B00 B:43-318  [code=3.60.10.10, no name defined]                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
     Sec.struct. author (1) .............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhheeeee..........-hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.....hhhh.............hhhhhhhhhhhhhhh..eehhhhhh.........................eeeee.hhhhh.eeeeee...........eeeee.. Sec.struct. author (1)
     Sec.struct. author (2) -------------------eeeeeee----------------------eeeee-----------------------------------eeeee-----eeee------------eeeee----eeeeee--------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) --------H------------V-----------------------------------------------------------------------------------E-------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------AP_NUCLEASE_F1_4  PDB: B:62-318 UniProt: 62-318                                                                                                                                                                                                                   PROSITE (1)
                PROSITE (2) ----------------------------------------------AP_NUCLEAS--------------------------------------------------------------------------------------------------------------------------------------------------------AP_NUCLEASE_F1_2 ---------AP_NUCLEASE_------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.3a  PDB: B:43-82 UniProt: 20-82  Exon 1.4  PDB: B:83-147 UniProt: 83-147                          --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------Exon 1.5a  PDB: B:147-318 UniProt: 147-318                                                                                                                                   Transcript 1 (2)
                 1de8 B  43 ALYEDPPDHKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL 318
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312

Chain U from PDB  Type:DNA  Length:11
                                           
                 1de8 U  31 GCTACxGATCG  41
                                 |  40 
                                36-3DR

Chain V from PDB  Type:DNA  Length:11
                                           
                 1de8 V  42 CGATCGGTAGC  52
                                    51

Chain X from PDB  Type:DNA  Length:11
                                           
                 1de8 X   1 GCTACxGATCG  11
                                 |  10 
                                 6-3DR

Chain Y from PDB  Type:DNA  Length:11
                                           
                 1de8 Y  12 CGATCGGTAGC  22
                                    21

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: DNase I-like (70)

Superfamily: DNase I-like (70)

Family: DNase I-like (31)

Protein domain: DNA repair endonuclease Hap1 (7)

Human (Homo sapiens) [TaxId: 9606] (7)

1a	d1de8a_	A:
1b	d1de8b_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 4-Layer Sandwich (459)

Topology: Deoxyribonuclease I; Chain A (35)

Homologous Superfamily: [code=3.60.10.10, no name defined] (35)

[unclassified] (5)

1a	1de8A00	A:43-318
1b	1de8B00	B:43-318

(no "Pfam Domain" information available for 1DE8)

Asymmetric Unit(hide GO term definitions)

Chain A,B (APEX1_HUMAN | P27695)

molecular function
	GO:0008408	3'-5' exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003906	DNA-(apurinic or apyrimidinic site) lyase activity	Catalysis of the cleavage of the C-O-P bond 3' to the apurinic or apyrimidinic site in DNA by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.
	GO:0051059	NF-kappaB binding	Interacting selectively and non-covalently with NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004523	RNA-DNA hybrid ribonuclease activity	Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
	GO:0031490	chromatin DNA binding	Interacting selectively and non-covalently with DNA that is assembled into chromatin.
	GO:0003684	damaged DNA binding	Interacting selectively and non-covalently with damaged DNA.
	GO:0008311	double-stranded DNA 3'-5' exodeoxyribonuclease activity	Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a double-stranded DNA molecule.
	GO:0008309	double-stranded DNA exodeoxyribonuclease activity	Catalysis of the sequential cleavage of mononucleotides from a free 5' or 3' terminus of a double-stranded DNA molecule.
	GO:0003691	double-stranded telomeric DNA binding	Interacting selectively and non-covalently with double-stranded telomere-associated DNA.
	GO:0004520	endodeoxyribonuclease activity	Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0004521	endoribonuclease activity	Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
	GO:0004527	exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0004528	phosphodiesterase I activity	Catalysis of the sequential hydrolytic removal of 5'-nucleotides from the 3'-hydroxy termini of 3'-hydroxy-terminated oligonucleotides.
	GO:0008081	phosphoric diester hydrolase activity	Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0032403	protein complex binding	Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0016890	site-specific endodeoxyribonuclease activity, specific for altered base	Catalysis of the hydrolysis of ester linkages at specific sites within a deoxyribonucleic acid molecule by creating internal breaks.
	GO:0003713	transcription coactivator activity	Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
	GO:0003714	transcription corepressor activity	Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
	GO:0004844	uracil DNA N-glycosylase activity	Catalysis of the cleavage of the N-C1' glycosidic bond between the damaged DNA base and the deoxyribose sugar, releasing a free base and leaving an apyrimidinic (AP) site. Enzymes with this activity recognize and remove uracil bases in DNA that result from the deamination of cytosine or the misincorporation of dUTP opposite an adenine.
biological process
	GO:0080111	DNA demethylation	The removal of a methyl group from one or more nucleotides within an DNA molecule.
	GO:0006310	DNA recombination	Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
	GO:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	GO:0007568	aging	A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
	GO:0006284	base-excision repair	In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
	GO:0006286	base-excision repair, base-free sugar-phosphate removal	Excision of the sugar phosphate residue at an AP site, i.e. a deoxyribose sugar with a missing base, by a phosphodiesterase enzyme.
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0071320	cellular response to cAMP	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
	GO:0070301	cellular response to hydrogen peroxide	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydrogen peroxide (H2O2) stimulus.
	GO:0071417	cellular response to organonitrogen compound	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond.
	GO:0071375	cellular response to peptide hormone stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals.
	GO:1903507	negative regulation of nucleic acid-templated transcription	Any process that stops, prevents or reduces the frequency, rate or extent of nucleic acid-templated transcription.
	GO:0014912	negative regulation of smooth muscle cell migration	Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle cell migration.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0045739	positive regulation of DNA repair	Any process that activates or increases the frequency, rate or extent of DNA repair.
	GO:1900087	positive regulation of G1/S transition of mitotic cell cycle	Any cell cycle regulatory process that promotes the commitment of a cell from G1 to S phase of the mitotic cell cycle.
	GO:0043488	regulation of mRNA stability	Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0042493	response to drug	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0010243	response to organonitrogen compound	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond.
	GO:0000723	telomere maintenance	Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins, the length of telomeric DNA and the replication and repair of the DNA. These processes includes those that shorten, lengthen, replicate and repair the telomeric DNA sequences.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005813	centrosome	A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0000784	nuclear chromosome, telomeric region	The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
	GO:0016607	nuclear speck	A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.
	GO:0005840	ribosome	An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
	GO:0005667	transcription factor complex	A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

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1bix	STRUCTURE OF UNCOMPLEXED HUMAN APE1.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 6)

PROSITE Motifs (4, 8)

Exons (3, 6)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (65, 65)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File