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(-) Description

Title :  CRYSTAL STRUCTURE OF CATALYTIC DOMAIN OF HUMAN POLY(ADP-RIBOSE) POLYMERASE COMPLEXED WITH A QUINOXALINE-TYPE INHIBITOR
 
Authors :  A. Iwashita, K. Hattori, H. Yamamoto, J. Ishida, Y. Kido, K. Kamijo, K. Murano, H. Miyake, T. Kinoshita, M. Warizaya, M. Ohkubo, N. Matsuoka, S. Mutoh
Date :  20 Aug 04  (Deposition) - 15 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protein-Inhibitor Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Iwashita, K. Hattori, H. Yamamoto, J. Ishida, Y. Kido, K. Kamijo, K. Murano, H. Miyake, T. Kinoshita, M. Warizaya, M. Ohkubo, N. Matsuoka, S. Mutoh
Discovery Of Quinazolinone And Quinoxaline Derivatives As Potent And Selective Poly(Adp-Ribose) Polymerase-1/2 Inhibitors.
Febs Lett. V. 579 1389 2005
PubMed-ID: 15733846  |  Reference-DOI: 10.1016/J.FEBSLET.2005.01.036
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - POLY [ADP-RIBOSE] POLYMERASE-1
    ChainsA, B, C, D
    EC Number2.4.2.30
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX4T-2
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN
    GenePPOL
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPARP-1, ADPRT, NAD+, ADP-RIBOSYLTRANSFERASE-1, POLY[ADP-RIBOSE] SYNTHETASE-1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1CNQ4Ligand/Ion3-(4-CHLOROPHENYL)QUINOXALINE-5-CARBOXAMIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:763 , ASP A:766 , HIS A:862 , GLY A:863 , TYR A:896 , PHE A:897 , SER A:904 , TYR A:907 , GLU A:988BINDING SITE FOR RESIDUE CNQ A 1
2AC2SOFTWAREGLU B:763 , ASP B:766 , HIS B:862 , GLY B:863 , TYR B:889 , TYR B:896 , SER B:904 , TYR B:907 , GLU B:988BINDING SITE FOR RESIDUE CNQ B 2
3AC3SOFTWAREGLU C:763 , ASP C:766 , HIS C:862 , GLY C:863 , TYR C:896 , PHE C:897 , LYS C:903 , SER C:904 , TYR C:907 , GLU C:988BINDING SITE FOR RESIDUE CNQ C 3
4AC4SOFTWAREASP D:766 , HIS D:862 , GLY D:863 , TYR D:889 , TYR D:896 , PHE D:897 , SER D:904 , TYR D:907BINDING SITE FOR RESIDUE CNQ D 4

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WOK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 8)

Asymmetric/Biological Unit (2, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_014715V762APARP1_HUMANPolymorphism1136410A/B/C/DV762A
2UniProtVAR_019173K940RPARP1_HUMANPolymorphism3219145A/B/C/DK940R

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

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PARP_ALPHA_HDPS51060 PARP alpha-helical domain profile.PARP1_HUMAN662-779
 
 
 
  4A:662-779
B:662-779
C:662-779
D:662-779
2PARP_CATALYTICPS51059 PARP catalytic domain profile.PARP1_HUMAN788-1014
 
 
 
  4A:788-1011
B:788-1011
C:788-1011
D:788-1011

(-) Exons   (10, 40)

Asymmetric/Biological Unit (10, 40)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003667941bENSE00001697768chr1:226595774-226595511264PARP1_HUMAN1-40400--
1.2aENST000003667942aENSE00000962007chr1:226590080-226589915166PARP1_HUMAN41-96560--
1.5bENST000003667945bENSE00000962008chr1:226580015-226579900116PARP1_HUMAN96-134390--
1.6ENST000003667946ENSE00000962009chr1:226578325-226578111215PARP1_HUMAN135-206720--
1.7bENST000003667947bENSE00000962010chr1:226576456-226576357100PARP1_HUMAN206-239340--
1.8ENST000003667948ENSE00000962011chr1:226574143-226574027117PARP1_HUMAN240-278390--
1.9ENST000003667949ENSE00000962012chr1:226573381-226573205177PARP1_HUMAN279-337590--
1.10ENST0000036679410ENSE00000962013chr1:226570884-226570737148PARP1_HUMAN338-387500--
1.11ENST0000036679411ENSE00000962014chr1:226568909-226568769141PARP1_HUMAN387-434480--
1.12ENST0000036679412ENSE00000962015chr1:226567865-226567623243PARP1_HUMAN434-515820--
1.13ENST0000036679413ENSE00000962016chr1:226567342-22656727469PARP1_HUMAN515-538240--
1.14ENST0000036679414ENSE00000962017chr1:226566975-226566843133PARP1_HUMAN538-582450--
1.15ENST0000036679415ENSE00000962018chr1:226565004-226564809196PARP1_HUMAN582-647660--
1.16ENST0000036679416ENSE00000962019chr1:226562055-226561927129PARP1_HUMAN648-690434A:662-690
B:662-690
C:662-690
D:662-690
29
29
29
29
1.17cENST0000036679417cENSE00000962020chr1:226558218-22655813584PARP1_HUMAN691-718284A:691-718
B:691-718
C:691-718
D:691-718
28
28
28
28
1.18ENST0000036679418ENSE00000962021chr1:226556022-226555900123PARP1_HUMAN719-759414A:719-759
B:719-759
C:719-759
D:719-759
41
41
41
41
1.19aENST0000036679419aENSE00000962022chr1:226555309-226555181129PARP1_HUMAN760-802434A:760-802
B:760-802
C:760-802
D:760-802
43
43
43
43
1.19cENST0000036679419cENSE00000962023chr1:226553753-22655365599PARP1_HUMAN803-835334A:803-835
B:803-835
C:803-835
D:803-835
33
33
33
33
1.20bENST0000036679420bENSE00000962024chr1:226552855-226552703153PARP1_HUMAN836-886514A:836-886
B:836-886
C:836-886
D:836-886
51
51
51
51
1.21bENST0000036679421bENSE00000962025chr1:226551771-226551644128PARP1_HUMAN887-929434A:887-929
B:887-929
C:887-929
D:887-929
43
43
43
43
1.22ENST0000036679422ENSE00000962026chr1:226550861-22655080062PARP1_HUMAN929-950224A:929-950
B:929-950
C:929-950
D:929-950
22
22
22
22
1.23bENST0000036679423bENSE00000962027chr1:226549784-226549670115PARP1_HUMAN950-988394A:950-988
B:950-988
C:950-988
D:950-988
39
39
39
39
1.24dENST0000036679424dENSE00001442633chr1:226549242-226548392851PARP1_HUMAN988-1014274A:988-1011
B:988-1011
C:988-1011
D:988-1011
24
24
24
24

(-) Sequences/Alignments

Asymmetric/Biological 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:350
 aligned with PARP1_HUMAN | P09874 from UniProtKB/Swiss-Prot  Length:1014

    Alignment length:350
                                   671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011
         PARP1_HUMAN    662 KSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKVEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT 1011
               SCOP domains d1woka1 A:662-796 automated matches                                                                                                    d1woka2 A:797-1011 automated matches                                                                                                                                                                                    SCOP domains
               CATH domains 1wokA01 A:662-797 Poly(ADP-ribose) Polymerase, domain 1                                                                                 1wokA02 A:798-1010  [code=3.90.228.10, no name defined]                                                                                                                                                              - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhheeeee....hhhhhhhhhhhhhh........eeeeeeeeeeee......hhhhh....eeeeeeeehhhhhhhhhhhh........hhhhh.....eee..hhhhhhhhhh......eeeeeeeeee....eee...............eee...eee.hhhh.....ee.....eee...........eeee.hhh.eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------A---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PARP_ALPHA_HD  PDB: A:662-779 UniProt: 662-779                                                                        --------PARP_CATALYTIC  PDB: A:788-1011 UniProt: 788-1014                                                                                                                                                                                PROSITE
           Transcript 1 (1) Exon 1.16  PDB: A:662-690    Exon 1.17c  PDB: A:691-718  Exon 1.18  PDB: A:719-759                Exon 1.19a  PDB: A:760-802 UniProt: 760-802Exon 1.19c  PDB: A:803-835       Exon 1.20b  PDB: A:836-886 UniProt: 836-886        Exon 1.21b  PDB: A:887-929 UniProt: 887-929--------------------Exon 1.23b  PDB: A:950-988             ----------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.22             -------------------------------------Exon 1.24d [INCOMPLETE]  Transcript 1 (2)
                1wok A  662 KSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKVEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT 1011
                                   671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011

Chain B from PDB  Type:PROTEIN  Length:350
 aligned with PARP1_HUMAN | P09874 from UniProtKB/Swiss-Prot  Length:1014

    Alignment length:350
                                   671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011
         PARP1_HUMAN    662 KSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKVEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT 1011
               SCOP domains d1wokb1 B:662-796 automated matches                                                                                                    d1wokb2 B:797-1011 automated matches                                                                                                                                                                                    SCOP domains
               CATH domains 1wokB01 B:662-797 Poly(ADP-ribose) Polymerase, domain 1                                                                                 1wokB02 B:798-1010  [code=3.90.228.10, no name defined]                                                                                                                                                              - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh......ee....hhhhhhhhhhhhhh.......eeeeeeeeee....hhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhh..................eee..hhhhhhh.........eeeeeeeeee...eeee..............eeee...eee.hhhh............eee...........eeee.hhh.eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------A---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PARP_ALPHA_HD  PDB: B:662-779 UniProt: 662-779                                                                        --------PARP_CATALYTIC  PDB: B:788-1011 UniProt: 788-1014                                                                                                                                                                                PROSITE
           Transcript 1 (1) Exon 1.16  PDB: B:662-690    Exon 1.17c  PDB: B:691-718  Exon 1.18  PDB: B:719-759                Exon 1.19a  PDB: B:760-802 UniProt: 760-802Exon 1.19c  PDB: B:803-835       Exon 1.20b  PDB: B:836-886 UniProt: 836-886        Exon 1.21b  PDB: B:887-929 UniProt: 887-929--------------------Exon 1.23b  PDB: B:950-988             ----------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.22             -------------------------------------Exon 1.24d [INCOMPLETE]  Transcript 1 (2)
                1wok B  662 KSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKVEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT 1011
                                   671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011

Chain C from PDB  Type:PROTEIN  Length:350
 aligned with PARP1_HUMAN | P09874 from UniProtKB/Swiss-Prot  Length:1014

    Alignment length:350
                                   671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011
         PARP1_HUMAN    662 KSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKVEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT 1011
               SCOP domains d1wokc1 C:662-796 automated matches                                                                                                    d1wokc2 C:797-1011 automated matches                                                                                                                                                                                    SCOP domains
               CATH domains 1wokC01 C:662-797 Poly(ADP-ribose) Polymerase, domain 1                                                                                 1wokC02 C:798-1010  [code=3.90.228.10, no name defined]                                                                                                                                                              - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh.hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhheeeee....hhhhhhhhhhhhhh.......ee......eeeee..hhhhhhhhhhh..eeeeeee.hhhhhhhhhhhh........hhhhh.....eee..hhhhhhh.........eeeeeeeeee.....ee...............eee...eee.hhhhee....ee....eee...........eeee.hhh.eeeeeeeeee.ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------A---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PARP_ALPHA_HD  PDB: C:662-779 UniProt: 662-779                                                                        --------PARP_CATALYTIC  PDB: C:788-1011 UniProt: 788-1014                                                                                                                                                                                PROSITE
           Transcript 1 (1) Exon 1.16  PDB: C:662-690    Exon 1.17c  PDB: C:691-718  Exon 1.18  PDB: C:719-759                Exon 1.19a  PDB: C:760-802 UniProt: 760-802Exon 1.19c  PDB: C:803-835       Exon 1.20b  PDB: C:836-886 UniProt: 836-886        Exon 1.21b  PDB: C:887-929 UniProt: 887-929--------------------Exon 1.23b  PDB: C:950-988             ----------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.22             -------------------------------------Exon 1.24d [INCOMPLETE]  Transcript 1 (2)
                1wok C  662 KSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKVEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT 1011
                                   671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011

Chain D from PDB  Type:PROTEIN  Length:350
 aligned with PARP1_HUMAN | P09874 from UniProtKB/Swiss-Prot  Length:1014

    Alignment length:350
                                   671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011
         PARP1_HUMAN    662 KSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKVEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT 1011
               SCOP domains d1wokd1 D:662-796 automated matches                                                                                                    d1wokd2 D:797-1011 automated matches                                                                                                                                                                                    SCOP domains
               CATH domains 1wokD01 D:662-797 Poly(ADP-ribose) Polymerase, domain 1                                                                                 1wokD02 D:798-1010  [code=3.90.228.10, no name defined]                                                                                                                                                              - CATH domains
           Pfam domains (1) PARP_reg-1wokD05 D:662-795                                                                                                            -PARP-1wokD01 D:797-1007                                                                                                                                                                                            ---- Pfam domains (1)
           Pfam domains (2) PARP_reg-1wokD06 D:662-795                                                                                                            -PARP-1wokD02 D:797-1007                                                                                                                                                                                            ---- Pfam domains (2)
           Pfam domains (3) PARP_reg-1wokD07 D:662-795                                                                                                            -PARP-1wokD03 D:797-1007                                                                                                                                                                                            ---- Pfam domains (3)
           Pfam domains (4) PARP_reg-1wokD08 D:662-795                                                                                                            -PARP-1wokD04 D:797-1007                                                                                                                                                                                            ---- Pfam domains (4)
         Sec.struct. author ....hhhhhhhhhhhhh.hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhh..........hhhhhhhhhhhhh......................hhhhhhhhhh...eeee.........hhhhhh.........hhhhh.....eee..hhhhhhh.........ee...eeeee......................eee.....................................eeee.hhh.eeeee...ee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------A---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PARP_ALPHA_HD  PDB: D:662-779 UniProt: 662-779                                                                        --------PARP_CATALYTIC  PDB: D:788-1011 UniProt: 788-1014                                                                                                                                                                                PROSITE
           Transcript 1 (1) Exon 1.16  PDB: D:662-690    Exon 1.17c  PDB: D:691-718  Exon 1.18  PDB: D:719-759                Exon 1.19a  PDB: D:760-802 UniProt: 760-802Exon 1.19c  PDB: D:803-835       Exon 1.20b  PDB: D:836-886 UniProt: 836-886        Exon 1.21b  PDB: D:887-929 UniProt: 887-929--------------------Exon 1.23b  PDB: D:950-988             ----------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.22             -------------------------------------Exon 1.24d [INCOMPLETE]  Transcript 1 (2)
                1wok D  662 KSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKVEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT 1011
                                   671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 8)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Family: PARP (21)
1aPARP-1wokD01D:797-1007
1bPARP-1wokD02D:797-1007
1cPARP-1wokD03D:797-1007
1dPARP-1wokD04D:797-1007

(-) Gene Ontology  (63, 63)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (PARP1_HUMAN | P09874)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003910    DNA ligase (ATP) activity    Catalysis of the reaction: ATP + deoxyribonucleotide(n) + deoxyribonucleotide(m) = AMP + diphosphate + deoxyribonucleotide(n+m).
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0003950    NAD+ ADP-ribosyltransferase activity    Catalysis of the reaction: NAD+ + (ADP-D-ribosyl)(n)-acceptor = nicotinamide + (ADP-D-ribosyl)(n+1)-acceptor.
    GO:0070412    R-SMAD binding    Interacting selectively and non-covalently with a receptor-regulated SMAD signaling protein.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0042826    histone deacetylase binding    Interacting selectively and non-covalently with the enzyme histone deacetylase.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0047485    protein N-terminus binding    Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0042769    DNA damage response, detection of DNA damage    The series of events required to receive a stimulus indicating DNA damage has occurred and convert it to a molecular signal.
    GO:0051103    DNA ligation involved in DNA repair    The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase, that contributes to DNA repair.
    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: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:0032869    cellular response to insulin 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 an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0034599    cellular response to oxidative stress    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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0006302    double-strand break repair    The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.
    GO:0000724    double-strand break repair via homologous recombination    The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule.
    GO:0070911    global genome nucleotide-excision repair    The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.
    GO:0006273    lagging strand elongation    The synthesis of DNA from a template strand in a net 3' to 5' direction. Lagging strand DNA elongation proceeds by discontinuous synthesis of short stretches of DNA, known as Okazaki fragments, from RNA primers; these fragments are then joined by DNA ligase. Although each segment of nascent DNA is synthesized in the 5' to 3' direction, the overall direction of lagging strand synthesis is 3' to 5', mirroring the progress of the replication fork.
    GO:0030225    macrophage differentiation    The process in which a relatively unspecialized monocyte acquires the specialized features of a macrophage.
    GO:0032042    mitochondrial DNA metabolic process    The chemical reactions and pathways involving mitochondrial DNA.
    GO:0043504    mitochondrial DNA repair    The process of restoring mitochondrial DNA after damage.
    GO:0007005    mitochondrion organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
    GO:1904357    negative regulation of telomere maintenance via telomere lengthening    Any process that stops, prevents or reduces the frequency, rate or extent of telomere maintenance via telomere lengthening.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0000715    nucleotide-excision repair, DNA damage recognition    The identification of lesions in DNA, such as pyrimidine-dimers, intrastrand cross-links, and bulky adducts. The wide range of substrate specificity suggests the repair complex recognizes distortions in the DNA helix.
    GO:0000717    nucleotide-excision repair, DNA duplex unwinding    The unwinding, or local denaturation, of the DNA duplex to create a bubble around the site of the DNA damage.
    GO:0033683    nucleotide-excision repair, DNA incision    A process that results in the endonucleolytic cleavage of the damaged strand of DNA. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound.
    GO:0006295    nucleotide-excision repair, DNA incision, 3'-to lesion    The endonucleolytic cleavage of the damaged strand of DNA 3' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision precedes the incision formed 5' to the site of damage.
    GO:0006296    nucleotide-excision repair, DNA incision, 5'-to lesion    The endonucleolytic cleavage of the damaged strand of DNA 5' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision follows the incision formed 3' to the site of damage.
    GO:0006294    nucleotide-excision repair, preincision complex assembly    The aggregation, arrangement and bonding together of proteins on DNA to form the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage. This assembly occurs before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage.
    GO:0006293    nucleotide-excision repair, preincision complex stabilization    The stabilization of the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage as well as the unwound DNA. The stabilization of the protein-DNA complex ensures proper positioning of the preincision complex before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage.
    GO:0060391    positive regulation of SMAD protein import into nucleus    Any process that increases the rate, frequency or extent of SMAD protein import into the nucleus, i.e. the directed movement of a SMAD proteins from the cytoplasm into the nucleus. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways.
    GO:0010613    positive regulation of cardiac muscle hypertrophy    Any process that increases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:2000679    positive regulation of transcription regulatory region DNA binding    Any process that activates or increases the frequency, rate or extent of transcription regulatory region DNA binding.
    GO:0006471    protein ADP-ribosylation    The transfer, from NAD, of ADP-ribose to protein amino acids.
    GO:0016540    protein autoprocessing    Processing which a protein carries out itself. This involves actions such as the autolytic removal of residues to generate the mature form of the protein.
    GO:0036211    protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0070212    protein poly-ADP-ribosylation    The transfer of multiple ADP-ribose residues from NAD to a protein amino acid, forming a poly(ADP-ribose) chain.
    GO:0016925    protein sumoylation    The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
    GO:1903827    regulation of cellular protein localization    Any process that modulates the frequency, rate or extent of cellular protein localization. Cellular protein localization is any process in which a protein is transported to, and/or maintained in, a specific location and encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0023019    signal transduction involved in regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression as a consequence of a process in which a signal is released and/or conveyed from one location to another.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0007179    transforming growth factor beta receptor signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0005635    nuclear envelope    The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
    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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PARP1_HUMAN | P098741uk0 1uk1 2cok 2cr9 2cs2 2dmj 2jvn 2l30 2l31 2n8a 2rcw 2rd6 2riq 3gjw 3gn7 3l3l 3l3m 3od8 3oda 3odc 3ode 4av1 4dqy 4gv7 4hhy 4hhz 4l6s 4opx 4oqa 4oqb 4pjt 4r5w 4r6e 4rv6 4und 4uxb 4xhu 4zzz 5a00 5ds3 5ha9 5kpn 5kpo 5kpp 5kpq 5wrq 5wry 5wrz 5ws0 5ws1 5wtc

(-) Related Entries Specified in the PDB File

1uk0 THE SAME PROTEIN COMPLEXED WITH FR257517