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(-) Description

Title :  CRYSTAL STRUCTURE OF CONSTITUTIVELY ACTIVE PARP-2
 
Authors :  A. A. Riccio, J. M. Pascal
Date :  17 Sep 15  (Deposition) - 27 Jul 16  (Release) - 27 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Adp-Ribosyl Transferase, Parp, Parp-2, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Dawicki-Mckenna, M. F. Langelier, J. E. Denizio, A. A. Riccio, C. D. Cao, K. R. Karch, M. Mccauley, J. D. Steffen, B. E. Black, J. M. Pascal
Parp-1 Activation Requires Local Unfolding Of An Autoinhibitory Domain.
Mol. Cell V. 60 755 2015
PubMed-ID: 26626480  |  Reference-DOI: 10.1016/J.MOLCEL.2015.10.013

(-) Compounds

Molecule 1 - POLY [ADP-RIBOSE] POLYMERASE 2
    Chains: A, B, C, D
    EC Number: 2.4.2.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 348-583
    Gene: PARP2, ADPRT2, ADPRTL2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HPARP-2,ADP-RIBOSYLTRANSFERASE DIPHTHERIA TOXIN-LIKE 2, ARTD2,NAD(+) ADP-RIBOSYLTRANSFERASE 2,ADPRT-2,POLY[ADP-RIBOSE] SYNTHASE 2,PADPRT-2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1UHB4Ligand/Ion2-[4-[(2S,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]CARBONYLPIPERAZIN-1-YL]-N-(1-OXIDANYLIDENE-2,3-DIHYDROISOINDOL-4-YL)ETHANAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1UHB1Ligand/Ion2-[4-[(2S,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]CARBONYLPIPERAZIN-1-YL]-N-(1-OXIDANYLIDENE-2,3-DIHYDROISOINDOL-4-YL)ETHANAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1UHB1Ligand/Ion2-[4-[(2S,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]CARBONYLPIPERAZIN-1-YL]-N-(1-OXIDANYLIDENE-2,3-DIHYDROISOINDOL-4-YL)ETHANAMIDE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1UHB1Ligand/Ion2-[4-[(2S,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]CARBONYLPIPERAZIN-1-YL]-N-(1-OXIDANYLIDENE-2,3-DIHYDROISOINDOL-4-YL)ETHANAMIDE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1UHB1Ligand/Ion2-[4-[(2S,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]CARBONYLPIPERAZIN-1-YL]-N-(1-OXIDANYLIDENE-2,3-DIHYDROISOINDOL-4-YL)ETHANAMIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:414 , HIS A:415 , GLY A:416 , SER A:417 , ASN A:421 , GLY A:424 , ILE A:425 , GLY A:429 , ARG A:431 , ALA A:433 , TYR A:449 , SER A:457 , TYR A:460 , GLU A:545 , HOH A:1112binding site for residue UHB A 1001
2AC2SOFTWARETRP B:414 , HIS B:415 , GLY B:416 , SER B:417 , GLY B:424 , ILE B:425 , GLY B:429 , LEU B:430 , ARG B:431 , ALA B:433 , PRO B:434 , TYR B:449 , SER B:457 , TYR B:460 , GLU B:545binding site for residue UHB B 1001
3AC3SOFTWARELEU A:466 , HIS C:415 , GLY C:416 , SER C:417 , ASN C:421 , GLY C:424 , ILE C:425 , GLY C:429 , ARG C:431 , ALA C:433 , TYR C:449 , SER C:457 , TYR C:460 , GLU C:545 , HOH C:1106 , HOH C:1114binding site for residue UHB C 1001
4AC4SOFTWARELEU B:466 , HIS D:415 , GLY D:416 , SER D:417 , ASN D:421 , GLY D:424 , ILE D:425 , GLY D:429 , ARG D:431 , PRO D:434 , TYR D:442 , TYR D:449 , SER D:457 , TYR D:460binding site for residue UHB D 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DSY)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:526 -Pro A:527
2Gly B:526 -Pro B:527
3Gly C:526 -Pro C:527
4Gly D:526 -Pro D:527

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DSY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DSY)

(-) Exons   (0, 0)

(no "Exon" information available for 5DSY)

(-) Sequences/Alignments

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:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh.....hhhhhhhhh..eeeee....hhhhhhhhhhhhhh.......eeeeeeeeeeeee.hhhhhh......eeeeeee.hhhhhhhhhhhh..................eee..hhhhhhh.........eeeeeeeeee...eeee.......hhhhh...eeee.eeeee.hhhheee..eee....eee..........eee.eeee.hhh.eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dsy A 217 PESQLDLRVQELIKLICNQSPEHPLDQHYRNLHCALRPLDHESYEFKVISQYLQSTHAPTHSDYTMTLLDLFEVEKDGEKEAFREDLHNRMLLWHGSRMSNWVGILSHGLRIAPPEAPITGYMFGKGIYFADMSSKSANYCFASRLKNTGLLLLSEVALGQCNELLEANPKAEGLLQGKHSTKGLGKMAPSSAHFVTLNGSTVPLGPASDTGILNPDGYTLNYNEYIVYNPNQVRMRYLLKVQFNFLQ 568
                                   226       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560        
                                           234|                                                                                                                                                                                                                                     
                                            339                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh......hhhhhhhhh..eeeee....hhhhhhhhhhhhhh.......eeeeeeeeeeeee.hhhhhh......eeeeeee.hhhhhhhhhhhh..................eee..hhhhhhhhhh......eeeeeeeeee...eeee.......hhhhh...eeee...eee.hhhheee..eee....eee..............eeee.hhh.eeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dsy B 217 PESQLDLRVQELIKLICNLQSPEHPLDQHYRNLHCALRPLDHESYEFKVISQYLQSTHAPTHSDYTMTLLDLFEVEKDGEKEAFREDLHNRMLLWHGSRMSNWVGILSHGLRIAPPEAPITGYMFGKGIYFADMSSKSANYCFASRLKNTGLLLLSEVALGQCNELLEANPKAEGLLQGKHSTKGLGKMAPSSAHFVTLNGSTVPLGPASDTGILNPDGYTLNYNEYIVYNPNQVRMRYLLKVQFNFLQLW 570
                                   226       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569 
                                           234|                                                                                                                                                                                                                                        
                                            338                                                                                                                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh....hhhhhhhhh..eeeee....hhhhhhhhhhhhhh.......eeeeeeeeeeeee.hhhhhh......eeeeeee.hhhhhhhhhhhh..................eee..hhhhhhhhhh......eeeeeeeeee...eeee...hhhhhhhhh...eeee.eeeee.hhhheee..eee....eee..........eee.eeee.hhh.eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dsy C 217 PESQLDLRVQELIKLICNQSPEHPLDQHYRNLHCALRPLDHESYEFKVISQYLQSTHAPTHSDYTMTLLDLFEVEKDGEKEAFREDLHNRMLLWHGSRMSNWVGILSHGLRIAPPEAPITGYMFGKGIYFADMSSKSANYCFASRLKNTGLLLLSEVALGQCNELLEANPKAEGLLQGKHSTKGLGKMAPSSAHFVTLNGSTVPLGPASDTGILNPDGYTLNYNEYIVYNPNQVRMRYLLKVQFNFLQ 568
                                   226       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560        
                                           234|                                                                                                                                                                                                                                     
                                            339                                                                                                                                                                                                                                     


Chain D from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh....hhhhhhhhh..eeeeee...hhhhhhhhhhhhhh.......eeeeeeeeeeeee.hhhhhh......eeeeeee.hhhhhhhhhhhh..................eeee.hhhhhhhhhh......eeeeeeeeee...eeee.......hhhhh...eeee.eeee.hhhhheee..eee.....ee..........eee.eeee.hhh.eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dsy D 217 PESQLDLRVQELIKLICNSPEHPLDQHYRNLHCALRPLDHESYEFKVISQYLQSTHAPTHSDYTMTLLDLFEVEKDGEKEAFREDLHNRMLLWHGSRMSNWVGILSHGLRIAPPEAPITGYMFGKGIYFADMSSKSANYCFASRLKNTGLLLLSEVALGQCNELLEANPKAEGLLQGKHSTKGLGKMAPSSAHFVTLNGSTVPLGPASDTGILNPDGYTLNYNEYIVYNPNQVRMRYLLKVQFNFLQ 568
                                   226       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       
                                           234|                                                                                                                                                                                                                                    
                                            340
   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  (0, 0)

(no "SCOP Domain" information available for 5DSY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DSY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DSY)

(-) Gene Ontology  (16, 16)

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        PARP2_HUMAN | Q9UGN5: 3kcz 3kjd 4pjv 4tvj 4zzx 4zzy 5d5k

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