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(-) Description

Title :  THE COMPLEX STRUCTURE OF TIMELESS_PAB AND PARP-1_CATALYTIC DOMAIN
 
Authors :  S. Xie, C. Qian
Date :  06 Jan 15  (Deposition) - 30 Sep 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  C,D  (1x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Dna Damage Response, Transferase-Replication Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Xie, O. Mortusewicz, H. T. Ma, P. Herr, R. R. Poon, T. Helleday, C. Qia
Timeless Interacts With Parp-1 To Promote Homologous Recombination Repair.
Mol. Cell V. 60 163 2015
PubMed-ID: 26344098  |  Reference-DOI: 10.1016/J.MOLCEL.2015.07.031

(-) Compounds

Molecule 1 - POLY [ADP-RIBOSE] POLYMERASE 1
    Chains: C, A
    EC Number: 2.4.2.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 661-1014
    Gene: PARP1, ADPRT, PPOL
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PARP-1,ADP-RIBOSYLTRANSFERASE DIPHTHERIA TOXIN-LIKE 1,ARTD1, NAD(+) ADP-RIBOSYLTRANSFERASE 1,ADPRT 1,POLY[ADP-RIBOSE] SYNTHASE 1
 
Molecule 2 - PROTEIN TIMELESS HOMOLOG
    Chains: D, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1000-1098
    Gene: TIMELESS, TIM, TIM1, TIMELESS1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HTIM

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):   CD
Biological Unit 2 (1x): AB  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CA1Ligand/IonCALCIUM ION
3GOL4Ligand/IonGLYCEROL
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3GOL3Ligand/IonGLYCEROL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3GOL1Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP C:770 , HIS C:862 , SER C:864 , ASN C:868 , HOH C:1230binding site for residue GOL C 1101
2AC2SOFTWAREARG C:841 , GLY C:843 , GLU C:844binding site for residue GOL C 1102
3AC3SOFTWAREHIS C:862 , GLY C:863 , SER C:904 , TYR C:907binding site for residue ACT C 1103
4AC4SOFTWAREASP A:957 , LEU D:25binding site for residue GOL D 201
5AC5SOFTWAREASP A:766 , ASP A:770 , HIS A:862 , SER A:864 , ASN A:868 , CA A:1103binding site for residue GOL A 1101
6AC6SOFTWAREHIS A:862 , GLY A:863 , TYR A:896 , SER A:904binding site for residue ACT A 1102
7AC7SOFTWAREASP A:766 , GOL A:1101 , HOH A:1220binding site for residue CA A 1103

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1C:845 -B:43
2D:43 -A:845

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr A:661 -Lys A:662

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XHU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XHU)

(-) Exons   (0, 0)

(no "Exon" information available for 4XHU)

(-) 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:341
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.eeeee....hhhhhhhhhhhhhh.......eeeeeeeeeeeee.hhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhh........hhhhh.....eee..hhhhhhhhhh......eeeeeeeeee...eeee..............eeee.eeeee.hhhheee..eee....eee.......eee.eeee.hhh.eeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xhu A  661 TKSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKVEMLDNLLDIEVAYSLLRSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKTS 1012
                                   670       680       690       700       710       720||     736       746       756       766       776  ||   791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011 
                                                                                      721|                                                779|                                                                                                                                                                                                                                   
                                                                                       728                                                 785                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:89
                                                                                                                          
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhh....ee....hhhhhhhhhhhhhhhhhhhh.............ee....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                4xhu B   15 LHQEGFSIPLLWLQNCLIRAADDREEDGCSQAVPLVPLTEENEEAMENEQFQQLLRKLGVRPPASGQETFWRIPAKLSPTQLRRAAASL  103
                                    24        34        44        54        64        74        84        94         


Chain C from PDB  Type:PROTEIN  Length:333
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.eeeee....hhhhhhhhhhhhhh...eeeeeeeeeeee.hhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhh........hhhhh.....eee..hhhhhhhhhh......eeeeeeeeee...eeee..............eeee.eeeee.hhhheee..eee....eee......eee.eeee.hhh.eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xhu C  665 LPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKVEMLDNLLDIEVAYSLLRSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVDTSLLYNEYIVYDIAQVNLKYLLKLKFNF 1009
                                   674       684       694       704       714       725       735       745       755       765       775   ||  790       800       810       820 ||    835       845       855       865       875       885       895       905       915       925       935       945       955       965       975   ||  986       996      1006   
                                                                                   722|                                                    779|                                  822|                                                                                                                                                    979|                            
                                                                                    724                                                     785                                   828                                                                                                                                                     981                            


Chain D from PDB  Type:PROTEIN  Length:83
                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh....ee....hhhhhhhhhhhhhhhhhhhhh............ee....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                4xhu D   21 SIPLLWLQNCLIRAADDREEDGCSQAVPLVPLTEENEEAMENEQFQQLLRKLGVRPPASGQETFWRIPAKLSPTQLRRAAASL  103
                                    30        40        50        60        70        80        90       100
   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 4XHU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XHU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XHU)

(-) Gene Ontology  (82, 90)

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    Thr A:661 - Lys A:662   [ RasMol ]  
 
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  4xhu
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  PARP1_HUMAN | P09874
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  TIM_HUMAN | Q9UNS1
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 Related Entries

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

UniProtKB/Swiss-Prot
        PARP1_HUMAN | P09874: 1uk0 1uk1 1wok 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 4zzz 5a00 5ds3 5ha9 5kpn 5kpo 5kpp 5kpq 5wrq 5wry 5wrz 5ws0 5ws1 5wtc
        TIM_HUMAN | Q9UNS1: 4xht 4xhw 5mqi

(-) Related Entries Specified in the PDB File

4xht 4xhw