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(-) Description

Title :  THE CATALYTIC CORE OF RAD2 IN COMPLEX WITH DNA SUBSTRATE (COMPLEX IV)
 
Authors :  M. Mietus, E. Nowak, M. Jaciuk, P. Kustosz, M. Nowotny
Date :  02 Apr 14  (Deposition) - 27 Aug 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ba Rossmann-Like, Dna Repair, Tfiih, Nucleus, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Mietus, E. Nowak, M. Jaciuk, P. Kustosz, J. Studnicka, M. Nowotny
Crystal Structure Of The Catalytic Core Of Rad2: Insights Into The Mechanism Of Substrate Binding.
Nucleic Acids Res. V. 42 10762 2014
PubMed-ID: 25120270  |  Reference-DOI: 10.1093/NAR/GKU729

(-) Compounds

Molecule 1 - DNA REPAIR PROTEIN RAD2
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3) ROSSETA
    Expression System Taxid: 469008
    Expression System Vector Type: PET
    Fragment: ENZYME CATALYTIC CORE, UNP RESIDUES 2-111, UNP RESIDUES 732-986
    Gene: RAD2, YGR258C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
 
Molecule 2 - DNA (5'- D(*TP*TP*TP*TP*GP*CP*TP*CP*CP*CP*TP*TP*GP*TP*CP*TP*CP*AP*GP*TP*TP*TP* T)-3')
    Chains: C
    Engineered: YES
    Other Details: DNA OLIGONUCLEOTIDE
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*TP*TP*TP*TP*CP*TP*GP*AP*GP*AP*CP*AP*AP*GP*GP*GP*AP*GP*CP*TP*TP*TP* T)-3')
    Chains: D
    Engineered: YES
    Other Details: DNA OLIGONUCLEOTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2K2Ligand/IonPOTASSIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:2 , GLU A:794 , ASP A:813 , ASP A:815 , HOH A:1114BINDING SITE FOR RESIDUE CA A 1001
2AC2SOFTWARELEU A:860 , LEU A:861 , LEU A:869 , MET A:872 , HOH A:1123 , HOH A:1140 , DG C:9 , DA D:9BINDING SITE FOR RESIDUE K A 1002
3AC3SOFTWAREGLY B:2 , GLU B:794 , ASP B:813 , ASP B:815 , ASP B:864BINDING SITE FOR RESIDUE CA B 1001
4AC4SOFTWARELEU B:860 , LEU B:861 , LEU B:869 , MET B:872 , HOH B:1119 , DG C:9 , DA D:9BINDING SITE FOR RESIDUE K B 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q10)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Phe A:929 -Pro A:930
2His B:830 -Glu B:831
3Phe B:929 -Pro B:930

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q10)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q10)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q10)

(-) 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:300
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhee.hhhhhh..eeeee..hhhhhhhhh....hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhh......hhhhhhhhhhhhhh....eee...hhhhhhhhhhhh.....ee...hhhhhh....eee.....eeehhhhhhhhhh.hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh...............hhhhhhhhhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4q10 A   2 GVHSFWDIAGPTARPVRLESLEDKRMAVDASIWIYQFLKAVRVKNSHITGFFRRICKLLYFGIRPVFVFDGGVPVLKRETIRQDEVTMDMIKEVQELLSRFGIPYITAPMEAEAQCAELLQLNLVDGIITDDSDVFLFGGTKIYKNMFHVEFYDAESILKLLGLDRKNMIELAQLLGSDYTNGLKGMGPVSSIEVIAEFGNLKNFKDWYNNGQFDKRKQETENKFEKDLRKKLVNNEIILDDDFPSVMVYDAYMRPEVDHDTTPFVWGVPDLDMLRSFMKTQLGWPHEKSDEILIPLIRD 985
                                    11        21        31        41 ||     57        67        77        87  ||   771       781       791       801       811       821       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985
                                                                    43|                                      90|                                                              830|                                                                                                                                                      
                                                                     50                                      765                                                               835                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:295
                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhheeehhhhhh..eeee...hhhhhhhhhh.....hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhh...hhhhhhhhhhhhhhh...eee...hhhhhhhhhhhh....eee...hhhhhh....eee........eeeehhhhhhhhhh.hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh........hhhhhhhhhh...............hhhhhhhhhhhhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q10 B   2 GVHSFWDIAGPTARPVRLESLEDKRMAVDASIWIYQFLKAVRDAVKNSHITGFFRRICKLLYFGIRPVFVFDGGVPVLKRETIRDEVTMDMIKEVQELLSRFGIPYITAPMEAEAQCAELLQLNLVDGIITDDSDVFLFGGTKIYKNMFHEKNYVEFYDAESILKLLGLDRKNMIELAQLLGSDYTNGLKGMGPVSSIEVIAEFGNLKNFKDWYNNGQFNKFEKDLRKKLVNNEIILDDDFPSVMVYDAYMRPEVDHDTTPFVWGVPDLDMLRSFMKTQLGWPHEKSDEILIPLI 983
                                    11        21        31        41  ||    55        65        75        85   ||  770       780       790       800       810       820       830       840       850       860       870       880       890       908       918       928       938       948       958       968       978     
                                                                     44|                                      89|                                                                                                                                   899|                                                                           
                                                                      49                                      765                                                                                                                                    908                                                                           


Chain C from PDB  Type:DNA  Length:17
                                                 
                 4q10 C   0 TGCTCCCTTGTCTCAGT  16
                                     9       


Chain D from PDB  Type:DNA  Length:17
                                                 
                 4q10 D   0 TCTGAGACAAGGGAGCT  16
                                     9
   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 4Q10)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q10)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q10)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    His B:830 - Glu B:831   [ RasMol ]  
    Phe A:929 - Pro A:930   [ RasMol ]  
    Phe B:929 - Pro B:930   [ RasMol ]  
 

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  RAD2_YEAST | P07276
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 Related Entries

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

UniProtKB/Swiss-Prot
        RAD2_YEAST | P07276: 2lox 4q0r 4q0w 4q0z

(-) Related Entries Specified in the PDB File

4q0w 4q0z 4q10