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(-) Description

Title :  THE CATALYTIC CORE OF RAD2 (COMPLEX I)
 
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 :  2.75
Chains :  Asym. Unit :  A,B,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Nuclease, Nucleotide Excision Repair, 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(*CP*TP*GP*AP*GP*TP*CP*AP*GP*AP*GP*CP*AP*AP*A)- 3')
    Chains: D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABD
Biological Unit 1 (1x): A D
Biological Unit 2 (1x):  B 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 24)

Asymmetric Unit (1, 24)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 4Q0R)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q0R)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:929 -Pro A:930
2Phe B:929 -Pro B:930

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q0R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q0R)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q0R)

(-) 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:293
                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhheeee.hhhh..eeeeehhhhhh...hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhh..hhhhhhhhhhhhh...eee...hhhhhhhhhhhh....eee...hhhhhh...eeee.......eeeeeehhhhhhhhh.hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.hhhhhhhhhhhhhh.........hhhhhhhhhh...............hhhhhhhhhhhhhh.hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q0r A   1 mGVHSFWDIAGPTARPVRLESLEDKRmAVDASIWIYQFSHITGFFRRICKLLYFGIRPVFVFDGGVPVLKRETIRQRKTmDmIKEVQELLSRFGIPYITAPmEAEAQCAELLQLNLVDGIITDDSDVFLFGGTKIYKNmFHEKNYVEFYDAESILKLLGLDRKNmIELAQLLGSDYTNGLKGmGPVSSIEVIAEFGNLKNFKDWYNNGQFDKRKQETENKFEKDLRKKLVNNEIILDDDFPSVmVYDAYmRPEVDHDTTPFVWGVPDLDmLRSFmKTQLGWPHEKSDEILIPL 982
                            |       10        20      | 30       |54        64        74        84       769 |     779       789 |     799       809       819       829       839       849    |  859       869  |    879       889       899       909       919       929   |   939       949       959    |  969       979   
                            |                        27-MSE     38|                                     92|| |                 791-MSE                              828-MSE                   854-MSE           872-MSE                                                      933-MSE |                 959-MSE|                  
                            1-MSE                                53                                     768| |                                                                                                                                                                     939-MSE                  964-MSE              
                                                                                                         769-MSE                                                                                                                                                                                                                 
                                                                                                           771-MSE                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:277
                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhheeee.hhh...eeee.hhhh.hhhhhhhhhhhhhhh..eeeeee....hhhhhhh.hhhhhhhhhhhhhh...eee...hhhhhhhhhhhh....eee...hhhhhh...eeee.......eeeeeehhhhhhhh..hhhhhhhhhhhhh..........hhhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhh........hhhhhhhhhh...............hhhhhhhhhhhhhh.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q0r B   0 SmGVHSFWDIAGPTARPVRLESLEDKRmAVDASIWSHITGFFRRICKLLYFGIRPVFVFDGGVPVLKRETTmDmIKEVQELLSRFGIPYITAPmEAEAQCAELLQLNLVDGIITDDSDVFLFGGTKIYKNmFHEKNYVEFYDAESILKLLGLDRKNmIELAQLLGSDYTNGLKGmGPVSSIEVIAEFGNLKNFKDWYNNGQFKFEKDLRKKLVNNEIILDDDFPSVmVYDAYmRPEVDHDTTPFVWGVPDLDmLRSFmKTQLGWPHEKSDEILIPLI 983
                             |       9        19       |29    ||  57        67        77        87|| |   777       787   |   797       807       817       827|      837       847      |857       867    |  877       887       897 ||    916       926      |936  |    946       956  |    966       976       
                             1-MSE                    27-MSE 34|                                87|| |                 791-MSE                              828-MSE                   854-MSE           872-MSE                    899|                     933-MSE |                 959-MSE|                   
                                                              53                                768| |                                                                                                                              909                           939-MSE                  964-MSE               
                                                                                                 769-MSE                                                                                                                                                                                                         
                                                                                                   771-MSE                                                                                                                                                                                                       


Chain D from PDB  Type:DNA  Length:4
                                    
                 4q0r D   7 GTCA  10
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4Q0R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q0R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q0R)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Phe B:929 - Pro B:930   [ RasMol ]  
 
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  4q0r
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  3.1.-.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        RAD2_YEAST | P07276: 2lox 4q0w 4q0z 4q10

(-) Related Entries Specified in the PDB File

4q0w 4q0z 4q10