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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HOLLIDAY JUNCTION-RESOLVING ENZYME GEN1 (WT) IN COMPLEX WITH PRODUCT DNA, MG2+ AND MN2+ IONS
 
Authors :  Y. J. Liu, A. D. J. Freeman, A. C. Declais, T. J. Wilson, A. Gartner, D. M. J
Date :  17 Jul 15  (Deposition) - 30 Dec 15  (Release) - 13 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,H,R
Keywords :  Gen1, 4-Way Holiday Junction, Resolvase, Dna Damage Repair, Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Liu, A. D. Freeman, A. C. Declais, T. J. Wilson, A. Gartner, D. M. Lilley
Crystal Structure Of A Eukaryotic Gen1 Resolving Enzyme Bound To Dna.
Cell Rep V. 13 2565 2015
PubMed-ID: 26686639  |  Reference-DOI: 10.1016/J.CELREP.2015.11.042

(-) Compounds

Molecule 1 - NUCLEASE-LIKE PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: CATALYTIC DOMAIN, UNP RESIDUES 2-465
    Gene: CTHT_0007290
    Organism Scientific: CHAETOMIUM THERMOPHILUM
    Organism Taxid: 209285
 
Molecule 2 - R
    Chains: R
    Engineered: YES
    Fragment: R-STEM
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: DNA OLIGO SYNTHESIS
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*TP*GP*AP*GP*CP*GP*GP*TP*GP*GP*TP*TP*GP*GP*T)- 3')
    Chains: H
    Engineered: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AHR

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION
2MSE7Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:122 , HOH A:608 , HOH A:630 , HOH A:653binding site for residue MN A 501
2AC2SOFTWAREASP A:141 , ASP A:143 , HOH A:604 , HOH A:611 , HOH A:631 , DG H:17 , HOH H:101binding site for residue MN A 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Gly A:2 -Ile A:3
2Cys A:208 -Gly A:209
3Lys A:223 -Glu A:224
4Phe A:268 -Pro A:269
5Phe A:295 -Pro A:296

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CNQ)

(-) 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:392
                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh....eeeehhhhhhhhhhhhh...eeeee.hhhhhh........hhhhhhhhhhhhhhhhhh.eeeeee........hhhhhhhhhhhh..eeee...hhhhhhhhhhhh....eee...hhhhhh...eeeeeee.......eeeeeehhhhh......hhhhhhhhhhhh.......hhhhhhhhhhh........hhhhhhhhhhhhhh....................hhhhhhhhhh....hhhhhhhhhhhh......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee.hhhhh...eeeeeehhhhhhh.hhhhh...........eeeeeehhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cnq A   2 GIKGIYKEIGSGERISLCKLAIDHLEQHNRPLRLAIDmAIWQFQIQAARGGSNPAIRTLFYRFVRLLSLGIHPIFVFDGPNKPGVSTAmAKRLIRLFGFTAHDAPGEAEAECAYLEQQGIVDAVLSEDVDTImFGSRVTLRDWSSEGGPPTHVTLHDAKKIAEGPSGLDREGmVLVALmSGGGIPGCGIKVACQAAKAGFGKELCAITEWKQRLLHELRTNESGFFRTKHKALEIPENFPNmEVLRYYTHPVVSSPATIERLRQEFPPSSTVDIAGLREFTRETFDWTFRPGAIKLIKVLAPGLLVQRCLDRYEESTLVKGISmRREHFSTDATPELRVSFIPAELVGLDPGQEPEVKPFDPWQPDLAWVPETILKLGVPVTVEDWEEGQRS 465
                                    11        21        31       |41        51        61        71        81  ||   103       113       123       133       143  |    153     ||166       176       186  |    196 ||    211       221    || 239       249       259       269 |     279       289       299       309       319       329       339  ||   363   |   373       383       393      |433       443       453       463  
                                                                39-MSE                                       84|    |                                         146-MSE      159|                       189-MSE |  ||                   226|                                 271-MSE                                                                342|       367-MSE                          400|                                  
                                                                                                              97    |                                                       163                             195-MSE                    235                                                                                                         357                                         431                                  
                                                                                                                  102-MSE                                                                                      198|                                                                                                                                                                                                                 
                                                                                                                                                                                                                204                                                                                                                                                                                                                 


Chain H from PDB  Type:DNA  Length:15
                                               
                 5cnq H  16 TGAGCGGTGGTTGGT  30
                                    25     


Chain R from PDB  Type:DNA  Length:16
                                                
                 5cnq R   0 TACCCACCACCGCTCA  15
                                     9
   Legend:   → Mismatch (orange background)
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    → 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 5CNQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Cys A:208 - Gly A:209   [ RasMol ]  
    Gly A:2 - Ile A:3   [ RasMol ]  
    Lys A:223 - Glu A:224   [ RasMol ]  
    Phe A:268 - Pro A:269   [ RasMol ]  
    Phe A:295 - Pro A:296   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        G0RYN2_CHATD | G0RYN2: 5co8

(-) Related Entries Specified in the PDB File

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