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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HOLLIDAY JUNCTION-RESOLVING ENZYME GEN1 (WT) IN COMPLEX WITH PRODUCT DNA AND MG2+ ION
 
Authors :  Y. J. Liu, A. D. J. Freeman, A. C. Declais, T. J. Wilson, A. Gartner, D. M. J
Date :  20 Jul 15  (Deposition) - 13 Jan 16  (Release) - 13 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,C,H,R,X
Keywords :  Holiday Junction, Resolvase, Complex, Dna, Hydrolase (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 - DNA (31-MER)
    Chains: R
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 2 - NUCLEASE-LIKE PROTEIN
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CTHT_0007290
    Organism Scientific: CHAETOMIUM THERMOPHILUM (STRAIN DSM 1495 / CBS 144.50 / IMI 039719)
    Organism Taxid: 759272
    Strain: DSM 1495 / CBS 144.50 / IMI 039719
 
Molecule 3 - DNA (5'-D(*AP*GP*AP*CP*TP*GP*CP*AP*GP*TP*TP*GP*AP*GP*TP*C)- 3')
    Chains: X
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - NUCLEASE-LIKE PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CTHT_0007290
    Organism Scientific: CHAETOMIUM THERMOPHILUM (STRAIN DSM 1495 / CBS 144.50 / IMI 039719)
    Organism Taxid: 759272
    Strain: DSM 1495 / CBS 144.50 / IMI 039719
 
Molecule 5 - DNA (5'-D(*TP*GP*AP*GP*CP*GP*GP*TP*GP*GP*TP*TP*GP*GP*A)- 3')
    Chains: H
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ACHRX

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric/Biological Unit (2, 14)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:122 , ASP A:141 , ASP A:143 , HOH A:601 , HOH A:611 , ASP C:141 , ASP C:143 , HOH C:603 , HOH C:612 , HOH H:601 , HOH H:602binding site for residue MG C 501
2AC2SOFTWAREGLU A:122 , ASP A:141 , ASP A:143 , HOH A:601 , HOH A:611 , ASP C:141 , ASP C:143 , HOH C:603 , HOH C:612 , HOH H:601 , HOH H:602binding site for residue MG A 501

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1C:226 -A:226

(-) Cis Peptide Bonds  (17, 17)

Asymmetric/Biological Unit
No.Residues
1Gly C:2 -Ile C:3
2Gln C:47 -Ala C:48
3Arg C:50 -Gly C:51
4Gly C:180 -Pro C:181
5Gly C:197 -Gly C:198
6Cys C:208 -Gly C:209
7Lys C:223 -Glu C:224
8Phe C:268 -Pro C:269
9Phe C:295 -Pro C:296
10Gly A:2 -Ile A:3
11Asn A:96 -Gly A:97
12Gly A:180 -Pro A:181
13Gly A:197 -Gly A:198
14Cys A:208 -Gly A:209
15Lys A:223 -Glu A:224
16Phe A:268 -Pro A:269
17Phe A:295 -Pro A:296

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CO8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CO8)

(-) Exons   (0, 0)

(no "Exon" information available for 5CO8)

(-) 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:393
                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh..eeeehhhhhhhhhhhhh...eeeee...hhhhhh......hhhhhhhhhhhhhhhhhh.eeeeee.........hhhhhhhhhhhh..eeee...hhhhhhhhhhhh....eee...hhhhh....eeeeeee.......eeeeeehhhhhh.....hhhhhhhhhhhh........hhhhhhhhhhh........hhhhhhhhhhhhhhh...................hhhhhhhhhh....hhhhhhhhhhhh......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee.hhhh..eeeeeeehhhhhhh................eeeeeehhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5co8 A   2 GIKGIYKEIGSGERISLCKLAIDHLEQHNRPLRLAIDMAIWQFQIQAARGGSNPAIRTLFYRFVRLLSLGIHPIFVFDGPNKPNGVSTAmAKRLIRLFGFTAHDAPGEAEAECAYLEQQGIVDAVLSEDVDTImFGSRVTLRDWSSEGGPPTHVTLHDAKKIAEGPSGLDREGmVLVALMSGGDGIPGCGIKVACQAAKAGFGKELCAITEWKQRLLHELRTNESGFFRTKHKALEIPENFPNmEVLRYYTHPVVSSPATIERLRQEFPPSSTVDIAGLREFTRETFDWTFRPGAIKLIKVLAPGLLVQRCLDRYEESTLVKGISmRREHFSTDATPELRVSFIPAELVGLDPGQEPEVPFDPWQPDLAWVPETILKLGVPVTVEDWEEGQRS 465
                                    11        21        31        41        51        61        71        81  ||   102       112       122       132       142   |   152      |165       175       185   |   195  ||   209       219      |237       247       257       267   |   277       287       297       307       317       327       337    || 361     | 371       381       391       432       442       452       462   
                                                                                                             84|     |                                         146-MSE      159|                       189-MSE  198|                    226|                                 271-MSE                                                                342|       367-MSE                          400|                                 
                                                                                                              96     |                                                       163                                 203                     235                                                                                                         357                                         432                                 
                                                                                                                   102-MSE                                                                                                                                                                                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:397
                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh..eeeehhhhhhhhhhhhh...eeeee..hhhhhhh......hhhhhhhhhhhhhhhhhh.eeeeee.........hhhhhhhhhhhh..eeee...hhhhhhhhhhhh....eee...hhhhhh...eeeeeee.......eeeeeehhhhhh.....hhhhhhhhhhhh............hhhhhhhhhhh........hhhhhhhhhhhhhhh...................hhhhhhhhhh....hhhhhhhhhhhh......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee.hhhh..eeeeeeehhhhhhh.hhhhh..........eeeeeehhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5co8 C   2 GIKGIYKEIGSGERISLCKLAIDHLEQHNRPLRLAIDmAIWQFQIQAARGGSNPAIRTLFYRFVRLLSLGIHPIFVFDGPNKPNGVSTAmAKRLIRLFGFTAHDAPGEAEAECAYLEQQGIVDAVLSEDVDTImFGSRVTLRDWSSEGGPPTHVTLHDAKKIAEGPSGLDREGmVLVALmSGGDYLPDGIPGCGIKVACQAAKAGFGKELCAITEWKQRLLHELRTNESGFFRTKHKALEIPENFPNmEVLRYYTHPVVSSPATIERLRQEFPPSSTVDIAGLREFTRETFDWTFRPGAIKLIKVLAPGLLVQRCLDRYEESTLVKGISmRREHFSTDATPELRVSFIPAELVGLDPGQEPEVPFDPWQPDLAWVPETILKLGVPVTVEDWEEGQRS 465
                                    11        21        31       |41        51        61        71        81  ||   102       112       122       132       142   |   152      |165       175       185   |   195       205       215       225||     243       253       263       273       283       293       303       313       323       333       357       367       377       387       397  ||   438       448       458       
                                                                39-MSE                                       84|     |                                         146-MSE      159|                       189-MSE |                            226|                                 271-MSE                                                                342|       367-MSE                          400|                                 
                                                                                                              96     |                                                       163                             195-MSE                         235                                                                                                         357                                         432                                 
                                                                                                                   102-MSE                                                                                                                                                                                                                                                                                                               


Chain H from PDB  Type:DNA  Length:15
                                               
                 5co8 H  16 TGAGCGGTGGTTGGA  30
                                    25     


Chain R from PDB  Type:DNA  Length:31
                                                               
                 5co8 R   0 TTCCAACCACCGCTCAACTCAACTGCAGTCT  30
                                     9        19        29 


Chain X from PDB  Type:DNA  Length:16
                                                
                 5co8 X   1 AGACTGCAGTTGAGTC  16
                                    10
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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 5CO8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CO8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CO8)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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        G0RYN2_CHATD | G0RYN2: 5cnq

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