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(-) Description

Title :  CRYSTAL STRUCTURE OF XERH SITE-SPECIFIC RECOMBINASE BOUND TO DIFH SUBSTRATE: PRE-CLEAVAGE COMPLEX
 
Authors :  A. Bebel, O. Barabas
Date :  25 Apr 16  (Deposition) - 28 Dec 16  (Release) - 11 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Xer, Tyrosine Recombinase, Site-Specific Recombinase, Chromosome Dimer Resolution, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Bebel, E. Karaca, B. Kumar, W. M. Stark, O. Barabas
Structural Snapshots Of Xer Recombination Reveal Activation By Synaptic Complex Remodeling And Dna Bending.
Elife V. 5 2016
PubMed-ID: 28009253  |  Reference-DOI: 10.7554/ELIFE.19706

(-) Compounds

Molecule 1 - TYROSINE RECOMBINASE XERH
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PETM-28
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: XERH, HP_0675
    Organism Scientific: HELICOBACTER PYLORI (STRAIN ATCC 700392 / 26695)
    Organism Taxid: 85962
    Strain: ATCC 700392 / 26695
 
Molecule 2 - DNA (30-MER)
    Chains: E, G
    Engineered: YES
    Organism Scientific: HELICOBACTER PYLORI 26695
    Organism Taxid: 85962
    Synthetic: YES
 
Molecule 3 - DNA (30-MER)
    Chains: F, H
    Engineered: YES
    Organism Scientific: HELICOBACTER PYLORI 26695
    Organism Taxid: 85962
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3GOL5Ligand/IonGLYCEROL
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:56 , HOH A:580 , HOH A:601 , LEU C:184 , PHE C:209binding site for residue GOL A 401
02AC2SOFTWARETYR A:232 , LEU A:261binding site for residue GOL A 402
03AC3SOFTWARETYR A:85 , PHE A:86 , LYS A:88 , PHE A:98binding site for residue EDO A 403
04AC4SOFTWARELEU A:326 , LEU C:326binding site for residue CL A 404
05AC5SOFTWAREASP B:140 , HOH B:598 , LYS D:141binding site for residue GOL B 401
06AC6SOFTWARETHR B:28 , LEU B:30 , SER B:31 , ASN B:32 , HOH B:535 , SER C:114binding site for residue GOL B 402
07AC7SOFTWARETYR B:267 , GLN B:278 , HOH B:584binding site for residue GOL B 403
08AC8SOFTWAREGLN B:38 , ASN B:39 , LYS C:88 , TYR C:116binding site for residue EDO B 404
09AC9SOFTWAREARG B:21 , ARG B:24 , LEU B:48 , ASN B:49binding site for residue PEG B 405
10AD1SOFTWAREASN A:154 , HOH A:532 , TYR C:25 , TYR C:138 , GLN C:142 , HOH C:557binding site for residue EDO C 401
11AD2SOFTWAREASN C:73 , THR C:74 , LEU C:77 , PRO C:78 , HOH C:534 , DA F:9 , HOH F:107binding site for residue EDO C 402
12AD3SOFTWARELYS D:81 , GLU D:84binding site for residue EDO D 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JK0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5JK0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JK0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JK0)

(-) Exons   (0, 0)

(no "Exon" information available for 5JK0)

(-) 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:347
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhh.hhh.eeee..eeeeeee.hhh.eeeeeee...hhhhhhhhhhhhh..................hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jk0 A   1 MKHPLEELKDPTENLLLWIGRFLRYKCTSLSNSQVKDQNKVFECLNELNQACSSSQLEKVCKKARNAGLLGINTYALPLLKFHEYFSKARLIAFNSLKNIDEVMLAEFLSVYTGGLSLATKKNYRIALLGLFSYIDKQNQDENEKSYIYNITLKKLPTHLNNEELEKFLESIDKIEMSAKVRARNRLLIKIIVFTGMRSNEALQLKIKDFTLENGCYTILIKGKGDKYRAVMLKAFHIESLLKEWLIERELYPVKNDLLFCNQKGSALTQAYLYKQVERIINFAGLRREKNGAHMLRHSFATLLYQKRHDLILVQEALGHASLNTSRIYTHFDKQRLEEAASIWEEN 362
                                    10        20        30        40        50        60        70        80        90 ||    104       114       124       134       144       154   ||  175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       
                                                                                                                      92|                                                          158|                                                                                                                                                                                                
                                                                                                                       97                                                           170                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:345
                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhh.hhh.eee...eeeeeee.hhh.eeeeeee...hhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jk0 B   1 MKHPLEELKDPTENLLLWIGRFLRYKCTSLSNSQVKDQNKVFECLNELNQACSSSQLEKVCKKARNAGLLGINTYALPLLKFHEYFSKARLITFNSLKNIDEVMLAEFLSVYTGGLSLATKKNYRIALLGLFSYIDKQNQDENEKSYIYNITLKKLPTHLNNEELEKFLESIDKIEMSAKVRARNRLLIKIIVFTGMRSNEALQLKIKDFTLENGCYTILIKGKGDKYRAVMLKAFHIESLLKEWLIERELYPVKNDLLFCNQKGSALTQAYLYKQVERIINFAGLRREKNGAHMLRHSFATLLYQKRHDLILVQEALGHASLNTSRIYTHFDKQRLEEAASIWE 360
                                    10        20        30        40        50        60        70        80        90  ||   104       114       124       134       144       154   ||  175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355     
                                                                                                                       93|                                                         158|                                                                                                                                                                                              
                                                                                                                        98                                                          170                                                                                                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:348
                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhh.hhh.eeee..eeeeeee.....eeeeeee...hhhhhhhhhhhhh..................hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5jk0 C   1 MKHPLEELKDPTENLLLWIGRFLRYKCTSLSNSQVKDQNKVFECLNELNQACSSSQLEKVCKKARNAGLLGINTYALPLLKFHEYFSKARLITERLAFNSLKNIDEVMLAEFLSVYTGGLSLATKKNYRIALLGLFSYIDKQNQDENEKSYIYNITLKNIKLPTHLNNEELEKFLESIDKIEMSAKVRARNRLLIKIIVFTGMRSNEALQLKIKDFTLENGCYTILIKGKGDKYRAVMLKAFHIESLLKEWLIERELYPVKNDLLFCNQKGSALTQAYLYKQVERIINFAGLRREKNGAHMLRHSFATLLYQKRHDLILVQEALGHASLNTSRIYTHFRLEEAASIWE 360
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160|      179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       352        
                                                                                                                                                                                         160|                                                                                                                                                                              347|         
                                                                                                                                                                                          170                                                                                                                                                                               351         


Chain D from PDB  Type:PROTEIN  Length:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhh.hhh.eeee..eeeeeee.....eeeeeee...hhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jk0 D   1 MKHPLEELKDPTENLLLWIGRFLRYKCTSLSNSQVKDQNKVFECLNELNQACSSSQLEKVCKKARNAGLLGINTYALPLLKFHEYFSKARLITERLAFNSLKNIDEVMLAEFLSVYTGGLSLATKKNYRIALLGLFSYIDKQNQDENEKSYIYNITLKNISKLPTHLNNEELEKFLESIDKIEMSAKVRARNRLLIKIIVFTGMRSNEALQLKIKDFTLENGCYTILIKGKGDKYRAVMLKAFHIESLLKEWLIERELYPVKNDLLFCNQKGSALTQAYLYKQVERIINFAGLRREKNGAHMLRHSFATLLYQKRHDLILVQEALGHASLNTSRIYTHRLEEAASIWEE 361
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160||     178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       352         
                                                                                                                                                                                          161|                                                                                                                                                                             346|          
                                                                                                                                                                                           170                                                                                                                                                                              351          


Chain E from PDB  Type:DNA  Length:30
                                                              
                 5jk0 E   1 GAGTTATGAAAACTGCACTTTTCAAACTTT  30
                                    10        20        30


Chain F from PDB  Type:DNA  Length:30
                                                              
                 5jk0 F   1 AAAGTTTGAAAAGTGCAGTTTTCATAACTA  30
                                    10        20        30


Chain G from PDB  Type:DNA  Length:30
                                                              
                 5jk0 G   1 GAGTTATGAAAACTGCACTTTTCAAACTTT  30
                                    10        20        30


Chain H from PDB  Type:DNA  Length:29
                                                             
                 5jk0 H   2 AAGTTTGAAAAGTGCAGTTTTCATAACTA  30
                                    11        21
   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 5JK0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JK0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JK0)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        XERH_HELPY | O25386: 5jjv

(-) Related Entries Specified in the PDB File

5jjv 5JJV CONTAINS THE SAME PROTEIN COMPLEXED WITH PALINDROMIC DIFH DNA RESULTING IN A POST-CLEAVAGE INTERMEDIATE.