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(-) Description

Title :  CRYSTAL STRUCTURE OF RECU(D88N) IN COMPLEX WITH PALINDROMIC DNA DUPLEX
 
Authors :  S. Khavnekar, J. B. Rafferty, A. Kale
Date :  16 Dec 15  (Deposition) - 07 Dec 16  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.21
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,C,E,F,G,H  (1x)
Biol. Unit 2:  B (1x),D (1x),E (1x),F (1x),G (1x),H (1x)
Keywords :  Resolvase, Holliday Junction, Recu, Dna, Complex, Dna-Binding Proteins, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Khavnekar, S. C. Dantu, S. Sedelnikova, S. Ayora, J. Rafferty, A. Kale
Structural Insights Into Dynamics Of Recu-Hj Complex Formation Elucidates Key Role Of Ntr And Stalk Region Towar Formation Of Reactive State.
Nucleic Acids Res. V. 45 975 2017
PubMed-ID: 27903910  |  Reference-DOI: 10.1093/NAR/GKW1165

(-) Compounds

Molecule 1 - HOLLIDAY JUNCTION RESOLVASE RECU
    Chains: A, B, C, D
    EC Number: 3.1.22.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PCB210
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector Type: PLASMID
    Gene: RECU, PRFA, YPPB, BSU22310
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
 
Molecule 2 - PALINDROMIC DNA
    Chains: E, F, G, H
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A C EFGH
Biological Unit 2 (1x):  B (1x) D (1x)E (1x)F (1x)G (1x)H (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5FDK)

(-) Sites  (0, 0)

(no "Site" information available for 5FDK)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Ser A:27 -Tyr A:28
2Arg A:31 -Gly A:32
3Thr A:34 -Leu A:35
4Ser A:72 -Ala A:73
5Tyr C:197 -Phe C:198
6Ser D:15 -Val D:16
7Arg D:24 -Ala D:25
8Arg D:31 -Gly D:32
9Tyr D:183 -Ala D:184

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FDK)

(-) 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:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhh....eeee....eeeee............eeee.......eeeee..eeeeeeeee.....eee.hhhhhhhhhhhhhhhhh..eeeeeee....eeeeehhhhhhhhhhhhhh...eeehhhhhhhhee..........hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fdk A  23 KRAPSYSNRGMTLEDDLNETNKYYLTNQIAVIHKKPTPVQIVNVHYPKRSAAVIKEAYFKQSSTTNYNGIYKGRYIDFEAKETKNKTSFPLQNFHDHQIEHMKQVKAQDGICFVIISAFDQVYFLEADKLFYFWDRKEKNGRKSIRKDELEETAYPISLGYAPRIDYISIIEQLYFS 199
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       


Chain B from PDB  Type:PROTEIN  Length:166
                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...eeee......eeee........eeeee.........eeeee..eeee..eee.....eee....hhhhhhhhhhhhhh..eeeeeeee..eeeeeehhhhhhhhhhhhh....eeehhhhhhhhee.........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fdk B  34 TLEDDLNETNKYYLTNQIAVIHKKPTPVQIVNVHYPKRSAAVIKEAYFKQSSTTNYNGIYKGRYIDFEAKETKNKTSFPLQNFHDHQIEHMKQVKAQDGICFVIISAFDQVYFLEADKLFYFWDRKEKNGRKSIRKDELEETAYPISLGYAPRIDYISIIEQLYFS 199
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193      


Chain C from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhh...ee......eeeeeee.......eeeeeee.......eeeee..eeeee.ee......eee.hhhhhhhhhhhhhhhh...ee..ee......ee.hhhhhhhhhhhhhh....eee..hhhhhhee.ee.....eehhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5fdk C  26 PSYSNRGMTLEDDLNETNKYYLTNQIAVIHKKPTPVQIVNVHYPKRSAAVIKEAYFKQSSTTNYNGIYKGRYIDFEAKETKNKTSFPLQNFHDHQIEHMKQVKAQDGICFVIISAFDQVYFLEADKLFYFWDRKEKNGRKSIRKDELEETAYPISLGYAPRIDYISIIEQLYFS 199
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195    


Chain D from PDB  Type:PROTEIN  Length:199
                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................................hhhhhhhhhhhhhhh...eeee....eeeeeee.......eeeeeee.......eeeee..eeee..ee........hhhhhhhhhhhhhhhhhhh..eeeeee......eeeehhhhhhhhhhh........hhhhhhhhhee.........hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fdk D   1 MIRYPNGKTFQPKHSVSSQNSQKRAPSYSNRGMTLEDDLNETNKYYLTNQIAVIHKKPTPVQIVNVHYPKRSAAVIKEAYFKQSSTTNYNGIYKGRYIDFEAKETKNKTSFPLQNFHDHQIEHMKQVKAQDGICFVIISAFDQVYFLEADKLFYFWDRKEKNGRKSIRKDELEETAYPISLGYAPRIDYISIIEQLYFS 199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190         


Chain E from PDB  Type:DNA  Length:12
                                            
                 5fdk E   1 ACGCAATTGCGT  12
                                    10  


Chain F from PDB  Type:DNA  Length:12
                                            
                 5fdk F   1 ACGCAATTGCGT  12
                                    10  


Chain G from PDB  Type:DNA  Length:11
                                           
                 5fdk G   2 CGCAATTGCGT  12
                                    11 


Chain H from PDB  Type:DNA  Length:11
                                           
                 5fdk H   1 ACGCAATTGCG  11
                                    10
   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 5FDK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

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  Cis Peptide Bonds
    Arg A:31 - Gly A:32   [ RasMol ]  
    Arg D:24 - Ala D:25   [ RasMol ]  
    Arg D:31 - Gly D:32   [ RasMol ]  
    Ser A:27 - Tyr A:28   [ RasMol ]  
    Ser A:72 - Ala A:73   [ RasMol ]  
    Ser D:15 - Val D:16   [ RasMol ]  
    Thr A:34 - Leu A:35   [ RasMol ]  
    Tyr C:197 - Phe C:198   [ RasMol ]  
    Tyr D:183 - Ala D:184   [ RasMol ]  
 
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  RECU_BACSU | P39792
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 Related Entries

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

UniProtKB/Swiss-Prot
        RECU_BACSU | P39792: 1rzn 1zp7

(-) Related Entries Specified in the PDB File

1zp7 1ZP7 IS AN UNCOMPLEXED STRUCTURE OF RECU.