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(-) Description

Title :  CRYSTAL STRUCTURE OF THE REPLICATION INITIATOR PROTEIN ENCODED ON PLASMID PMV158 (REPB), TETRAGONAL FORM, TO 3.6 ANG RESOLUTION
 
Authors :  D. R. Boer, J. A. Ruiz-Maso, A. G. Blanco, M. Vives-Llacer, I. Uson, F. X. Gomis-Ruth, M. Espinosa, G. Del Solar, M. Coll
Date :  26 Jun 08  (Deposition) - 30 Jun 09  (Release) - 30 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.60
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Replication Initiation, Plasmid Replication, Nuclease, Hexamer, Flexible Nuclease Domains, Dna Replication, Plasmid, Replication Initiator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. R. Boer, J. A. Ruiz-Maso, J. R. Lopez-Blanco, A. G. Blanco, M. Vives-Llacer, P. Chacon, I. Uson, F. X. Gomis-Ruth, M. Espinosa, O. Llorca, G. Del Solar, M. Coll
Plasmid Replication Initiator Repb Forms A Hexamer Reminiscent Of Ring Helicases And Has Mobile Nuclease Domains
Embo J. V. 28 1666 2009
PubMed-ID: 19440202  |  Reference-DOI: 10.1038/EMBOJ.2009.125
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REPLICATION PROTEIN REPB
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEM-T
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: REPB
    Organism Scientific: STREPTOCOCCUS AGALACTIAE
    Organism Taxid: 1311

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MN4Ligand/IonMANGANESE (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:39 , ASP A:42 , HIS A:55 , HIS A:57BINDING SITE FOR RESIDUE MN A 301
2AC2SOFTWAREHIS B:39 , ASP B:42 , HIS B:55 , HIS B:57BINDING SITE FOR RESIDUE MN B 301
3AC3SOFTWAREHIS C:39 , ASP C:42 , HIS C:55 , HIS C:57BINDING SITE FOR RESIDUE MN C 301
4AC4SOFTWAREHIS F:39 , ASP F:42 , HIS F:55 , HIS F:57BINDING SITE FOR RESIDUE MN F 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DKY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3DKY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DKY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3DKY)

(-) Exons   (0, 0)

(no "Exon" information available for 3DKY)

(-) 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:200
 aligned with REPB_STRAG | P13921 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:200
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203
           REPB_STRAG     4 EKARYFTFLLYPESIPSDWELKLETLGVPMAISPLHDKDKSSIKGQKYKKAHYHVLYIAKNPVTADSVRKKIKLLLGEKSLAMVQVVLNVENMYLYLTHESKDAIAKKKHVYDKADIKLINNFDIDRYVTLDVEEKTELFNVVVSLIRAYTLQNIFDLYDFIDENGETYGLTINLVNEVIAGKTGFMKLLFDGAYQRSKR 203
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeehhhhh..hhhhhhhhh...eee....................eeeeeeeeeeeehhhhhhhhhhhhh......eee..hhhhhhhhh...hhhhhhh..........eee...hhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dky A   4 EKARYFTFLLYPESIPSDWELKLETLGVPMAISPLHDKDKSSIKGQKYKKAHYHVLYIAKNPVTADSVRKKIKLLLGEKSLAMVQVVLNVENMYLYLTHESKDAIAKKKHVYDKADIKLINNFDIDRYVTLDVEEKTELFNVVVSLIRAYTLQNIFDLYDFIDENGETYGLTINLVNEVIAGKTGFMKLLFDGAYQRSKR 203
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203


Chain B from PDB  Type:PROTEIN  Length:201
 aligned with REPB_STRAG | P13921 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:201
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203 
           REPB_STRAG     4 EKARYFTFLLYPESIPSDWELKLETLGVPMAISPLHDKDKSSIKGQKYKKAHYHVLYIAKNPVTADSVRKKIKLLLGEKSLAMVQVVLNVENMYLYLTHESKDAIAKKKHVYDKADIKLINNFDIDRYVTLDVEEKTELFNVVVSLIRAYTLQNIFDLYDFIDENGETYGLTINLVNEVIAGKTGFMKLLFDGAYQRSKRG 204
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeehhhhh..hhhhhhhhh...eee....................eeeeeeeeeeeehhhhhhhhhhhhh.......ee..hhhhhhhhh...hhhhhhh.....hhhhheee...hhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dky B   4 EKARYFTFLLYPESIPSDWELKLETLGVPMAISPLHDKDKSSIKGQKYKKAHYHVLYIAKNPVTADSVRKKIKLLLGEKSLAMVQVVLNVENMYLYLTHESKDAIAKKKHVYDKADIKLINNFDIDRYVTLDVEEKTELFNVVVSLIRAYTLQNIFDLYDFIDENGETYGLTINLVNEVIAGKTGFMKLLFDGAYQRSKRG 204
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203 


Chain C from PDB  Type:PROTEIN  Length:201
 aligned with REPB_STRAG | P13921 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:201
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203 
           REPB_STRAG     4 EKARYFTFLLYPESIPSDWELKLETLGVPMAISPLHDKDKSSIKGQKYKKAHYHVLYIAKNPVTADSVRKKIKLLLGEKSLAMVQVVLNVENMYLYLTHESKDAIAKKKHVYDKADIKLINNFDIDRYVTLDVEEKTELFNVVVSLIRAYTLQNIFDLYDFIDENGETYGLTINLVNEVIAGKTGFMKLLFDGAYQRSKRG 204
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeehhhhh..hhhhhhhhh...eee....................eeeeeeeeeeeehhhhhhhhhhhhh.......ee..hhhhhhhhh...hhhhhhh..........eeehhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dky C   4 EKARYFTFLLYPESIPSDWELKLETLGVPMAISPLHDKDKSSIKGQKYKKAHYHVLYIAKNPVTADSVRKKIKLLLGEKSLAMVQVVLNVENMYLYLTHESKDAIAKKKHVYDKADIKLINNFDIDRYVTLDVEEKTELFNVVVSLIRAYTLQNIFDLYDFIDENGETYGLTINLVNEVIAGKTGFMKLLFDGAYQRSKRG 204
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203 


Chain D from PDB  Type:PROTEIN  Length:189
 aligned with REPB_STRAG | P13921 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:200
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203
           REPB_STRAG     4 EKARYFTFLLYPESIPSDWELKLETLGVPMAISPLHDKDKSSIKGQKYKKAHYHVLYIAKNPVTADSVRKKIKLLLGEKSLAMVQVVLNVENMYLYLTHESKDAIAKKKHVYDKADIKLINNFDIDRYVTLDVEEKTELFNVVVSLIRAYTLQNIFDLYDFIDENGETYGLTINLVNEVIAGKTGFMKLLFDGAYQRSKR 203
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeehhhhh..hhhhhhhhh...eee.......-----------..eeeeeeeeeeeehhhhhhhhhhhhh.......ee..hhhhhhhhh...hhhhhhh..........eeehhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dky D   4 EKARYFTFLLYPESIPSDWELKLETLGVPMAISPLHDKD-----------AHYHVLYIAKNPVTADSVRKKIKLLLGEKSLAMVQVVLNVENMYLYLTHESKDAIAKKKHVYDKADIKLINNFDIDRYVTLDVEEKTELFNVVVSLIRAYTLQNIFDLYDFIDENGETYGLTINLVNEVIAGKTGFMKLLFDGAYQRSKR 203
                                    13        23        33        |-         -|       63        73        83        93       103       113       123       133       143       153       163       173       183       193       203
                                                                 42          54                                                                                                                                                     


Chain E from PDB  Type:PROTEIN  Length:180
 aligned with REPB_STRAG | P13921 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:198
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196        
           REPB_STRAG     7 RYFTFLLYPESIPSDWELKLETLGVPMAISPLHDKDKSSIKGQKYKKAHYHVLYIAKNPVTADSVRKKIKLLLGEKSLAMVQVVLNVENMYLYLTHESKDAIAKKKHVYDKADIKLINNFDIDRYVTLDVEEKTELFNVVVSLIRAYTLQNIFDLYDFIDENGETYGLTINLVNEVIAGKTGFMKLLFDGAYQRSKRG 204
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeehhhhh..hhhhhhhhh...eee.......------------.eeeeee.....hhhhhhhhhhhhhh------.ee..hhhhhhhhh...hhhhhhh..........eeehhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3dky E   7 RYFTFLLYPESIPSDWELKLETLGVPMAISPLHDKD------------HYHVLYIAKNPVTADSVRKKIKLLLG------VQVVLNVENMYLYLTHESKDAIAKKKHVYDKADIKLINNFDIDRYVTLDVEEKTELFNVVVSLIRAYTLQNIFDLYDFIDENGETYGLTINLVNEVIAGKTGFMKLLFDGAYQRSKRG 204
                                    16        26        36     |   -        56        66        76   |     -|       96       106       116       126       136       146       156       166       176       186       196        
                                                              42           55                       80     87                                                                                                                     


Chain F from PDB  Type:PROTEIN  Length:190
 aligned with REPB_STRAG | P13921 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:201
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203 
           REPB_STRAG     4 EKARYFTFLLYPESIPSDWELKLETLGVPMAISPLHDKDKSSIKGQKYKKAHYHVLYIAKNPVTADSVRKKIKLLLGEKSLAMVQVVLNVENMYLYLTHESKDAIAKKKHVYDKADIKLINNFDIDRYVTLDVEEKTELFNVVVSLIRAYTLQNIFDLYDFIDENGETYGLTINLVNEVIAGKTGFMKLLFDGAYQRSKRG 204
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeehhhhh..hhhhhhhhh...eee.......-----------..eeeeeeeeeeeehhhhhhhhhhhhh......eee..hhhhhhhhh...hhhhhhh..........eeehhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dky F   4 EKARYFTFLLYPESIPSDWELKLETLGVPMAISPLHDKD-----------AHYHVLYIAKNPVTADSVRKKIKLLLGEKSLAMVQVVLNVENMYLYLTHESKDAIAKKKHVYDKADIKLINNFDIDRYVTLDVEEKTELFNVVVSLIRAYTLQNIFDLYDFIDENGETYGLTINLVNEVIAGKTGFMKLLFDGAYQRSKRG 204
                                    13        23        33        |-         -|       63        73        83        93       103       113       123       133       143       153       163       173       183       193       203 
                                                                 42          54
   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 3DKY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3DKY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DKY)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (REPB_STRAG | P13921)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003916    DNA topoisomerase activity    Catalysis of the transient cleavage and passage of individual DNA strands or double helices through one another, resulting a topological transformation in double-stranded DNA.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
cellular component
    GO:0005727    extrachromosomal circular DNA    Circular DNA structures that are not part of a chromosome.

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 Related Entries

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

UniProtKB/Swiss-Prot
        REPB_STRAG | P13921: 3dkx 4u87

(-) Related Entries Specified in the PDB File

1ksx X-RAY STRUCTURE OF AN ASSEMBLY INTERMEDIATE OF THE ORIGIN BINDING DOMAIN OF THE E1 PAPILLOMAVIRUS REP WITH THE E1 RECOGNITION DNA SEQUENCE
1ksy X-RAY STRUCTURE OF AN ASSEMBLY INTERMEDIATE OF THE ORIGIN BINDING DOMAIN OF THE E1 PAPILLOMAVIRUS REP WITH THE E1 RECOGNITION DNA SEQUENCE
1l2m MINIMIZED SOLUTION STRUCTURE OF A SIMILAR PROTEIN FROM TOMATO YELLOW LEAF CURL VIRUS (SARDINIA), ORIGIN BINDING DOMAIN ONLY
1rz9 THE ORIGIN BINDING DOMAIN OF ADENO-ASSOCIATED VIRUS (AAV) REP IN COMPLEX WITH THE RECOGNITION DNA SEQUENCE
2gxa X-RAY STRUCTURE OF THE OLIGOMERIZATION AND HELICASE DOMAINS OF THE E1 PAPILLOMAVIRUS REP COMPLEX WITH SSDNA AND MGADP
2hw0 SOLUTION STRUCTURE OF A SIMILAR PROTEIN FROM PORCINE CIRCOVIRUS 2, ORIGIN BINDING DOMAIN ONLY
3dkx TRIGONAL FORM OF FULL-LENGTH PMV158 REPB