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(-) Description

Title :  CRYSTAL STRUCTURE OF REPLICATION INITIATOR PROTEIN REPE54 OF MINI-F PLASMID COMPLEXED WITH AN ITERON DNA
 
Authors :  H. Komori, F. Matsunaga, Y. Higuchi, M. Ishiai, C. Wada, K. Miki
Date :  29 Apr 99  (Deposition) - 09 Feb 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Replication Initiator, Dna-Binding, , Replication/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Komori, F. Matsunaga, Y. Higuchi, M. Ishiai, C. Wada, K. Miki
Crystal Structure Of A Prokaryotic Replication Initiator Protein Bound To Dna At 2. 6 A Resolution.
Embo J. V. 18 4597 1999
PubMed-ID: 10469640  |  Reference-DOI: 10.1093/EMBOJ/18.17.4597
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP *AP*GP*T)-3')
    Chains: A
    Engineered: YES
    Synonym: ITERON
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP *GP*GP*T)-3')
    Chains: B
    Engineered: YES
    Synonym: ITERON
    Synthetic: YES
 
Molecule 3 - PROTEIN (REPLICATION INITIATION PROTEIN)
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: HIS-TAGGED PROTEIN
    Synonym: REPE54

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:23 , GLU C:77 , ASP C:81 , HOH C:253 , HOH C:254 , HOH C:255BINDING SITE FOR RESIDUE MG C 252

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1REP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1REP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1REP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1REP)

(-) Exons   (0, 0)

(no "Exon" information available for 1REP)

(-) 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:DNA  Length:21
                                                     
                 1rep A   1 CCTGTGACAAATTGCCCTCAG  21
                                    10        20 


Chain B from PDB  Type:DNA  Length:21
                                                     
                 1rep B  23 CTGAGGGCAATTTGTCACAGG  43
                                    32        42 


Chain C from PDB  Type:PROTEIN  Length:214
 aligned with REPE1_ECOLI | P03856 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:232
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244  
          REPE1_ECOLI    15 SPRIVQSNDLTEAAYSLSRDQKRMLYLFVDQIRKSDGTLQEHDGICEIHVAKYAEIFGLTSAEASKDIRQALKSFAGKEVVFYRPEEDAGDEKGYESFPWFIKRAHSPSRGLYSVHINPYLIPFFIGLQNRFTQFRLSETKEITNPYAMRLYESLCQYRKPDGSGIVSLKIDWIIERYQLPQSYQRMPDFRRRFLQVCVNEINSRTPMRLSYIEKKKGRQTTHIVFSFRDIT 246
               SCOP domains d1repc1 C:15-143 RepE54                                                                                                          d1repc2 C:144-246 RepE54                                                                                SCOP domains
               CATH domains 1repC01 C:15-155 'winged helix' rep      ressor DNA binding domain                                                                           1repC02 C:156-246 'winged helix' repressor DNA binding domain                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhhhh......hhhhhhhhhhhhhhh..------...eeeeehhhhhhh....hhhhhhhhhhhhh.....eee..------------.eee......eeee..eeeee..hhhhhhh.......eeeehhhh.....hhhhhhhhhhh.......eeeeeeehhhhhhh........hhhhhhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rep C  15 SPRIVQSNDLTEAAYSLSRDQKRMLYLFVDQIRKS------HDGICEIHVAKYAEIFGLTSAEASKDIRQALKSFAGKEVVFY------------ESFPWFIKPAHSPSRGLYSVHINPYLIPFFIGLQNRFTQFRLSETKEITNPYAMRLYESLCQYRKPDGSGIVSLKIDWIIERYQLPQSYQRMPDFRRRFLQVCVNEINSRTPMRLSYIEKKKGRQTTHIVFSFRDIT 246
                                    24        34        44    |    - |      64        74        84        94  |      -     | 114       124       134       144       154       164       174       184       194       204       214       224       234       244  
                                                             49     56                                       97          110
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1REP)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain C   (REPE1_ECOLI | P03856)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    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.
    GO:0006270    DNA replication initiation    The process in which DNA-dependent DNA replication is started; this involves the separation of a stretch of the DNA double helix, the recruitment of DNA polymerases and the initiation of polymerase action.
    GO:0006276    plasmid maintenance    The maintenance of the integrity of extrachromosomal plasmid DNA; includes processes that ensure plasmids are retained in the daughter cells after cell division.
cellular component
    GO:0005727    extrachromosomal circular DNA    Circular DNA structures that are not part of a chromosome.

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  1rep
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 Related Entries

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

UniProtKB/Swiss-Prot
        REPE1_ECOLI | P03856: 2z9o

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