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(-) Description

Title :  CRYSTAL STRUCTURE OF THE E.COLI SEQA PROTEIN COMPLEXED WITH N6-METHYLADENINE- GUANINE MISMATCH DNA
 
Authors :  N. Fujikawa, H. Kurumizaka, O. Nureki, Y. Tanaka, M. Yamazoe, S. Hiraga, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  24 Jan 03  (Deposition) - 18 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Protein-Dna Complex, Recognition Of Hemimethylated Dna, Mismatched Dna, Replication, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Replication/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Fujikawa, H. Kurumizaka, O. Nureki, Y. Tanaka, M. Yamazoe, S. Hiraga, S. Yokoyama
Structural And Biochemical Analyses Of Hemimethylated Dna Binding By The Seqa Protein
Nucleic Acids Res. V. 32 82 2004
PubMed-ID: 14704346  |  Reference-DOI: 10.1093/NAR/GKH173
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*AP*AP*GP*GP*(6MA)P*TP*CP*CP*AP*A)-3'
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-D(*TP*TP*GP*GP*AP*GP*CP*CP*TP*T)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - SEQA PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX6P-1
    Expression System Strain: DH5A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DNA BINDING DOMAIN
    Gene: SEQA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 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
16MA1Mod. NucleotideN6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 1J3E)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:92 -A:113

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1J3E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J3E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J3E)

(-) Exons   (0, 0)

(no "Exon" information available for 1J3E)

(-) 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:115
 aligned with SEQA_ECOL6 | P0AFY9 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:121
                                    70        80        90       100       110       120       130       140       150       160       170       180 
           SEQA_ECOL6    61 PVKTIKDKVRAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 181
               SCOP domains d1j      3ea_ A: Replication modulator SeqA, C-terminal DNA-binding domain                                                SCOP domains
               CATH domains 1j3      eA00 A:2-116 Replication modulator SeqA, C-terminal DNA-binding domain                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhh------hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh........ee..hhhhhhh......ee......ee....hhhhhhhhhhhhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j3e A   2 PLG------SAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 116
                              |      5        15        25        35        45        55        65        75        85        95       105       115 
                              4      5                                                                                                               


Chain A from PDB  Type:PROTEIN  Length:115
 aligned with SEQA_ECOLI | P0AFY8 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:121
                                    70        80        90       100       110       120       130       140       150       160       170       180 
           SEQA_ECOLI    61 PVKTIKDKVRAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 181
               SCOP domains d1j      3ea_ A: Replication modulator SeqA, C-terminal DNA-binding domain                                                SCOP domains
               CATH domains 1j3      eA00 A:2-116 Replication modulator SeqA, C-terminal DNA-binding domain                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhh------hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh........ee..hhhhhhh......ee......ee....hhhhhhhhhhhhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j3e A   2 PLG------SAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 116
                              |      5        15        25        35        45        55        65        75        85        95       105       115 
                              4      5                                                                                                               


Chain A from PDB  Type:PROTEIN  Length:115
 aligned with SEQA_SHIFL | P0AFZ0 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:121
                                    70        80        90       100       110       120       130       140       150       160       170       180 
           SEQA_SHIFL    61 PVKTIKDKVRAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 181
               SCOP domains d1j      3ea_ A: Replication modulator SeqA, C-terminal DNA-binding domain                                                SCOP domains
               CATH domains 1j3      eA00 A:2-116 Replication modulator SeqA, C-terminal DNA-binding domain                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhh------hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh........ee..hhhhhhh......ee......ee....hhhhhhhhhhhhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j3e A   2 PLG------SAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 116
                              |      5        15        25        35        45        55        65        75        85        95       105       115 
                              4      5                                                                                                               


Chain B from PDB  Type:DNA  Length:10
                                          
                 1j3e B 201 AAGGaTCCAA 210
                                |  210
                              205-6MA 


Chain C from PDB  Type:DNA  Length:10
                                          
                 1j3e C 211 TTGGAGCCTT 220
                                   220
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J3E)

(-) Gene Ontology  (15, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SEQA_ECOL6 | P0AFY9)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0008156    negative regulation of DNA replication    Any process that stops, prevents, or reduces the frequency, rate or extent of DNA replication.
    GO:0032297    negative regulation of DNA-dependent DNA replication initiation    Any process that stops, prevents, or reduces the frequency, rate or extent of initiation of DNA-dependent DNA replication.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A   (SEQA_ECOLI | P0AFY8)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003688    DNA replication origin binding    Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally.
    GO:0010385    double-stranded methylated DNA binding    Interacting selectively and non-covalently with double-stranded methylated DNA. Methylation of cytosine or adenine in DNA is an important mechanism for establishing stable heritable epigenetic marks.
    GO:0044729    hemi-methylated DNA-binding    Interacting selectively and non-covalently with double-stranded hemi-methylated DNA at replication foci (one strand methylated, while the other strand is unmethylated). Methylation of cytosine or adenine in DNA is an important mechanism for establishing stable heritable epigenetic marks.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0008156    negative regulation of DNA replication    Any process that stops, prevents, or reduces the frequency, rate or extent of DNA replication.
    GO:0032297    negative regulation of DNA-dependent DNA replication initiation    Any process that stops, prevents, or reduces the frequency, rate or extent of initiation of DNA-dependent DNA replication.
    GO:0090143    nucleoid organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleoid. The nucleoid is the region of a bacterial cell, virion, mitochondrion or chloroplast to which the DNA is confined.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007062    sister chromatid cohesion    The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other.
cellular component
    GO:1990097    SeqA-DNA complex    A protein-DNA complex that contains an oligomer of SeqA bound to GATC sites in methylated or newly-synthesized, hemi-methylated double-stranded DNA, with preference for the latter. Binding of SeqA to hemimethylated DNA sequesters oriC, prevents re-methylation of DNA by Dam and in turn stops premature re-initiation of replication during one replication cycle.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain A   (SEQA_SHIFL | P0AFZ0)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0008156    negative regulation of DNA replication    Any process that stops, prevents, or reduces the frequency, rate or extent of DNA replication.
    GO:0032297    negative regulation of DNA-dependent DNA replication initiation    Any process that stops, prevents, or reduces the frequency, rate or extent of initiation of DNA-dependent DNA replication.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SEQA_ECOL6 | P0AFY9: 1iu3 1lrr 1xrx
        SEQA_ECOLI | P0AFY8: 1iu3 1lrr 1xrx 2ch3 3fmt
        SEQA_SHIFL | P0AFZ0: 1iu3 1lrr 1xrx

(-) Related Entries Specified in the PDB File

1iu3 RELATED ID: TRT001000146.2 RELATED DB: TARGETDB