1IU3 | PD0297 - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE E.COLI SEQA PROTEIN COMPLEXED WITH HEMIMETHYLATED DNA

Authors :   N. Fujikawa, H. Kurumizaka, O. Nureki, Y. Tanaka, M. Yamazoe, S. Hiraga, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   26 Feb 02 (Deposition) - 17 Jun 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym./Biol. Unit : A,B,C,D,E,F

Keywords :   Protein-Dna Complex, Recognition Of Hemimethylated Dna, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Replication Inhibitor/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)

*Molecule 1 - 5'-D(APAPGPGPAPTPCPCPAPA)-3'*
	Chains	:	A, D
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - 5'-D(TPTPGPGPAPTPCPCPTPT)-3'*
	Chains	:	B, E
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - SEQA PROTEIN
	Chains	:	C, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P1
	Expression System Strain	:	DH5A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	DNA BINDING DOMAIN, RESIDUES 71-181
	Gene	:	SEQA
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1IU3)

(no "Site" information available for 1IU3)

(no "SS Bond" information available for 1IU3)

(no "Cis Peptide Bond" information available for 1IU3)

(no "SAP(SNP)/Variant" information available for 1IU3)

(no "PROSITE Motif" information available for 1IU3)

(no "Exon" information available for 1IU3)

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:10
                                          
                 1iu3 A 201 AAGGATCCAA 210
                                   210

Chain B from PDB  Type:DNA  Length:10
                                          
                 1iu3 B 211 TTGGATCCTT 220
                                   220

Chain C 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 d1i      u3c_ C: Replication modulator SeqA, C-terminal DNA-binding domain                                                SCOP domains
               CATH domains 1iu      3C00 C:2-116 Replication modulator SeqA, C-terminal DNA-binding domain                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..h------hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh........ee.hhhhhhhh..............ee....hhhhhhhhhhhhhhhh..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iu3 C   2 PLG------SAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 116
                              |      5        15        25        35        45        55        65        75        85        95       105       115 
                              4      5

Chain C 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 d1i      u3c_ C: Replication modulator SeqA, C-terminal DNA-binding domain                                                SCOP domains
               CATH domains 1iu      3C00 C:2-116 Replication modulator SeqA, C-terminal DNA-binding domain                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..h------hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh........ee.hhhhhhhh..............ee....hhhhhhhhhhhhhhhh..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iu3 C   2 PLG------SAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 116
                              |      5        15        25        35        45        55        65        75        85        95       105       115 
                              4      5

Chain C 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 d1i      u3c_ C: Replication modulator SeqA, C-terminal DNA-binding domain                                                SCOP domains
               CATH domains 1iu      3C00 C:2-116 Replication modulator SeqA, C-terminal DNA-binding domain                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..h------hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh........ee.hhhhhhhh..............ee....hhhhhhhhhhhhhhhh..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iu3 C   2 PLG------SAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 116
                              |      5        15        25        35        45        55        65        75        85        95       105       115 
                              4      5

Chain D from PDB  Type:DNA  Length:10
                                          
                 1iu3 D 201 AAGGATCCAA 210
                                   210

Chain E from PDB  Type:DNA  Length:10
                                          
                 1iu3 E 211 TTGGATCCTT 220
                                   220

Chain F 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 d1i      u3f_ F: Replication modulator SeqA, C-terminal DNA-binding domain                                                SCOP domains
               CATH domains 1iu      3F00 F:2-116 Replication modulator SeqA, C-terminal DNA-binding domain                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..h------hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh........ee.hhhhhhhh..............ee....hhhhhhhhhhhhhhh...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iu3 F   2 PLG------SAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 116
                              |      5        15        25        35        45        55        65        75        85        95       105       115 
                              4      5

Chain F 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 d1i      u3f_ F: Replication modulator SeqA, C-terminal DNA-binding domain                                                SCOP domains
               CATH domains 1iu      3F00 F:2-116 Replication modulator SeqA, C-terminal DNA-binding domain                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..h------hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh........ee.hhhhhhhh..............ee....hhhhhhhhhhhhhhh...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iu3 F   2 PLG------SAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 116
                              |      5        15        25        35        45        55        65        75        85        95       105       115 
                              4      5

Chain F 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 d1i      u3f_ F: Replication modulator SeqA, C-terminal DNA-binding domain                                                SCOP domains
               CATH domains 1iu      3F00 F:2-116 Replication modulator SeqA, C-terminal DNA-binding domain                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..h------hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh........ee.hhhhhhhh..............ee....hhhhhhhhhhhhhhh...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iu3 F   2 PLG------SAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 116
                              |      5        15        25        35        45        55        65        75        85        95       105       115 
                              4      5

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Replication modulator SeqA, C-terminal DNA-binding domain (4)

Homologous Superfamily: Replication modulator SeqA, C-terminal DNA-binding domain (4)

[unclassified] (3)

1a	1iu3C00	C:2-116
1b	1iu3F00	F:2-116

(no "Pfam Domain" information available for 1IU3)

Asymmetric/Biological Unit(hide GO term definitions)

Chain C,F (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 C,F (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.

Chain C,F (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.

Asymmetric/Biological Unit
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(no "Sites" information available for 1iu3)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1iu3)

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	1iu3
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	SEQA_ECOL6 \| P0AFY9
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	SEQA_ECOLI \| P0AFY8
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	SEQA_ECOL6 \| P0AFY9
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	SEQA_ECOL6 \| P0AFY9	:	1j3e 1lrr 1xrx
	SEQA_ECOLI \| P0AFY8	:	1j3e 1lrr 1xrx 2ch3 3fmt
	SEQA_SHIFL \| P0AFZ0	:	1j3e 1lrr 1xrx

(no "Related Entries Specified in the PDB File" available for 1IU3)

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SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (15, 25)

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