1LRR | PD0315 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

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

Authors :   A. Guarne, Q. Zhao, R. Guirlando, W. Yang

Date :   15 May 02 (Deposition) - 11 Dec 02 (Release) - 29 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.65

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: D,E,F  (1x)

Keywords :   Protein-Dna Complex, Replication, Methylated Gatc, Replication Inhibitor-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Guarne, Q. Zhao, R. Guirlando, W. Yang
Insights Into Negative Modulation Of E. Coli Replication Initiation From The Structure Of Seqa-Hemimethylated Dna Complex
Nat. Struct. Biol. V. 9 839 2002
PubMed-ID: 12379844

*Molecule 1 - 5'-D(CPAPCPCPGPAPTPCPGPAPCPT)-3'*
	Chains	:	B, E
	Engineered	:	YES
	Other Details	:	SYNTHETIC OLIGONUCLOTIDE
	Synthetic	:	YES

*Molecule 2 - 5'-D(APGPTPCPGP(6MA)PTPCPGPGPTPG)-3'*
	Chains	:	C, F
	Engineered	:	YES
	Other Details	:	SYNTHETIC OLIGONUCLOTIDE
	Synthetic	:	YES

Molecule 3 - SEQA PROTEIN
	Chains	:	A, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 51-181
	Gene	:	SEQA
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	6MA	2	Mod. Nucleotide	N6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	6MA	1	Mod. Nucleotide	N6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	6MA	1	Mod. Nucleotide	N6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE

(no "Site" information available for 1LRR)

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

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

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

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

(no "Exon" information available for 1LRR)

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:118
 aligned with SEQA_ECOL6 | P0AFY9 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:118
                                    73        83        93       103       113       123       133       143       153       163       173        
           SEQA_ECOL6    64 TIKDKVRAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 181
               SCOP domains d1lrra_ A: Replication modulator SeqA, C-terminal DNA-binding domain                                                   SCOP domains
               CATH domains 1lrrA00 A:64-181 Replication modulator SeqA, C-terminal DNA-binding domain                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh........ee.hhhhhhhhh.....ee......ee....hhhhhhhhhhhhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1lrr A  64 TIKDKVRAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 181
                                    73        83        93       103       113       123       133       143       153       163       173

Chain A from PDB  Type:PROTEIN  Length:118
 aligned with SEQA_ECOLI | P0AFY8 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:118
                                    73        83        93       103       113       123       133       143       153       163       173        
           SEQA_ECOLI    64 TIKDKVRAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 181
               SCOP domains d1lrra_ A: Replication modulator SeqA, C-terminal DNA-binding domain                                                   SCOP domains
               CATH domains 1lrrA00 A:64-181 Replication modulator SeqA, C-terminal DNA-binding domain                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh........ee.hhhhhhhhh.....ee......ee....hhhhhhhhhhhhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1lrr A  64 TIKDKVRAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 181
                                    73        83        93       103       113       123       133       143       153       163       173

Chain A from PDB  Type:PROTEIN  Length:118
 aligned with SEQA_SHIFL | P0AFZ0 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:118
                                    73        83        93       103       113       123       133       143       153       163       173        
           SEQA_SHIFL    64 TIKDKVRAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 181
               SCOP domains d1lrra_ A: Replication modulator SeqA, C-terminal DNA-binding domain                                                   SCOP domains
               CATH domains 1lrrA00 A:64-181 Replication modulator SeqA, C-terminal DNA-binding domain                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh........ee.hhhhhhhhh.....ee......ee....hhhhhhhhhhhhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1lrr A  64 TIKDKVRAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 181
                                    73        83        93       103       113       123       133       143       153       163       173

Chain B from PDB  Type:DNA  Length:12
                                            
                 1lrr B   1 CACCGATCGACT  12
                                    10

Chain C from PDB  Type:DNA  Length:12
                                            
                 1lrr C   1 AGTCGaTCGGTG  12
                                 |  10  
                                 6-6MA

Chain D from PDB  Type:PROTEIN  Length:118
 aligned with SEQA_ECOL6 | P0AFY9 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:118
                                    73        83        93       103       113       123       133       143       153       163       173        
           SEQA_ECOL6    64 TIKDKVRAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 181
               SCOP domains d1lrrd_ D: Replication modulator SeqA, C-terminal DNA-binding domain                                                   SCOP domains
               CATH domains 1lrrD00 D:64-181 Replication modulator SeqA, C-terminal DNA-binding domain                                             CATH domains
           Pfam domains (1) SeqA-1lrrD01 D:64-181                                                                                                  Pfam domains (1)
           Pfam domains (2) SeqA-1lrrD02 D:64-181                                                                                                  Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh........ee.hhhhhhhh......ee......ee....hhhhhhhhhhhhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1lrr D  64 TIKDKVRAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 181
                                    73        83        93       103       113       123       133       143       153       163       173

Chain D from PDB  Type:PROTEIN  Length:118
 aligned with SEQA_ECOLI | P0AFY8 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:118
                                    73        83        93       103       113       123       133       143       153       163       173        
           SEQA_ECOLI    64 TIKDKVRAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 181
               SCOP domains d1lrrd_ D: Replication modulator SeqA, C-terminal DNA-binding domain                                                   SCOP domains
               CATH domains 1lrrD00 D:64-181 Replication modulator SeqA, C-terminal DNA-binding domain                                             CATH domains
           Pfam domains (1) SeqA-1lrrD01 D:64-181                                                                                                  Pfam domains (1)
           Pfam domains (2) SeqA-1lrrD02 D:64-181                                                                                                  Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh........ee.hhhhhhhh......ee......ee....hhhhhhhhhhhhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1lrr D  64 TIKDKVRAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 181
                                    73        83        93       103       113       123       133       143       153       163       173

Chain D from PDB  Type:PROTEIN  Length:118
 aligned with SEQA_SHIFL | P0AFZ0 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:118
                                    73        83        93       103       113       123       133       143       153       163       173        
           SEQA_SHIFL    64 TIKDKVRAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 181
               SCOP domains d1lrrd_ D: Replication modulator SeqA, C-terminal DNA-binding domain                                                   SCOP domains
               CATH domains 1lrrD00 D:64-181 Replication modulator SeqA, C-terminal DNA-binding domain                                             CATH domains
           Pfam domains (1) SeqA-1lrrD01 D:64-181                                                                                                  Pfam domains (1)
           Pfam domains (2) SeqA-1lrrD02 D:64-181                                                                                                  Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh........ee.hhhhhhhh......ee......ee....hhhhhhhhhhhhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1lrr D  64 TIKDKVRAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 181
                                    73        83        93       103       113       123       133       143       153       163       173

Chain E from PDB  Type:DNA  Length:12
                                            
                 1lrr E   1 CACCGATCGACT  12
                                    10

Chain F from PDB  Type:DNA  Length:12
                                            
                 1lrr F   1 AGTCGaTCGGTG  12
                                 |  10  
                                 6-6MA

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 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	1lrrA00	A:64-181
1b	1lrrD00	D:64-181

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: SeqA] (2)

Family: SeqA (2)

Escherichia coli O6 (2)

1a	SeqA-1lrrD01	D:64-181
1b	SeqA-1lrrD02	D:64-181

Asymmetric Unit(hide GO term definitions)

Chain A,D (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,D (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,D (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.

Asymmetric Unit
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	1lrr
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(no "Related Entries Specified in the PDB File" available for 1LRR)

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Ligands, Modified Residues, Ions (1, 2)

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