2Z9O - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE DIMERIC FORM OF REPE IN COMPLEX WITH THE REPE OPERATOR DNA

Authors :   A. Nakamura, C. Wada, K. Miki

Date :   21 Sep 07 (Deposition) - 27 Nov 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.14

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

Keywords :   Replication Initiator, Autogenous Repressor, Protein-Dna Complex, Winged Helix-Turn-Helix, Dna Replication, Dna-Binding, Replication- Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Nakamura, C. Wada, K. Miki
Structural Basis For Regulation Of Bifunctional Roles In Replication Initiator Protein
Proc. Natl. Acad. Sci. Usa V. 104 18484 2007
PubMed-ID: 18000058 | Reference-DOI: 10.1073/PNAS.0705623104

Molecule 1 - REPLICATION INITIATION PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE-9
	Expression System Strain	:	M15
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	REPE
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	PROTEIN REP, PROTEIN E, PROTEIN F4

Molecule 2 - DNA (33-MER)
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - DNA (33-MER)
	Chains	:	D
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2Z9O)

(no "Site" information available for 2Z9O)

(no "SS Bond" information available for 2Z9O)

(no "Cis Peptide Bond" information available for 2Z9O)

(no "SAP(SNP)/Variant" information available for 2Z9O)

(no "PROSITE Motif" information available for 2Z9O)

(no "Exon" information available for 2Z9O)

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:222
 aligned with REPE1_ECOLI | P03856 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:231
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250 
          REPE1_ECOLI    21 SNDLTEAAYSLSRDQKRMLYLFVDQIRKSDGTLQEHDGICEIHVAKYAEIFGLTSAEASKDIRQALKSFAGKEVVFYRPEEDAGDEKGYESFPWFIKRAHSPSRGLYSVHINPYLIPFFIGLQNRFTQFRLSETKEITNPYAMRLYESLCQYRKPDGSGIVSLKIDWIIERYQLPQSYQRMPDFRRRFLQVCVNEINSRTPMRLSYIEKKKGRQTTHIVFSFRDITSMTTG 251
               SCOP domains d2z9oa1 A:21-143 RepE54                                                                                                    d2z9oa2 A:144-251 RepE54                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh..hhhhhhhhhhhhh..---------..eee..hhhhhhhh...hhhhhhhhhhhhhhh....eeeee.........eeeee..eeeeeee....eeeeee.hhhhhhhhhhhhhhhhh.hhh......hhhhhhhhhhhhh....eeeeeeeehhhhhhhh...hhhh.hhhhhhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z9o A  21 SNDLTEAAYSLSRDQKRMLYLFVDQIR---------DGICEIHVAKYAEIFGLTSAEASKDIRQALKSFAGKEVVFYRPEEDAGDEKGYESFPWFIKRAHSPSRGLYSVHINPYLIPFFIGLQNRFTQFRLSETKEITNPYAMRLYESLCQYRKPDGSGIVSLKIDWIIERYQLPQSYQRMPDFRRRFLQVCVNEINSRTPMRLSYIEKKKGRQTTHIVFSFRDITSMTTG 251
                                    30        40      |  -      | 60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250 
                                                     47        57

Chain B from PDB  Type:PROTEIN  Length:218
 aligned with REPE1_ECOLI | P03856 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:228
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239        
          REPE1_ECOLI    20 QSNDLTEAAYSLSRDQKRMLYLFVDQIRKSDGTLQEHDGICEIHVAKYAEIFGLTSAEASKDIRQALKSFAGKEVVFYRPEEDAGDEKGYESFPWFIKRAHSPSRGLYSVHINPYLIPFFIGLQNRFTQFRLSETKEITNPYAMRLYESLCQYRKPDGSGIVSLKIDWIIERYQLPQSYQRMPDFRRRFLQVCVNEINSRTPMRLSYIEKKKGRQTTHIVFSFRDITS 247
               SCOP domains d2z9ob1 B:20-143 RepE54                                                                                                     d2z9ob2 B:144-247 RepE54                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) Rep_3-2z9oB01 B:20-242                                                                                                                                                                                                         ----- Pfam domains (1)
           Pfam domains (2) Rep_3-2z9oB02 B:20-242                                                                                                                                                                                                         ----- Pfam domains (2)
         Sec.struct. author ...hhhhhhhh..hhhhhhhhhhhhh.----------..eeeeehhhhhhhh...hhhhhhhhhhhhhhhh...eeeee.........eeeee...eeeee.....eeeeee.hhhhhhhhhhhhhhhhh.hhhh.....hhhhhhhhhhh........eeeeee.hhhhhh....hhhh.hhhhhhhhhhhhhhhhhh......eeeeee....eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2z9o B  20 QSNDLTEAAYSLSRDQKRMLYLFVDQI----------DGICEIHVAKYAEIFGLTSAEASKDIRQALKSFAGKEVVFYRPEEDAGDEKGYESFPWFIKRAHSPSRGLYSVHINPYLIPFFIGLQNRFTQFRLSETKEITNPYAMRLYESLCQYRKPDGSGIVSLKIDWIIERYQLPQSYQRMPDFRRRFLQVCVNEINSRTPMRLSYIEKKKGRQTTHIVFSFRDITS 247
                                    29        39      |  -       |59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239        
                                                     46         57

Chain C from PDB  Type:DNA  Length:33
                                                                 
                 2z9o C   1 TTAGTGTGACAATCTAAAAACTTGTCACACTTC  33
                                    10        20        30

Chain D from PDB  Type:DNA  Length:33
                                                                 
                 2z9o D  34 GAAGTGTGACAAGTTTTTAGATTGTCACACTAA  66
                                    43        53        63

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: Winged helix DNA-binding domain (576)

Family: Replication initiation protein (4)

Protein domain: RepE54 (2)

Escherichia coli, mini-F plasmid [TaxId: 562] (2)

1a	d2z9oa1	A:21-143
1b	d2z9oa2	A:144-251
1c	d2z9ob1	B:20-143
1d	d2z9ob2	B:144-247

(no "CATH Domain" information available for 2Z9O)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: Rep_3 (2)

Escherichia coli (strain K12) (1)

1a	Rep_3-2z9oB01	B:20-242
1b	Rep_3-2z9oB02	B:20-242

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric/Biological Unit
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	2z9o
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	REPE1_ECOLI \| P03856
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	REPE1_ECOLI \| P03856	:	1rep

(no "Related Entries Specified in the PDB File" available for 2Z9O)

Description

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Ligands, Modified Residues, Ions (0, 0)

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