1J1V | PD0371 - JenaLib

Title :   CRYSTAL STRUCTURE OF DNAA DOMAINIV COMPLEXED WITH DNAABOX DNA

Authors :   N. Fujikawa, H. Kurumizaka, O. Nureki, T. Terada, M. Shirouzu, T. Katayama, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   18 Dec 02 (Deposition) - 22 Apr 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Protein-Dna Complex, 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, T. Terada, M. Shirouzu, T. Katayama, S. Yokoyama
Structural Basis Of Replication Origin Recognition By The Dnaa Protein
Nucleic Acids Res. V. 31 2077 2003
PubMed-ID: 12682358 | Reference-DOI: 10.1093/NAR/GKG309
(for further references see the PDB file header)

Compounds

*Molecule 1 - 5'-D(TPGPTPTPAPTPCPCPAPCPAPGPG)-3'**
	Chains	:	B
	Engineered	:	YES
	Synonym	:	DNAABOX DNA
	Synthetic	:	YES

*Molecule 2 - 5'-D(CPCPTPGPTPGPGPAPTPAPAPCPA)-3'**
	Chains	:	C
	Engineered	:	YES
	Synonym	:	DNAABOX DNA
	Synthetic	:	YES

Molecule 3 - CHROMOSOMAL REPLICATION INITIATOR PROTEIN DNAA
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	PET15B
	Expression System Vector Type	:	PLASMID
	Fragment	:	DNA BINDING DOMAIN, DNAA DOMAINIV
	Gene	:	DNAA
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS SYSTEM

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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)
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Chain A from PDB  Type:PROTEIN  Length:94
 aligned with DNAA_ECOLI | P03004 from UniProtKB/Swiss-Prot  Length:467

    Alignment length:94
                                   383       393       403       413       423       433       443       453       463    
           DNAA_ECOLI   374 VTIDNIQKTVAEYYKIKVADLLSKRRSRSVARPRQMAMALAKELTNHSLPEIGDAFGGRDHTTVLHACRKIEQLREESHDIKEDFSNLIRTLSS 467
               SCOP domains d1j1va_ A: Chromosomal replication initiation factor DnaA C-terminal domain IV                 SCOP domains
               CATH domains 1j1vA00 A:374-467  [code=1.10.1750.10, no name defined]                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..hhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------DNAA  PDB: A:425-444----------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 1j1v A 374 VTIDNIQKTVAEYYKIKVADLLSKRRSRSVARPRQmAmALAKELTNHSLPEIGDAFGGRDHTTVLHACRKIEQLREESHDIKEDFSNLIRTLSS 467
                                   383       393       403     | 413       423       433       443       453       463    
                                                             409-MSE                                                      
                                                               411-MSE

Chain B from PDB  Type:DNA  Length:13
                                             
                 1j1v B 101 TGTTATCCACAGG 113
                                   110

Chain C from PDB  Type:DNA  Length:13
                                             
                 1j1v C 201 CCTGTGGATAACA 213
                                   210

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Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DNAA_ECOLI | P03004)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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).
	GO:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
	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:0008156	negative regulation of DNA replication	Any process that stops, prevents, or reduces the frequency, rate or extent of DNA replication.
	GO:0006275	regulation of DNA replication	Any process that modulates the frequency, rate or extent of DNA replication.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	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.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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