2CCZ | PD0871 - JenaLib

Title :   CRYSTAL STRUCTURE OF E. COLI PRIMOSOMOL PROTEIN PRIB BOUND TO SSDNA

Authors :   C. -Y. Huang, C. -H. Hsu, H. -N. Wu, Y. -J. Sun, C. -D. Hsiao

Date :   19 Jan 06 (Deposition) - 18 Sep 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Dna/Replication, Primosome, Prib, Dna Replication, Dna Repair, Dna Recombination, Ssdna, Single-Stranded Dna, Dna/Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. -Y. Huang, C. -H. Hsu, Y. -J. Sun, H. -N. Wu, C. -D. Hsiao
Complexed Crystal Structure Of Replication Restart Primsome Protein Prib Reveals A Novel Single-Stranded Dna-Binding Mode.
Nucleic Acids Res. V. 34 3878 2006
PubMed-ID: 16899446 | Reference-DOI: 10.1093/NAR/GKL536

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (2, 2)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

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)
	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:122
 aligned with PRIB_ECOLI | P07013 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:122
                                  1                                                                                                    104            
                                  |  4        14        24        34        44        54        64        74        84        94       104         -  
           PRIB_ECOLI     - ------MTNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFISCHKAKNGLSKMVLHAEQIELIDSGD------------   -
               SCOP domains d2ccza_ A: automated matches                                                                                               SCOP domains
               CATH domains 2cczA00 A:-6-116 Nucleic acid-binding proteins                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeee..eeeeeeeeeeeeee...hhhhhhh.....eeeeee.ee...........eee..eeee..hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------SSB  PDB: A:1-101 UniProt: 1-101                                                                     --------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ccz A  -6 MDPNSLMTNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFISCHKAKNGLSKMVLHAEQIELIDSVDKLAAALEHHHHH 116
                                 ||  4        14        24        34        44        54        64        74        84        94       104       114  
                                -1|                                                                                                                   
                                  1

Chain B from PDB  Type:PROTEIN  Length:119
 aligned with PRIB_ECOLI | P07013 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:119
                                1                                                                                                    104           
                                |    6        16        26        36        46        56        66        76        86        96       | -         
           PRIB_ECOLI     - ----MTNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFISCHKAKNGLSKMVLHAEQIELIDSGD-----------   -
               SCOP domains d2cczb_ B: automated matches                                                                                            SCOP domains
               CATH domains 2cczB00 B:-4-115 Nucleic acid-binding proteins                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee............................................hhhhhhhhh...................................hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----SSB  PDB: B:1-101 UniProt: 1-101                                                                     -------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 2ccz B  -4 PNSLMTNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFISCHKAKNGLSKMVLHAEQIELIDSVDKLAAALEHHHH 115
                               ||    6        16        26        36        46        56        66        76        86        96       106         
                              -1|                                                                                                                  
                                1

Chain C from PDB  Type:DNA  Length:15
                                               
                 2ccz C   1 TTTTTTTTTTTTTTT  15
                                    10

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, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PRIB_ECOLI | P07013)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0003697	single-stranded DNA binding	Interacting selectively and non-covalently with single-stranded DNA.
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:0006269	DNA replication, synthesis of RNA primer	The synthesis of a short RNA polymer, usually 4-15 nucleotides long, using one strand of unwound DNA as a template; the RNA then serves as a primer from which DNA polymerases extend synthesis.
	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:1990077	primosome complex	Any of a family of protein complexes that form at the origin of replication or stalled replication forks and function in replication primer synthesis in all organisms. Early complexes initiate double-stranded DNA unwinding. The core unit consists of a replicative helicase and a primase. The helicase further unwinds the DNA and recruits the polymerase machinery. The primase synthesizes RNA primers that act as templates for complementary stand replication by the polymerase machinery. The primosome contains a number of associated proteins and protein complexes and contributes to the processes of replication initiation, lagging strand elongation, and replication restart.
	GO:0030894	replisome	A multi-component enzymatic machine at the replication fork which mediates DNA replication. Includes DNA primase, one or more DNA polymerases, DNA helicases, and other proteins.

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	Cis Peptide Bonds
		Ala B:14 - Pro B:15	[ RasMol ]

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