3K8A - JenaLib

Title :   NEISSERIA GONORRHOEAE PRIB

Authors :   M. E. Lopper, J. Dong, N. P. George, K. L. Duckett, M. A. Debeer

Date :   14 Oct 09 (Deposition) - 12 Jan 10 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Beta-Barrel, Ob-Fold, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Dong, N. P. George, K. L. Duckett, M. A. Debeer, M. E. Lopper
The Crystal Structure Of Neisseria Gonorrhoeae Prib Reveals Mechanistic Differences Among Bacterial Dna Replication Restart Pathways
Nucleic Acids Res. V. 38 499 2010
PubMed-ID: 19906704 | Reference-DOI: 10.1093/NAR/GKP1031

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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:100
 aligned with PRIB_NEIG1 | Q5F924 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:100
                                    10        20        30        40        50        60        70        80        90       100
           PRIB_NEIG1     1 MGFTNLVSLAALIEKAFPIRYTPAGIPVLDIILKHESWQEENGQQCLVQLEIPARILGRQAEEWQYRQGDCATVEGFLAQKSRRSLMPMLRIQNIKEYKG 100
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeee...ee.....eeeeeeeeeeeeeee..eeeeeeeeeeeeeehhhhhhh......eeeeeeeeee.......eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SSB  PDB: A:4-99 UniProt: 4-99                                                                  - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 3k8a A   1 MGFTNLVSLAALIEKAFPIRYTPAGIPVLDIILKHESWQEENGQQCLVQLEIPARILGRQAEEWQYRQGDCATVEGFLAQKSRRSLMPMLRIQNIKEYKG 100
                                    10        20        30        40        50        60        70        80        90       100

Chain B from PDB  Type:PROTEIN  Length:103
 aligned with PRIB_NEIG1 | Q5F924 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:103
                               1                                                                                                   
                               |     7        17        27        37        47        57        67        77        87        97   
           PRIB_NEIG1     - ---MGFTNLVSLAALIEKAFPIRYTPAGIPVLDIILKHESWQEENGQQCLVQLEIPARILGRQAEEWQYRQGDCATVEGFLAQKSRRSLMPMLRIQNIKEYKG 100
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeee...ee.....eeeeeeeeeeeeeee..eeeeeeeeeeeeeehhhhhhh......eeeeeeeeee.......eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------SSB  PDB: B:4-99 UniProt: 4-99                                                                  - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 3k8a B  -2 GSHMGFTNLVSLAALIEKAFPIRYTPAGIPVLDIILKHESWQEENGQQCLVQLEIPARILGRQAEEWQYRQGDCATVEGFLAQKSRRSLMPMLRIQNIKEYKG 100
                                     7        17        27        37        47        57        67        77        87        97

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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PRIB_NEIG1 | Q5F924)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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: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.
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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