2PNH - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   ESCHERICHIA COLI PRIB E39A VARIANT

Authors :   M. E. Lopper, J. L. Keck

Date :   24 Apr 07 (Deposition) - 07 Aug 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

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

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

Reference :   M. Lopper, R. Boonsombat, S. J. Sandler, J. L. Keck
A Hand-Off Mechanism For Primosome Assembly In Replication Restart.
Mol. Cell V. 26 781 2007
PubMed-ID: 17588514 | Reference-DOI: 10.1016/J.MOLCEL.2007.05.012

Molecule 1 - PRIMOSOMAL REPLICATION PROTEIN N
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PRIB
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2PNH)

Asymmetric/Biological Unit

No.	Residues
1	A:80	-	B:48

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

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SSB	PS50935	Single-strand binding (SSB) domain profile.	PRIB_ECOLI	1-101	2	A:1-100 B:1-100

(no "Exon" information available for 2PNH)

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:96
 aligned with PRIB_ECOLI | P07013 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:100
                                    10        20        30        40        50        60        70        80        90       100
           PRIB_ECOLI     1 MTNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFISCHKAKNGLSKMVLHAEQIELI 100
               SCOP domains d2pnha_ A: automated matches                                                                         SCOP domains
               CATH domains 2pnhA00 A:1-100 Nucleic acid-binding proteins                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeee..eeeeeeeeeeeeee.....hhhhhh....eeeeeeeeeee.----..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE SSB  PDB: A:1-100 UniProt: 1-101                                                                     PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 2pnh A   1 MTNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEAAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFISCHK----LSKMVLHAEQIELI 100
                                    10        20        30        40        50        60        70        80 |    | 90       100
                                                                                                            82   87

Chain B from PDB  Type:PROTEIN  Length:94
 aligned with PRIB_ECOLI | P07013 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:100
                                    10        20        30        40        50        60        70        80        90       100
           PRIB_ECOLI     1 MTNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFISCHKAKNGLSKMVLHAEQIELI 100
               SCOP domains d2pnhb_ B: automated matches                                                                         SCOP domains
               CATH domains 2pnhB00 B:1-100 Nucleic acid-binding proteins                                                        CATH domains
           Pfam domains (1) -SSB-2pnhB01 B:2-100                                                                                 Pfam domains (1)
           Pfam domains (2) -SSB-2pnhB02 B:2-100                                                                                 Pfam domains (2)
         Sec.struct. author ..eeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeee..eeeeeeeeeeeeee......hhhhh....eeeeeeeeee..------.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE SSB  PDB: B:1-100 UniProt: 1-101                                                                     PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 2pnh B   1 MTNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEAAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFISCHK------KMVLHAEQIELI 100
                                    10        20        30        40        50        60        70        80 |      90       100
                                                                                                            82     89

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 beta proteins (24004)

Fold: OB-fold (1179)

Superfamily: Nucleic acid-binding proteins (590)

Family: Single strand DNA-binding domain, SSB (96)

Protein domain: automated matches (30)

Escherichia coli K-12 [TaxId: 83333] (3)

1a	d2pnha_	A:
1b	d2pnhb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P) (1040)

Homologous Superfamily: Nucleic acid-binding proteins (483)

Escherichia coli k12. Organism_taxid: 83333. Strain: k12. (3)

1a	2pnhA00	A:1-100
1b	2pnhB00	B:1-100

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: OB (224)

Family: SSB (18)

Escherichia coli (strain K12) (4)

1a	SSB-2pnhB01	B:2-100
1b	SSB-2pnhB02	B:2-100

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.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
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	2pnh
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	PRIB_ECOLI \| P07013
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	PRIB_ECOLI \| P07013
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	PRIB_ECOLI \| P07013	:	1txy 1v1q 1woc 2ccz

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (9, 9)

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