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(-) Description

Title :  CRYSTAL STRUCTURE OF PRIB- A PRIMOSOMAL DNA REPLICATION PROTEIN OF ESCHERICHIA COLI
 
Authors :  J. -H. Liu, T. -W. Chang, C. -Y. Huang, M. -C. Chang, S. -U. Chen, H. -N. Wu, C. -D. Hsiao
Date :  22 Apr 04  (Deposition) - 25 Oct 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Primosome, Dna Replication, Dna Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. -H. Liu, T. -W. Chang, C. -Y. Huang, S. -U. Chen, H. -N. Wu, M. -C. Chang, C. -D. Hsiao
Crystal Structure Of Prib- A Primosomal Dna Replication Protein Of Escherichia Coli
J. Biol. Chem. V. 279 50465 2004
PubMed-ID: 15383524  |  Reference-DOI: 10.1074/JBC.M406773200

(-) Compounds

Molecule 1 - PRIMOSOMAL REPLICATION PROTEIN N
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B-PRIB
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1CYS3Mod. Amino AcidCYSTEINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:12 , ARG A:13 , VAL A:30 , GLN A:49 , HOH A:2075BINDING SITE FOR RESIDUE CYS A 201
2AC2SOFTWAREPRO A:15 , LEU A:16 , ARG A:17 , CYS A:27 , THR A:63 , HIS A:64 , HOH A:2049 , ARG B:34 , GLN B:45 , HOH B:2032BINDING SITE FOR RESIDUE CYS A 202
3AC3SOFTWARECYS B:12 , ARG B:13 , VAL B:30 , GLN B:49 , HOH B:2058 , HOH B:2059BINDING SITE FOR RESIDUE CYS B 203

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:48 -B:80
2A:80 -B:48

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V1Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V1Q)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SSBPS50935 Single-strand binding (SSB) domain profile.PRIB_ECOLI1-101
 		  2A:1-101
B:1-101

(-) Exons   (0, 0)

(no "Exon" information available for 1V1Q)

(-) 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:113
 aligned with PRIB_ECOLI | P07013 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:113
                                1                                                                                                    104     
                                |    6        16        26        36        46        56        66        76        86        96       | -   
           PRIB_ECOLI     - ----MTNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFISCHKAKNGLSKMVLHAEQIELIDSGD-----   -
               SCOP domains d1v1qa_ A: Primosomal replication protein N, PriB                                                                 SCOP domains
               CATH domains 1v1qA00 A:-4-107 Nucleic acid-binding proteins                                                                 -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeee..eeeeeeeeeeeeee.hhhhhhhh........................eeeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----SSB  PDB: A:1-101 UniProt: 1-101                                                                     -------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1v1q A  -4 PNSLMTNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFISCHKAKNGLSKMVLHAEQIELIDSVDKLACC 202
                               ||    6        16        26        36        46        56        66        76        86        96       106|| 
                              -1|                                                                                                       107| 
                                1                                                                                                        201 


Chain B from PDB  Type:PROTEIN  Length:113
 aligned with PRIB_ECOLI | P07013 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:113
                                   1                                                                                                    104  
                                   | 3        13        23        33        43        53        63        73        83        93       103|  
           PRIB_ECOLI     - -------MTNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFISCHKAKNGLSKMVLHAEQIELIDSGD--   -
               SCOP domains d1v1qb_ B: Primosomal replication protein N, PriB                                                                 SCOP domains
               CATH domains 1v1qB00 B:-7-105 Nucleic acid-binding proteins                                                                  - CATH domains
           Pfam domains (1) --------SSB-1v1qB01 B:2-100                                                                                ------ Pfam domains (1)
           Pfam domains (2) --------SSB-1v1qB02 B:2-100                                                                                ------ Pfam domains (2)
         Sec.struct. author ...hhhhh.eeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeee..eeeeeeeeeeeeee....hhhhh......eeeeeeeee...........eeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------SSB  PDB: B:1-101 UniProt: 1-101                                                                     ----- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1v1q B  -7 GRDPNSLMTNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFISCHKAKNGLSKMVLHAEQIELIDSVDKC 203
                                  || 3        13        23        33        43        53        63        73        83        93       103 ||
                                 -1|                                                                                                     105|
                                   1                                                                                                      203
   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)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: OB (224)

(-) 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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  1v1q
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PRIB_ECOLI | P07013: 1txy 1woc 2ccz 2pnh

(-) Related Entries Specified in the PDB File

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