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(-) Description

Title :  STRUCTURE OF THE DNAG PRIMASE CATALYTIC DOMAIN BOUND TO SSDNA
 
Authors :  J. E. Corn, J. G. Pelton, J. M. Berger
Date :  19 Oct 07  (Deposition) - 15 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Protein-Dna Complex, Toprim Fold, Dna Replication, Dna-Directed Rna Polymerase, Metal-Binding, Nucleotidyltransferase, Primosome, Transcription, Transferase, Zinc-Finger, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. E. Corn, J. G. Pelton, J. M. Berger
Identification Of A Dna Primase Template Tracking Site Redefines The Geometry Of Primer Synthesis.
Nat. Struct. Mol. Biol. V. 15 163 2008
PubMed-ID: 18193061  |  Reference-DOI: 10.1038/NSMB.1373

(-) Compounds

Molecule 1 - DNA PRIMASE
    Chains: A, B
    EC Number: 2.7.7.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSV271
    Expression System Strain: BL21 CODON+
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RNA POLYMERASE DOMAIN
    Gene: DNAG, DNAP, PARB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
 
Molecule 2 - DNA (5'- D(*DCP*DAP*DAP*DAP*DGP*DCP*DCP*DAP*DAP*DAP*DAP*DGP*DGP*DAP*DC)-3')
    Chains: C, D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3B39)

(-) Sites  (0, 0)

(no "Site" information available for 3B39)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3B39)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:227 -Pro A:228
2Thr B:227 -Pro B:228

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3B39)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TOPRIMPS50880 Toprim domain profile.DNAG_ECOLI259-341
 		  2A:259-341
B:259-341
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TOPRIMPS50880 Toprim domain profile.DNAG_ECOLI259-341
 		  1A:259-341
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TOPRIMPS50880 Toprim domain profile.DNAG_ECOLI259-341
 		  1-
B:259-341

(-) Exons   (0, 0)

(no "Exon" information available for 3B39)

(-) Sequences/Alignments

Asymmetric 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:317
 aligned with DNAG_ECOLI | P0ABS5 from UniProtKB/Swiss-Prot  Length:581

    Alignment length:319
                                   118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418         
           DNAG_ECOLI   109 ERHQRQTLYQLMDGLNTFYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDAGMLVTNDQGRSYDRFRERVMFPIRDKRGRVIGFGGRVLGNDTPKYLNSPETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVASLGTSTTADHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLPDGEDPDTLVRKEGKEAFEARMEQAMPLSAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVPGETLRIYLRQELGNKLGILDDSQL 427
               SCOP domains d3b39a_ A: automated matches                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 3b39A01 A:109-240  [code=3.90.980.10, no name defined]                                                                              3b39A02 A:241-367  [code=3.40.1360.10, no name defined]                                                                        3b39A03 A:368-426  [code=1.20.50.20, no name defined]      - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..eee....hhhhhhhh.hhhhhhhhhhh..eee..--.eee....eeeeeee.....eeeeeeee.......eee.......hhhh.eehhhhhhhhh.....eeee.hhhhhhhhhhh....eeee.....hhhhhhhhhhhh.eeeeeee.hhhhhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------TOPRIM  PDB: A:259-341 UniProt: 259-341                                            -------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b39 A 109 NAHQRQTLYQLMDGLNTFYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDAGMLVTND--RSYDRFRERVMFPIRDKRGRVIGFGGRVLGNDTPKYLNSPETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVASLGTSTTADHIQLLFRATNNVICCYDGDRAGRDAAWCALETALPYMTDGRQLRFMFLPDGEDPDTLVRKEGKEAFEARMEQAMPLSAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVPGETLRIYLRQELGNKLGILDDSQL 427
                                   118       128       138       148       158       168       178       188   |  |198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418         
                                                                                                             192  |                                                                                                                                                                                                                                        
                                                                                                                195                                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:310
 aligned with DNAG_ECOLI | P0ABS5 from UniProtKB/Swiss-Prot  Length:581

    Alignment length:310
                                   118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418
           DNAG_ECOLI   109 ERHQRQTLYQLMDGLNTFYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDAGMLVTNDQGRSYDRFRERVMFPIRDKRGRVIGFGGRVLGNDTPKYLNSPETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVASLGTSTTADHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLPDGEDPDTLVRKEGKEAFEARMEQAMPLSAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVPGETLRIYLRQELGNK 418
               SCOP domains d3b39b_ B: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3b39B01 B:109-240  [code=3.90.980.10, no name defined]                                                                              3b39B02 B:241-367  [code=3.40.1360.10, no name defined]                                                                        3b39B03 B:368-418                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..eee....hhhhhhhh.hhhhhhhhhhh..eee.....eee....eeeeeee.....eeeeeeee.......eee.......hhhh.eehhhhhhhhh.....eeee.hhhhhhhhhhh....eeee.....hhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------TOPRIM  PDB: B:259-341 UniProt: 259-341                                            ----------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b39 B 109 NAHQRQTLYQLMDGLNTFYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDAGMLVTNDQGRSYDRFRERVMFPIRDKRGRVIGFGGRVLGNDTPKYLNSPETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVASLGTSTTADHIQLLFRATNNVICCYDGDRAGRDAAWCALETALPYMTDGRQLRFMFLPDGEDPDTLVRKEGKEAFEARMEQAMPLSAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVPGETLRIYLRQELGNK 418
                                   118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418


Chain C from PDB  Type:DNA  Length:6
                                      
                 3b39 C   2 AAAGCC   7


Chain D from PDB  Type:DNA  Length:8
                                        
                 3b39 D   3 AAGCCAAA  11
                                ||  
                                7|  
                                 9
   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 Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (3, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3B39)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DNAG_ECOLI | P0ABS5)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003896    DNA primase activity    Catalysis of the synthesis of a short RNA primer on a DNA template, providing a free 3'-OH that can be extended by DNA-directed DNA polymerases.
    GO:0003899    DNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

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  3b39
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  2.7.7.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        DNAG_ECOLI | P0ABS5: 1dd9 1dde 1eqn 1t3w 2haj

(-) Related Entries Specified in the PDB File

1dd9 DNAG PRIMASE CATALYTIC CORE
1dde DNAG PRIMASE CATALYTIC CORE
1eqn DNAG PRIMASE CATALYTIC CORE