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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF PCNA1 FROM THERMOCOCCUS KODAKARAENSIS TK0535
 
Authors :  J. E. Ladner, Z. Kelman, M. Pan
Date :  24 Feb 10  (Deposition) - 26 Jan 11  (Release) - 20 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Pcna, Dna Processivity Factor, Trimer, Toroidal, Dna Replication, Dna-Binding, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. E. Ladner, M. Pan, J. Hurwitz, Z. Kelman
Crystal Structures Of Two Active Proliferating Cell Nuclear Antigens (Pcnas) Encoded By Thermococcus Kodakaraensis.
Proc. Natl. Acad. Sci. Usa V. 108 2711 2011
PubMed-ID: 21270332  |  Reference-DOI: 10.1073/PNAS.1019179108

(-) Compounds

Molecule 1 - DNA POLYMERASE SLIDING CLAMP 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3) ROSETTA
    Expression System Taxid: 562
    Gene: PCN1, TK0535
    Organism Common: THERMOCOCCUS KODAKARAENSIS
    Organism Scientific: THERMOCOCCUS KODAKARENSIS
    Organism Taxid: 311400
    Synonym: PROLIFERATING CELL NUCLEAR ANTIGEN HOMOLOG 1, PCNA 1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 1 (1, 9)
No.NameCountTypeFull Name
1SO49Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:55 , LYS A:60 , TYR A:61 , ASP A:153 , ARG A:202 , ARG A:246 , HOH A:268BINDING SITE FOR RESIDUE SO4 A 256
2AC2SOFTWAREARG A:45 , VAL A:46 , LEU A:242 , ALA A:244 , HOH A:295BINDING SITE FOR RESIDUE SO4 A 257
3AC3SOFTWAREGLU A:64 , GLU A:65 , PHE A:130 , THR A:131 , GLU A:190BINDING SITE FOR RESIDUE SO4 A 258

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LX1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LX1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LX1)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PCNA_1PS01251 Proliferating cell nuclear antigen signature 1.PCNA1_THEKO35-58  1A:35-58
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PCNA_1PS01251 Proliferating cell nuclear antigen signature 1.PCNA1_THEKO35-58  3A:35-58

(-) Exons   (0, 0)

(no "Exon" information available for 3LX1)

(-) 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:246
 aligned with PCNA1_THEKO | Q5JF32 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:246
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241      
          PCNA1_THEKO     2 PFEVVFDGAKEFADLIATASNLIDEAAFKFTEEGISMRAMDPSRVVLIDLNLPESIFSKYEVEEPETIGINMDQFKKILKRGKAKDTLILRKGDENFLEITFEGTAKRTFRLPLIDVEELELELPELPFTAKVVLLGEVLKEGIKDASLVSDAIKFIAKENEFTMKAEGETNEVEIRLTLEDEGLLDLEVEEETKSAYGIRYLSDMVKGIGKADEVILRFGNEMPLQMEYMIRDEGRLTFLLAPRV 247
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeehhhhhhhhhhhhhhhh.eeeeee...eeeeeee.....eeeeeeee.hhh.eeee...eeeeeehhhhhhhhh......eeeeee....eeeeeee...eeeeeee.................eeeeeehhhhhhhhhhhhhhh.eeeeeee..eeeeeee....eeeeeee.....eeeeee...eeeeeehhhhhhhhh......eeeeee.....eeeeeee...eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------PCNA_1  PDB: A:35-58    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lx1 A   2 PFEVVFDGAKEFADLIATASNLIDEAAFKFTEEGISMRAMDPSRVVLIDLNLPESIFSKYEVEEPETIGINMDQFKKILKRGKAKDTLILRKGDENFLEITFEGTAKRTFRLPLIDVEELELELPELPFTAKVVLLGEVLKEGIKDASLVSDAIKFIAKENEFTMKAEGETNEVEIRLTLEDEGLLDLEVEEETKSAYGIRYLSDMVKGIGKADEVILRFGNEMPLQMEYMIRDEGRLTFLLAPRV 247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3LX1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LX1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3LX1)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (PCNA1_THEKO | Q5JF32)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0030337    DNA polymerase processivity factor activity    An enzyme regulator activity that increases the processivity of polymerization by DNA polymerase, by allowing the polymerase to move rapidly along DNA while remaining topologically bound to it.
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:0006275    regulation of DNA replication    Any process that modulates the frequency, rate or extent of DNA replication.

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 Related Entries

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UniProtKB/Swiss-Prot
        PCNA1_THEKO | Q5JF32: 5da7 5dai

(-) Related Entries Specified in the PDB File

3lx2