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(-)Asym./Biol. Unit
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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  A CONSERVED PROTEIN BINDING-SITE ON BACTERIAL SLIDING CLAMPS
 
Authors :  D. Y. Burnouf, V. Olieric, J. Wagner, S. Fujii, J. Reinbolt, R. P. P. Fuch P. Dumas
Date :  18 Jul 03  (Deposition) - 15 Jul 04  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Transferase, Dna Polymerase Iv, Peptide Inhibition, Sliding Clamp, Translesion Synthesis, Transferase; Dna-Directed Dna Polymerase, Dna Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Y. Burnouf, V. Olieric, J. Wagner, S. Fujii, J. Reinbolt, R. P. P. Fuchs, P. Dumas
Structural And Biochemical Analysis Of Sliding Clamp/Ligand Interactions Suggest A Competition Between Replicative And Translesion Dna Polymerases
J. Mol. Biol. V. 335 1187 2004
PubMed-ID: 14729336  |  Reference-DOI: 10.1016/J.JMB.2003.11.049
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA POLYMERASE III
    Chains: A, B
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: ESCHERICHIA COLI
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: DNAN GENE
    Synonym: POLYMERASE, DNAN, B3701, C4623, Z5192, ECS4636
 
Molecule 2 - DNA POLYMERASE IV
    Chains: C
    EC Number: 2.7.7.7
    Fragment: C-TERMINUS OF DNA POL IV RESIDUES 336-351
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: C-TERMINUS (16 RESIDUES) OF DNA POL IV E.COLI
    Synonym: POL IV
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1OK7)

(-) Sites  (0, 0)

(no "Site" information available for 1OK7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OK7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OK7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OK7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OK7)

(-) Exons   (0, 0)

(no "Exon" information available for 1OK7)

(-) 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:366
 aligned with DPO3B_ECO57 | P0A990 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:366
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360      
          DPO3B_ECO57     1 MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL 366
               SCOP domains d1ok7a1 A:1-122 DNA polymerase III, beta subunit                                                                          d1ok7a2 A:123-244 DNA polymerase III, beta subunit                                                                        d1ok7a3 A:245-366 DNA polymerase III, beta subunit                                                                         SCOP domains
               CATH domains 1ok7A01 A:1-123 DNA Polymerase III, subunit A, domain 2                                                                    1ok7A02 A:124-247 DNA Polymerase III, subunit A, domain 2                                                                   1ok7A03 A:248-366 DNA Polymerase III, subunit A, domain 2                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhhh.......hhhh.eeeeeee..eeeeeee...eeeeeeee.......eeeeeehhhhhhhhhhh....eeeeeee..eeeeee..eeeeee..hhhhh.......eeeeeeeehhhhhhhhhhhhhhh.....hhhh.eeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeeehhhhhhhhhh......eeeeeee..eeeeee..eeeeee.......hhhhh......eeeeeehhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeeeeee.......eeeeeehhhhhhhhhhhh..eeeeee......eeeee..eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ok7 A   1 MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL 366
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360      


Chain A from PDB  Type:PROTEIN  Length:366
 aligned with DPO3B_ECOL6 | P0A989 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:366
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360      
          DPO3B_ECOL6     1 MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL 366
               SCOP domains d1ok7a1 A:1-122 DNA polymerase III, beta subunit                                                                          d1ok7a2 A:123-244 DNA polymerase III, beta subunit                                                                        d1ok7a3 A:245-366 DNA polymerase III, beta subunit                                                                         SCOP domains
               CATH domains 1ok7A01 A:1-123 DNA Polymerase III, subunit A, domain 2                                                                    1ok7A02 A:124-247 DNA Polymerase III, subunit A, domain 2                                                                   1ok7A03 A:248-366 DNA Polymerase III, subunit A, domain 2                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhhh.......hhhh.eeeeeee..eeeeeee...eeeeeeee.......eeeeeehhhhhhhhhhh....eeeeeee..eeeeee..eeeeee..hhhhh.......eeeeeeeehhhhhhhhhhhhhhh.....hhhh.eeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeeehhhhhhhhhh......eeeeeee..eeeeee..eeeeee.......hhhhh......eeeeeehhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeeeeee.......eeeeeehhhhhhhhhhhh..eeeeee......eeeee..eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ok7 A   1 MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL 366
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360      


Chain A from PDB  Type:PROTEIN  Length:366
 aligned with DPO3B_ECOLI | P0A988 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:366
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360      
          DPO3B_ECOLI     1 MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL 366
               SCOP domains d1ok7a1 A:1-122 DNA polymerase III, beta subunit                                                                          d1ok7a2 A:123-244 DNA polymerase III, beta subunit                                                                        d1ok7a3 A:245-366 DNA polymerase III, beta subunit                                                                         SCOP domains
               CATH domains 1ok7A01 A:1-123 DNA Polymerase III, subunit A, domain 2                                                                    1ok7A02 A:124-247 DNA Polymerase III, subunit A, domain 2                                                                   1ok7A03 A:248-366 DNA Polymerase III, subunit A, domain 2                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhhh.......hhhh.eeeeeee..eeeeeee...eeeeeeee.......eeeeeehhhhhhhhhhh....eeeeeee..eeeeee..eeeeee..hhhhh.......eeeeeeeehhhhhhhhhhhhhhh.....hhhh.eeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeeehhhhhhhhhh......eeeeeee..eeeeee..eeeeee.......hhhhh......eeeeeehhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeeeeee.......eeeeeehhhhhhhhhhhh..eeeeee......eeeee..eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ok7 A   1 MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL 366
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360      


Chain B from PDB  Type:PROTEIN  Length:366
 aligned with DPO3B_ECO57 | P0A990 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:366
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360      
          DPO3B_ECO57     1 MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL 366
               SCOP domains d1ok7b1 B:1-122 DNA polymerase III, beta subunit                                                                          d1ok7b2 B:123-244 DNA polymerase III, beta subunit                                                                        d1ok7b3 B:245-366 DNA polymerase III, beta subunit                                                                         SCOP domains
               CATH domains 1ok7B01 B:1-123 DNA Polymerase III, subunit A, domain 2                                                                    1ok7B02 B:124-247 DNA Polymerase III, subunit A, domain 2                                                                   1ok7B03 B:248-366 DNA Polymerase III, subunit A, domain 2                                                               CATH domains
           Pfam domains (1) DNA_pol3_beta-1ok7B01 B:1-120                                                                                           --------DNA_pol3_beta_2-1ok7B03 B:129-243                                                                                  -DNA_pol3_beta_3-1ok7B05 B:245-365                                                                                        - Pfam domains (1)
           Pfam domains (2) DNA_pol3_beta-1ok7B02 B:1-120                                                                                           --------DNA_pol3_beta_2-1ok7B04 B:129-243                                                                                  -DNA_pol3_beta_3-1ok7B06 B:245-365                                                                                        - Pfam domains (2)
         Sec.struct. author .eeeeehhhhhhhhhhhh........hhhh.eeeeeee..eeeeeee...eeeeeeee.......eeeeeehhhhhhhhhhh....eeeeeee..eeeeee..eeeeee..hhhhh.........eeeeehhhhhhhhhhhhhhhh.....hhhhhheeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeehhhhhhhhhhh.......eeeee...eeeeee..eeeeee.......hhhhhh.....eeeeeehhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeeeeee.......eeeeeehhhhhhhhhhh...eeeeee......eeeee..eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ok7 B   1 MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL 366
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360      


Chain B from PDB  Type:PROTEIN  Length:366
 aligned with DPO3B_ECOL6 | P0A989 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:366
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360      
          DPO3B_ECOL6     1 MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL 366
               SCOP domains d1ok7b1 B:1-122 DNA polymerase III, beta subunit                                                                          d1ok7b2 B:123-244 DNA polymerase III, beta subunit                                                                        d1ok7b3 B:245-366 DNA polymerase III, beta subunit                                                                         SCOP domains
               CATH domains 1ok7B01 B:1-123 DNA Polymerase III, subunit A, domain 2                                                                    1ok7B02 B:124-247 DNA Polymerase III, subunit A, domain 2                                                                   1ok7B03 B:248-366 DNA Polymerase III, subunit A, domain 2                                                               CATH domains
           Pfam domains (1) DNA_pol3_beta-1ok7B01 B:1-120                                                                                           --------DNA_pol3_beta_2-1ok7B03 B:129-243                                                                                  -DNA_pol3_beta_3-1ok7B05 B:245-365                                                                                        - Pfam domains (1)
           Pfam domains (2) DNA_pol3_beta-1ok7B02 B:1-120                                                                                           --------DNA_pol3_beta_2-1ok7B04 B:129-243                                                                                  -DNA_pol3_beta_3-1ok7B06 B:245-365                                                                                        - Pfam domains (2)
         Sec.struct. author .eeeeehhhhhhhhhhhh........hhhh.eeeeeee..eeeeeee...eeeeeeee.......eeeeeehhhhhhhhhhh....eeeeeee..eeeeee..eeeeee..hhhhh.........eeeeehhhhhhhhhhhhhhhh.....hhhhhheeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeehhhhhhhhhhh.......eeeee...eeeeee..eeeeee.......hhhhhh.....eeeeeehhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeeeeee.......eeeeeehhhhhhhhhhh...eeeeee......eeeee..eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ok7 B   1 MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL 366
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360      


Chain B from PDB  Type:PROTEIN  Length:366
 aligned with DPO3B_ECOLI | P0A988 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:366
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360      
          DPO3B_ECOLI     1 MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL 366
               SCOP domains d1ok7b1 B:1-122 DNA polymerase III, beta subunit                                                                          d1ok7b2 B:123-244 DNA polymerase III, beta subunit                                                                        d1ok7b3 B:245-366 DNA polymerase III, beta subunit                                                                         SCOP domains
               CATH domains 1ok7B01 B:1-123 DNA Polymerase III, subunit A, domain 2                                                                    1ok7B02 B:124-247 DNA Polymerase III, subunit A, domain 2                                                                   1ok7B03 B:248-366 DNA Polymerase III, subunit A, domain 2                                                               CATH domains
           Pfam domains (1) DNA_pol3_beta-1ok7B01 B:1-120                                                                                           --------DNA_pol3_beta_2-1ok7B03 B:129-243                                                                                  -DNA_pol3_beta_3-1ok7B05 B:245-365                                                                                        - Pfam domains (1)
           Pfam domains (2) DNA_pol3_beta-1ok7B02 B:1-120                                                                                           --------DNA_pol3_beta_2-1ok7B04 B:129-243                                                                                  -DNA_pol3_beta_3-1ok7B06 B:245-365                                                                                        - Pfam domains (2)
         Sec.struct. author .eeeeehhhhhhhhhhhh........hhhh.eeeeeee..eeeeeee...eeeeeeee.......eeeeeehhhhhhhhhhh....eeeeeee..eeeeee..eeeeee..hhhhh.........eeeeehhhhhhhhhhhhhhhh.....hhhhhheeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeehhhhhhhhhhh.......eeeee...eeeeee..eeeeee.......hhhhhh.....eeeeeehhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeeeeee.......eeeeeehhhhhhhhhhh...eeeeee......eeeee..eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ok7 B   1 MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL 366
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360      


Chain C from PDB  Type:PROTEIN  Length:7
 aligned with DPO4_ECOLI | Q47155 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:7
           DPO4_ECOLI   345 RQLVLGL 351
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 1ok7 C  10 RQLVLGL  16
   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, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Clan: DNA_clamp (33)

(-) Gene Ontology  (23, 51)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DPO3B_ECO57 | P0A990)
molecular function
    GO:0008408    3'-5' exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    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:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
    GO:0009360    DNA polymerase III complex    The DNA polymerase III holoenzyme is a complex that contains 10 different types of subunits. These subunits are organized into 3 functionally essential sub-assemblies: the pol III core, the beta sliding clamp processivity factor and the clamp-loading complex. The pol III core carries out the polymerase and the 3'-5' exonuclease proofreading activities. The polymerase is tethered to the template via the sliding clamp processivity factor. The clamp-loading complex assembles the beta processivity factor onto the primer template and plays a central role in the organization and communication at the replication fork.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A,B   (DPO3B_ECOL6 | P0A989)
molecular function
    GO:0008408    3'-5' exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    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:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
    GO:0009360    DNA polymerase III complex    The DNA polymerase III holoenzyme is a complex that contains 10 different types of subunits. These subunits are organized into 3 functionally essential sub-assemblies: the pol III core, the beta sliding clamp processivity factor and the clamp-loading complex. The pol III core carries out the polymerase and the 3'-5' exonuclease proofreading activities. The polymerase is tethered to the template via the sliding clamp processivity factor. The clamp-loading complex assembles the beta processivity factor onto the primer template and plays a central role in the organization and communication at the replication fork.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A,B   (DPO3B_ECOLI | P0A988)
molecular function
    GO:0008408    3'-5' exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    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:0006271    DNA strand elongation involved in DNA replication    The process in which a DNA strand is synthesized from template DNA during replication by the action of polymerases, which add nucleotides to the 3' end of the nascent DNA strand.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
    GO:0009360    DNA polymerase III complex    The DNA polymerase III holoenzyme is a complex that contains 10 different types of subunits. These subunits are organized into 3 functionally essential sub-assemblies: the pol III core, the beta sliding clamp processivity factor and the clamp-loading complex. The pol III core carries out the polymerase and the 3'-5' exonuclease proofreading activities. The polymerase is tethered to the template via the sliding clamp processivity factor. The clamp-loading complex assembles the beta processivity factor onto the primer template and plays a central role in the organization and communication at the replication fork.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain C   (DPO4_ECOLI | Q47155)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    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.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    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:0000731    DNA synthesis involved in DNA repair    Synthesis of DNA that proceeds from the broken 3' single-strand DNA end and uses the homologous intact duplex as the template.
    GO:0006261    DNA-dependent DNA replication    A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.
    GO:0009432    SOS response    An error-prone process for repairing damaged microbial DNA.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0019985    translesion synthesis    The replication of damaged DNA by synthesis across a lesion in the template strand; a specialized DNA polymerase or replication complex inserts a defined nucleotide across from the lesion which allows DNA synthesis to continue beyond the lesion. This process can be mutagenic depending on the damaged nucleotide and the inserted nucleotide.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  DPO4_ECOLI | Q47155
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 Related Entries

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

UniProtKB/Swiss-Prot
        DPO3B_ECO57 | P0A990: 1unn 1wai
        DPO3B_ECOL6 | P0A989: 1unn 1wai
        DPO3B_ECOLI | P0A988: 1jqj 1jql 1mmi 1unn 1wai 2pol 2xur 3bep 3d1e 3d1f 3d1g 3f1v 3pwe 3q4j 3q4k 3q4l 3qsb 4k3k 4k3l 4k3m 4k3o 4k3p 4k3q 4k3r 4k3s 4mjp 4mjq 4mjr 4n94 4n95 4n96 4n97 4n98 4n99 4n9a 5fku 5fkv 5fkw 5m1s
        DPO4_ECOLI | Q47155: 1unn 4ir1 4ir9 4irc 4ird 4irk 4q43 4q44 4q45 4r8u 5c5j

(-) Related Entries Specified in the PDB File

1jqj MECHANISM OF PROCESSIVITY CLAMP OPENING BY THE DELTASUBUNIT WRENCH OF THE CLAMP LOADER COMPLEX OF E. COLI DNAPOLYMERASE III: STRUCTURE OF THE BETA-DELTA COMPLEX
1jql MECHANISM OF PROCESSIVITY CLAMP OPENING BY THE DELTASUBUNIT WRENCH OF THE CLAMP LOADER COMPLEX OF E. COLI DNAPOLYMERASE III: STRUCTURE OF BETA-DELTA (1-140)
2pol POL III (BETA SUBUNIT)