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(-) Description

Title :  CRYSTAL STRUCTURE OF A DNA POLYMERASE III ALPHA-EPSILON CHIMERA
 
Authors :  A. Robinson, N. Horan, Z. -Q. Xu, N. E. Dixon, A. J. Oakley
Date :  04 Sep 12  (Deposition) - 03 Apr 13  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Dna Polymerase Iii, Poliii Epsilon, Poliii Alpha, Dnaq, Dnae, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Ozawa, N. P. Horan, A. Robinson, H. Yagi, F. R. Hill, S. Jergic, Z. Q. Xu, K. V. Loscha, N. Li, M. Tehei, A. J. Oakley, G. Otting, T. Huber, N. E. Dixon
Proofreading Exonuclease On A Tether: The Complex Between The E. Coli Dna Polymerase Iii Subunits Alpha, {Varepsilon} Theta And Beta Reveals A Highly Flexible Arrangement Of The Proofreading Domain
Nucleic Acids Res. V. 41 5354 2013
PubMed-ID: 23580545  |  Reference-DOI: 10.1093/NAR/GKT162

(-) Compounds

Molecule 1 - DNA POLYMERASE III SUBUNIT EPSILON,DNA POLYMERASE III SUBUNIT ALPHA
    Chains: A, B, C, D
    EC Number: 2.7.7.7, 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETMCS1
    Expression System Strain: BL21 P LYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: POLIII EPSILON C-TERMINAL DOMAIN (UNP RESIDUES 209-243), POLIII ALPHA PHP DOMAIN (UNP RESIDUES 1-270)
    Gene: DNAQ, MUTD, B0215, JW0205, DNAE, POLC, B0184, JW0179
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:38 , HOH A:579 , HOH A:581BINDING SITE FOR RESIDUE CL A 401
2AC2SOFTWAREARG B:38 , HOH B:620 , HOH B:651BINDING SITE FOR RESIDUE CL B 401
3AC3SOFTWAREARG C:38 , HOH C:563 , HOH C:569BINDING SITE FOR RESIDUE CL C 401
4AC4SOFTWAREARG D:38 , HOH D:654 , HOH D:657BINDING SITE FOR RESIDUE CL D 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GX8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GX8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GX8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GX8)

(-) Exons   (0, 0)

(no "Exon" information available for 4GX8)

(-) 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:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhh.hhhhh.....hhhhh......................hhhhhhhhhhh...eeeeeee....hhhhhhhhhhhh..eeeeeeeeeeehhhhh...eeeeeee.hhhhhhhhhhhhhhhhhh........ee.hhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhh............hhhhhhhhh..hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gx8 A   3 SKLRVVFATDEEIAAHEARLDLVQKKGGSCLWRATRESGSIGSMSEPRFVHLRVHSDYSMIDGPAKTAPLVKKAAALGMPALAITDFTNLCGLVKFYGAGHGAGIKPIVGADFNVQCDLLGDELTHLTVLAANNTGYQNLTLLISKAYQRGYGAAGPIIDRDWLIELNEGLILLSGGRMGDVGRSLLRGNSALVDECVAFYEEHFPDRYFLELIRTGRPDEESYLHAAVELAEARGLPVVATNDVRFIDSSDFDAHEIRVAIHDGFPRNYSPQQYMRSEEEMCELFADIPEALANTVEIAKRCNVT 315
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262     ||279       289       299       309      
                                                                                                                                                                                                                                                                                                   268|                                       
                                                                                                                                                                                                                                                                                                    276                                       


Chain B from PDB  Type:PROTEIN  Length:312
                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhh.hhhhh................................hhhhhhhhhhh...eeee.......hhhhhhhhhhhh..eeeeeeeeeeehhhhh...eeeeeee.hhhhhhhhhhhhhhhhhh........ee.hhhhhhh..eeee.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhh....................hhhhhhhhh..hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gx8 B   4 KLRVVFATDEEIAAHEARLDLVQKKGGSCLWRATRESGSIGSMSEPRFVHLRVHSDYSMIDGPAKTAPLVKKAAALGMPALAITDFTNLCGLVKFYGAGHGAGIKPIVGADFNVQCDLLGDELTHLTVLAANNTGYQNLTLLISKAYQRGYGAAGPIIDRDWLIELNEGLILLSGGRMGDVGRSLLRGNSALVDECVAFYEEHFPDRYFLELIRTGRPDEESYLHAAVELAEARGLPVVATNDVRFIDSSDFDAHEIRVAIHDGFTLDDPKRPRNYSPQQYMRSEEEMCELFADIPEALANTVEIAKRCNVT 315
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313  


Chain C from PDB  Type:PROTEIN  Length:312
                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhh.hhhhh................................hhhhhhhhhhh...eeeeeee....hhhhhhhhhhhh..eeeeeeeeeeehhhhh...eeeeeee.hhhhhhhhhhhhhhhhhh........ee.hhhhhhh..eeee.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhh...................hhhhhhhhh..hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gx8 C   4 KLRVVFATDEEIAAHEARLDLVQKKGGSCLWRATRESGSIGSMSEPRFVHLRVHSDYSMIDGPAKTAPLVKKAAALGMPALAITDFTNLCGLVKFYGAGHGAGIKPIVGADFNVQCDLLGDELTHLTVLAANNTGYQNLTLLISKAYQRGYGAAGPIIDRDWLIELNEGLILLSGGRMGDVGRSLLRGNSALVDECVAFYEEHFPDRYFLELIRTGRPDEESYLHAAVELAEARGLPVVATNDVRFIDSSDFDAHEIRVAIHDGFTLDDPKRPRNYSPQQYMRSEEEMCELFADIPEALANTVEIAKRCNVT 315
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313  


Chain D from PDB  Type:PROTEIN  Length:312
                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhh.hhhhh.....hhhhh......................hhhhhhhhhhh...eeeeeee....hhhhhhhhhhhh..eeeeeeeeeeehhhhh...eeeeeee.hhhhhhhhhhhhhhhhhh........ee.hhhhhh...eeee.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhh...................hhhhhhhhh..hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gx8 D   4 KLRVVFATDEEIAAHEARLDLVQKKGGSCLWRATRESGSIGSMSEPRFVHLRVHSDYSMIDGPAKTAPLVKKAAALGMPALAITDFTNLCGLVKFYGAGHGAGIKPIVGADFNVQCDLLGDELTHLTVLAANNTGYQNLTLLISKAYQRGYGAAGPIIDRDWLIELNEGLILLSGGRMGDVGRSLLRGNSALVDECVAFYEEHFPDRYFLELIRTGRPDEESYLHAAVELAEARGLPVVATNDVRFIDSSDFDAHEIRVAIHDGFTLDDPKRPRNYSPQQYMRSEEEMCELFADIPEALANTVEIAKRCNVT 315
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313
   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  (0, 0)

(no "SCOP Domain" information available for 4GX8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GX8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GX8)

(-) Gene Ontology  (19, 28)

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  DPO3E_ECOLI | P03007
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  2.7.7.7
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 Related Entries

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

UniProtKB/Swiss-Prot
        DPO3A_ECOLI | P10443: 2hnh 2hqa 4gx9 4jom 5fku 5fkv 5fkw 5m1s
        DPO3E_ECOLI | P03007: 1j53 1j54 1mgz 2gui 2ido 2xy8 4gx9 5fku 5fkv 5fkw 5m1s

(-) Related Entries Specified in the PDB File

1j53 STRUCTURE OF THE N-TERMINAL EXONUCLEASE DOMAIN OF THE EPSILON SUBUNIT OF E.COLI DNA POLYMERASE III AT PH 8.5
1j54 STRUCTURE OF THE N-TERMINAL EXONUCLEASE DOMAIN OF THE EPSILON SUBUNIT OF E.COLI DNA POLYMERASE III AT PH 5.8
2axd SOLUTION STRUCTURE OF THE THETA SUBUNIT OF ESCHERICHIA COLI DNA POLYMERASE III IN COMPLEX WITH THE EPSILON SUBUNIT
2gui STRUCTURE AND FUNCTION OF CYCLIZED VERSIONS OF THE PROOFREADING EXONUCLEASE SUBUNIT OF E. COLI DNA POLYMERASE III
2hnh CRYSTAL STRUCTURE OF THE CATALYTIC ALPHA SUBUNIT OF E. COLI REPLICATIVE DNA POLYMERASE III
2hqa CRYSTAL STRUCTURE OF THE CATALYTIC ALPHA SUBUNIT OF E. COLI REPLICATIVE DNA POLYMERASE III
2ido STRUCTURE OF THE E. COLI POL III EPSILON-HOT PROOFREADING COMPLEX
4gx9