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(-) Description

Title :  CRYSTAL STRUCTURE OF A DNA POLYMERASE III ALPHA-EPSILON CHIMERA
 
Authors :  N. Li, N. Horan, Z. -Q. Xu, D. Jacques, N. E. Dixon, A. J. Oakley
Date :  04 Sep 12  (Deposition) - 03 Apr 13  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
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 200-243), 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4GX9)

(-) Sites  (0, 0)

(no "Site" information available for 4GX9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GX9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GX9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GX9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GX9)

(-) Exons   (0, 0)

(no "Exon" information available for 4GX9)

(-) 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: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.hhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhh...................hhhhhhhhh..hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gx9 A   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 B from PDB  Type:PROTEIN  Length:313
                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhh.hhhhh................................hhhhhhhhhhh...eeee.......hhhhhhhhhhhhh.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
                 4gx9 B  -5 IQRSKLRVVFATDEEIAAHEARLDLVQKKGGSCLWRATRESGSIGSMSEPRFVHLRVHSDYSMIDGPAKTAPLVKKAAALGMPALAITDFTNLCGLVKFYGAGHGAGIKPIVGADFNVQCDLLGDELTHLTVLAANNTGYQNLTLLISKAYQRGYGAAGPIIDRDWLIELNEGLILLSGGRMGDVGRSLLRGNSALVDECVAFYEEHFPDRYFLELIRTGRPDEESYLHAAVELAEARGLPVVATNDVRFIDSSDFDAHEIRVAIHDGFTPKRPRNYSPQQYMRSEEEMCELFADIPEALANTVEIAKRCNVT 315
                              ||     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269|      282       292       302       312   
                             -3|                                                                                                                                                                                                                                                                       269|                                          
                               3                                                                                                                                                                                                                                                                        273                                          


Chain C from PDB  Type:PROTEIN  Length:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhhh.hhhhh................................hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh.eeeeeeeeeeehhhhh...eeeeeee.hhhhhhhhhhhhhhhhhh.......eee.hhhhhh...eeee.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhh....................hhhhhhhhh..hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gx9 C  -5 IQRISKLRVVFATDEEIAAHEARLDLVQKKGGSCLWRATRESGSIGSMSEPRFVHLRVHSDYSMIDGPAKTAPLVKKAAALGMPALAITDFTNLCGLVKFYGAGHGAGIKPIVGADFNVQCDLLGDELTHLTVLAANNTGYQNLTLLISKAYQRGYGAAGPIIDRDWLIELNEGLILLSGGRMGDVGRSLLRGNSALVDECVAFYEEHFPDRYFLELIRTGRPDEESYLHAAVELAEARGLPVVATNDVRFIDSSDFDAHEIRVAIHDGFTLDDPKRPRNYSPQQYMRSEEEMCELFADIPEALANTVEIAKRCNVT 315
                               ||    8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       
                              -2|                                                                                                                                                                                                                                                                                                                        
                                3                                                                                                                                                                                                                                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:312
                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhh......................................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
                 4gx9 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 4GX9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GX9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GX9)

(-) 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 4gx8 4jom 5fku 5fkv 5fkw 5m1s
        DPO3E_ECOLI | P03007: 1j53 1j54 1mgz 2gui 2ido 2xy8 4gx8 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
2gui STRUCTURE AND FUNCTION OF CYCLIZED VERSIONS OF THE PROOFREADING EXONUCLEASE SUBUNIT OF E. COLI DNA
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
4gx8