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(-) Description

Title :  STRUCTURE OF THE E. COLI POL III EPSILON-HOT PROOFREADING COMPLEX
 
Authors :  T. W. Kirby, S. Harvey, E. F. Derose, S. Chalov, A. K. Chikova, F. W. Perri R. M. Schaaper, R. E. London, L. C. Pedersen
Date :  15 Sep 06  (Deposition) - 14 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Polymerase, Exonuclease, Hot, Epsilon, Pol Iii, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. W. Kirby, S. Harvey, E. F. Derose, S. Chalov, A. K. Chikova, F. W. Perrino, R. M. Schaaper, R. E. London, L. C. Pedersen
Structure Of The Escherichia Coli Dna Polymerase Iii Epsilon-Hot Proofreading Complex.
J. Biol. Chem. V. 281 38466 2006
PubMed-ID: 16973612  |  Reference-DOI: 10.1074/JBC.M606917200

(-) Compounds

Molecule 1 - DNA POLYMERASE III EPSILON SUBUNIT
    Chains: A, C
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: POXO4
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: EXONUCLEASE DOMAIN
    Gene: DNAQ, MUTD
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 2 - HOT PROTEIN
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30A
    Expression System Strain: BLR(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HOT
    Organism Scientific: ENTEROBACTERIA PHAGE
    Organism Taxid: 10678
    Strain: P1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MN5Ligand/IonMANGANESE (II) ION
3TMP2Ligand/IonTHYMIDINE-5'-PHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2MN-1Ligand/IonMANGANESE (II) ION
3TMP1Ligand/IonTHYMIDINE-5'-PHOSPHATE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MN-1Ligand/IonMANGANESE (II) ION
3TMP1Ligand/IonTHYMIDINE-5'-PHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:12 , TMP A:2001 , HOH A:2003 , HOH A:2016 , HOH A:2081BINDING SITE FOR RESIDUE MN A 1001
2AC2SOFTWAREASP A:12 , GLU A:14 , ASP A:167 , TMP A:2001 , HOH A:2017BINDING SITE FOR RESIDUE MN A 1002
3AC3SOFTWAREASP C:12 , GLU C:14 , ASP C:167 , TMP C:2002 , HOH C:2008BINDING SITE FOR RESIDUE MN C 1003
4AC4SOFTWAREASP C:12 , TMP C:2002 , HOH C:2003 , HOH C:2089 , HOH C:2090BINDING SITE FOR RESIDUE MN C 1004
5AC5SOFTWAREHIS C:162 , HOH C:2149 , HOH C:2150 , HOH C:2151BINDING SITE FOR RESIDUE MN C 1005
6AC6SOFTWAREASP A:12 , THR A:13 , GLU A:14 , THR A:15 , MET A:18 , GLU A:61 , HIS A:66 , PHE A:102 , ASP A:167 , MN A:1001 , MN A:1002 , HOH A:2017 , HOH A:2051 , HOH A:2074BINDING SITE FOR RESIDUE TMP A 2001
7AC7SOFTWAREASP C:12 , THR C:13 , GLU C:14 , THR C:15 , GLU C:61 , HIS C:66 , PHE C:102 , ASP C:167 , EDO C:1000 , MN C:1003 , MN C:1004 , HOH C:2008 , HOH C:2027 , HOH C:2044BINDING SITE FOR RESIDUE TMP C 2002
8AC8SOFTWAREHIS C:98 , TMP C:2002 , HOH C:2019 , HOH C:2038BINDING SITE FOR RESIDUE EDO C 1000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2IDO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2IDO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2IDO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2IDO)

(-) Exons   (0, 0)

(no "Exon" information available for 2IDO)

(-) 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:173
 aligned with DPO3E_ECOLI | P03007 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:175
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175     
          DPO3E_ECOLI     6 TRQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALLDAQILAEVYLAMTG 180
               SCOP domains d2idoa_ A: automated matches                                                                                                                                                    SCOP domains
               CATH domains 2idoA00 A:6-180  [code=3.30.420.10, no name defined]                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..............eeeeeeeeee..ee....eeee.......hhhhhhhhh.hhhhhh...hhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhh.....hhhhh.eeeehhhhhhhhh.....hhhhhhhhh.....-.-..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ido A   6 TRQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNS-R-LHGALLDAQILAEVYLAMTG 180
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155 | | | 165       175     
                                                                                                                                                                                 157 | |                   
                                                                                                                                                                                   159 |                   
                                                                                                                                                                                     161                   


Chain B from PDB  Type:PROTEIN  Length:75
 aligned with Q71T70_BPP1 | Q71T70 from UniProtKB/TrEMBL  Length:87

    Alignment length:75
                                    15        25        35        45        55        65        75     
          Q71T70_BPP1     6 YDWNIAAKSQEERDKVNVDLAASGVAYKERLNIPVIAEQVAREQPENLRTYFMERLRHYRQLSLQLPKGSDPAYQ  80
               SCOP domains d2idob_ B: Homolog of theta (HOT)                                           SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 2ido B   2 YDWNIAAKSQEERDKVNVDLAASGVAYKERLNIPVIAEQVAREQPENLRTYFMERLRHYRQLSLQLPKGSDPAYQ  76
                                    11        21        31        41        51        61        71     


Chain C from PDB  Type:PROTEIN  Length:175
 aligned with DPO3E_ECOLI | P03007 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:175
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175     
          DPO3E_ECOLI     6 TRQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALLDAQILAEVYLAMTG 180
               SCOP domains d2idoc_ C: automated matches                                                                                                                                                    SCOP domains
               CATH domains 2idoC00 C:6-180  [code=3.30.420.10, no name defined]                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..............eeeeeeeeee..ee....eeee.......hhhhhhhhh.hhhhhh...hhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhh.....hhhhh.eeeehhhhhhhhh.....hhhhhhhhh.........hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ido C   6 TRQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALLDAQILAEVYLAMTG 180
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175     


Chain D from PDB  Type:PROTEIN  Length:76
 aligned with Q71T70_BPP1 | Q71T70 from UniProtKB/TrEMBL  Length:87

    Alignment length:76
                                    14        24        34        44        54        64        74      
          Q71T70_BPP1     5 MYDWNIAAKSQEERDKVNVDLAASGVAYKERLNIPVIAEQVAREQPENLRTYFMERLRHYRQLSLQLPKGSDPAYQ  80
               SCOP domains d2idod_ D: Homolog of theta (HOT)                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 2ido D   1 MYDWNIAAKSQEERDKVNVDLAASGVAYKERLNIPVIAEQVAREQPENLRTYFMERLRHYRQLSLQLPKGSDPAYQ  76
                                    10        20        30        40        50        60        70
   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  (2, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IDO)

(-) Gene Ontology  (15, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (DPO3E_ECOLI | P03007)
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:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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:0045004    DNA replication proofreading    Correction of replication errors by DNA polymerase using a 3'-5' exonuclease activity.
    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:0044776    DNA polymerase III, core complex    The DNA polymerase III core complex consists of the alpha,epsilon and theta subunits and is carries out the polymerase and the 3'-5' exonuclease proofreading activities.

Chain B,D   (Q71T70_BPP1 | Q71T70)
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.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DPO3E_ECOLI | P03007: 1j53 1j54 1mgz 2gui 2xy8 4gx8 4gx9 5fku 5fkv 5fkw 5m1s
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        Q71T70_BPP1 | Q71T70: 1se7

(-) Related Entries Specified in the PDB File

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