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(-) Description

Title :  CRYSTAL STRUCTURE OF CHI AND PSI SUBUNIT HETERODIMER FROM DNA POL III
 
Authors :  J. M. Gulbis, J. Finkelstein, M. O'Donnell, J. Kuriyan
Date :  16 Mar 00  (Deposition) - 26 Aug 03  (Release) - 24 Feb 09  (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 :  Dna Pol Iii, Heterodimer, Clamp-Loader, Alpha-Beta Fold, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. M. Gulbis, S. L. Kazmirski, J. Finkelstein, Z. Kelman, M. O'Donnell, J. Kuriyan
Crystal Structure Of The Chi:Psi Sub-Assembly Of The Escherichia Coli Dna Polymerase Clamp-Loader Complex.
Eur. J. Biochem. V. 271 439 2004
PubMed-ID: 14717711  |  Reference-DOI: 10.1046/J.1432-1033.2003.03944.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA POLYMERASE III CHI SUBUNIT
    ChainsA, C
    EC Number2.7.7.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-147
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
 
Molecule 2 - DNA POLYMERASE III PSI SUBUNIT
    ChainsB, D
    EC Number2.7.7.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 26-137
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1EM8)

(-) Sites  (0, 0)

(no "Site" information available for 1EM8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1EM8)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Arg A:59 -Pro A:60
2Arg C:59 -Pro C:60

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1EM8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1EM8)

(-) Exons   (0, 0)

(no "Exon" information available for 1EM8)

(-) 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:147
 aligned with HOLC_ECOLI | P28905 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       
           HOLC_ECOLI     1 MKNATFYLLDNDTTVDGLSAVEQLVCEIAAERWRSGKRVLIACEDEKQAYRLDEALWARPAESFVPHNLAGEGPRGGAPVEIAWPQKRSSSRRDILISLRTSFADFATAFTEVVDFVPYEDSLKQLARERYKAYRVAGFNLNTATWK 147
               SCOP domains d1em8a_ A: DNA polymerase III chi subunit                                                                                                           SCOP domains
               CATH domains 1em8A00 A:1-147  [code=3.40.50.10110, no name defined]                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..........hhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhh.......eee..........eeee...........eeee.....hhhhhhh.eeeeee..hhhhhhhhhhhhhhhhhh.eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1em8 A   1 MKNATFYLLDNDTTVDGLSAVEQLVCEIAAERWRSGKRVLIACEDEKQAYRLDEALWARPAESFVPHNLAGEGPRGGAPVEIAWPQKRSSSRRDILISLRTSFADFATAFTEVVDFVPYEDSLKQLARERYKAYRVAGFNLNTATWK 147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       

Chain B from PDB  Type:PROTEIN  Length:110
 aligned with HOLD_ECOLI | P28632 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:110
                                    36        46        56        66        76        86        96       106       116       126       136
           HOLD_ECOLI    27 GEIAIAIPAHVRLVMVANDLPALTDPLVSDVLRALTVSPDQVLQLTPEKIAMLPQGSHCNSWRLGTDEPLSLEGAQVASPALTDLRANPTARAALWQQICTYEHDFFPRN 136
               SCOP domains d1em8b_ B: DNA polymerase III psi subunit                                                                      SCOP domains
               CATH domains 1em8B00 B:27-136 DNA polymerase iii psi subunit. Chain: B                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee........hhhhhhhhhhh..hhh.eeee..hhhhhh......eeeee...........eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1em8 B  27 GEIAIAIPAHVRLVMVANDLPALTDPLVSDVLRALTVSPDQVLQLTPEKIAMLPQGSHCNSWRLGTDEPLSLEGAQVASPALTDLRANPTARAALWQQICTYEHDFFPRN 136
                                    36        46        56        66        76        86        96       106       116       126       136

Chain C from PDB  Type:PROTEIN  Length:147
 aligned with HOLC_ECOLI | P28905 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       
           HOLC_ECOLI     1 MKNATFYLLDNDTTVDGLSAVEQLVCEIAAERWRSGKRVLIACEDEKQAYRLDEALWARPAESFVPHNLAGEGPRGGAPVEIAWPQKRSSSRRDILISLRTSFADFATAFTEVVDFVPYEDSLKQLARERYKAYRVAGFNLNTATWK 147
               SCOP domains d1em8c_ C: DNA polymerase III chi subunit                                                                                                           SCOP domains
               CATH domains 1em8C00 C:1-147  [code=3.40.50.10110, no name defined]                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..........hhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh..........eee..........eeee...........eeee.....hhhhhhh.eeeeee..hhhhhhhhhhhhhhhhhh..eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1em8 C   1 MKNATFYLLDNDTTVDGLSAVEQLVCEIAAERWRSGKRVLIACEDEKQAYRLDEALWARPAESFVPHNLAGEGPRGGAPVEIAWPQKRSSSRRDILISLRTSFADFATAFTEVVDFVPYEDSLKQLARERYKAYRVAGFNLNTATWK 147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       

Chain D from PDB  Type:PROTEIN  Length:112
 aligned with HOLD_ECOLI | P28632 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:112
                                    35        45        55        65        75        85        95       105       115       125       135  
           HOLD_ECOLI    26 QGEIAIAIPAHVRLVMVANDLPALTDPLVSDVLRALTVSPDQVLQLTPEKIAMLPQGSHCNSWRLGTDEPLSLEGAQVASPALTDLRANPTARAALWQQICTYEHDFFPRND 137
               SCOP domains d1em8d_ D: DNA polymerase III psi subunit                                                                        SCOP domains
               CATH domains 1em8D00 D:26-137 DNA polymerase iii psi subunit. Chain: B                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeee........hhhhhhhhhhh..hhh.eeeehhhhhhhh.......eeee...........eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1em8 D  26 QGEIAIAIPAHVRLVMVANDLPALTDPLVSDVLRALTVSPDQVLQLTPEKIAMLPQGSHCNSWRLGTDEPLSLEGAQVASPALTDLRANPTARAALWQQICTYEHDFFPRND 137
                                    35        45        55        65        75        85        95       105       115       125       135  

   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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EM8)

(-) Gene Ontology  (11, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (HOLC_ECOLI | P28905)
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: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:0032298    positive regulation of DNA-dependent DNA replication initiation    Any process that activates or increases the frequency, rate or extent of initiation of DNA-dependent DNA replication.
cellular component
    GO:0043847    DNA polymerase III, clamp loader chi/psi subcomplex    A dimer composed of the chi and psi subunits which is a subassembly of the DNA polymerase III clamp loader complex and serves as a bridge between the DnaX complex and the single-stranded DNA-binding protein (SSB).

Chain B,D   (HOLD_ECOLI | P28632)
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: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: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:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HOLC_ECOLI | P289053sxu
        HOLD_ECOLI | P286323gli 3sxu

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1EM8)