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(-) Description

Title :  NUCLEOTIDE-FREE FORM OF AN ISOLATED E. COLI CLAMP LOADER GAMMA SUBUNIT
 
Authors :  M. Podobnik, T. F. Weitze, M. O'Donnell, J. Kuriyan
Date :  30 Dec 02  (Deposition) - 01 Apr 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rossman-Like Fold, Aaa+ Atpase Domains, Sensor 1, Sensor 2, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Podobnik, T. F. Weitze, M. O'Donnell, J. Kuriyan
Nucleotide-Induced Conformational Changes In An Isolated Escherichia Coli Dna Polymerase Iii Clamp Loader Subunit
Structure V. 11 253 2003
PubMed-ID: 12623013  |  Reference-DOI: 10.1016/S0969-2126(03)00027-3
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA POLYMERASE III SUBUNIT GAMMA
    ChainsA, B
    EC Number2.7.7.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL DOMAINS 1 AND 2
    GeneDNAX
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:64 , CYS A:73 , GLY A:74 , CYS A:76 , CYS A:79BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWARETHR A:46 , ARG A:47 , GLY A:48 , VAL A:49 , GLY A:50 , LYS A:51 , THR A:52 , ARG A:215BINDING SITE FOR RESIDUE SO4 A 501
3AC3SOFTWAREARG A:47 , ARG A:215 , LYS B:141BINDING SITE FOR RESIDUE SO4 A 601
4AC4SOFTWARECYS B:64 , CYS B:73 , GLY B:74 , CYS B:76 , CYS B:79BINDING SITE FOR RESIDUE ZN B 402
5AC5SOFTWARETHR B:46 , ARG B:47 , GLY B:48 , VAL B:49 , GLY B:50 , LYS B:51 , THR B:52 , HOH B:503 , HOH B:562BINDING SITE FOR RESIDUE SO4 B 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NJG)

(-) 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:240
 aligned with DPO3X_ECOLI | P06710 from UniProtKB/Swiss-Prot  Length:643

    Alignment length:240
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243
          DPO3X_ECOLI     4 QVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLGT 243
               SCOP domains d1njga_ A: delta prime subunit of DNA polymerase III, N-domain                                                                                                                                                                                   SCOP domains
               CATH domains 1njgA01 A:4-177 P-loop containing nucleotide triphosphate hydrolases                                                                                                          1njgA02 A:178-243  [code=1.10.8.60, no name defined]               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhh...hhhhh..hhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhh...........hhhhhhhhh.....eeeee..hhhhhhhhhhhhhh..........eeeeeehhhhhhhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.hhhhhhhhhhhhhh......hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1njg A   4 QVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLGT 243
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243

Chain B from PDB  Type:PROTEIN  Length:239
 aligned with DPO3X_ECOLI | P06710 from UniProtKB/Swiss-Prot  Length:643

    Alignment length:239
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234         
          DPO3X_ECOLI     5 VLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLGT 243
               SCOP domains d1njgb_ B: delta prime subunit of DNA polymerase III, N-domain                                                                                                                                                                                  SCOP domains
               CATH domains 1njgB01-1njgB02 B:13-177 P-loop containing nucleotide triphosphate hydrolases                                                                                                1njgB01 B:5-11,B:178-243  [code=1.10.8.60, no name defined]        CATH domains
           Pfam domains (1) ---------------DNA_pol3_delta2-1njgB01 B:20-179                                                                                                                                ----------------------------------------------------DNA_pol3_gam Pfam domains (1)
           Pfam domains (2) ---------------DNA_pol3_delta2-1njgB02 B:20-179                                                                                                                                ----------------------------------------------------DNA_pol3_gam Pfam domains (2)
         Sec.struct. author hhhhhh...hhhhh..hhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhh...........hhhhhhhhh.....eeeee.....hhhhhhhhhh...........eeeeee.hhhhhhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1njg B   5 VLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLGT 243
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234         

   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, 2)

Asymmetric Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DPO3X_ECOLI | P06710)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003689    DNA clamp loader activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the opening of the ring structure of the PCNA complex, or any of the related sliding clamp complexes, and their closing around the DNA duplex.
    GO:0030337    DNA polymerase processivity factor activity    An enzyme regulator activity that increases the processivity of polymerization by DNA polymerase, by allowing the polymerase to move rapidly along DNA while remaining topologically bound to it.
    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:0017111    nucleoside-triphosphatase activity    Catalysis of the reaction: a nucleoside triphosphate + H2O = nucleoside diphosphate + phosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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: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.
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:0043846    DNA polymerase III, clamp loader complex    A heptamer that includes the tau and gamma products of the dnaX gene and the chi/psi subcomplex. Confers structural asymmetry that allows the polymerase to replicate both leading and lagging strands.
    GO:0005663    DNA replication factor C complex    A complex that loads the DNA polymerase processivity factor proliferating cell nuclear antigen (PCNA) onto DNA, thereby permitting processive DNA synthesis catalyzed by DNA polymerase. In eukaryotes the complex consists of five polypeptides.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DPO3X_ECOLI | P067101jr3 1njf 1xxh 1xxi 2aya 3glf 3glg 3glh 3gli 5fku 5fkv

(-) Related Entries Specified in the PDB File

1njf NUCLEOTIDE BOUND FORM OF AN ISOLATED E. COLI CLAMP LOADER GAMMA SUBUNIT