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(-) Description

Title :  CRYSTAL STRUCTURE OF A DINB FAMILY ERROR PRONE DNA POLYMERASE FROM SULFOLOBUS SOLFATARICUS
 
Authors :  L. F. Silvian, E. A. Toth, P. Pham, M. F. Goodman, T. Ellenberger
Date :  25 Sep 01  (Deposition) - 31 Oct 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Dna Polymerase, Error-Prone Polymerase, Lesion-Bypass Polymerase, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. F. Silvian, E. A. Toth, P. Pham, M. F. Goodman, T. Ellenberger
Crystal Structure Of A Dinb Family Error-Prone Dna Polymerase From Sulfolobus Solfataricus.
Nat. Struct. Biol. V. 8 984 2001
PubMed-ID: 11685247  |  Reference-DOI: 10.1038/NSB1101-984
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DBH PROTEIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET17
    Expression System StrainBL21(DE3)RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneDBH
    MutationYES
    Organism ScientificSULFOLOBUS SOLFATARICUS
    Organism Taxid2287

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1K1Q)

(-) Sites  (0, 0)

(no "Site" information available for 1K1Q)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K1Q)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys B:160 -Pro B:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K1Q)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UMUCPS50173 UmuC domain profile.DPO4_SULSF3-188
 
  2A:3-188
B:3-188
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UMUCPS50173 UmuC domain profile.DPO4_SULSF3-188
 
  1A:3-188
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UMUCPS50173 UmuC domain profile.DPO4_SULSF3-188
 
  1-
B:3-188

(-) Exons   (0, 0)

(no "Exon" information available for 1K1Q)

(-) 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:333
 aligned with DPO4_SULSF | P96022 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:344
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340    
           DPO4_SULSF     1 MIVIFVDFDYFFAQVEEVLNPQYKGKPLVVCVYSGRTKTSGAVATANYEARKLGVKAGMPIIKAMQIAPSAIYVPMRKPIYEAFSNRIMNLLNKHADKIEVASIDEAYLDVTNKVEGNFENGIELARKIKQEILEKEKITVTVGVAPNKILAKIIADKSKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEKITGKAKALYLLKLAQNKYSEPVENKSKIPHGRYLTLPYNTRDVKVILPYLKKAINEAYNKVNGIPMRITVIAIMEDLDILSKGKKFKHGISIDNAYKVAEDLLRELLVRDKRRNVRRIGVKLDNIIIN 344
               SCOP domains d1k1qa2 A:1-239 DinB homolog (DBH)                                                                                                                                                                                                             d1k1qa1 A:240-344 DinB homolog (DBH)                                                                      SCOP domains
               CATH domains -1k1qA02  -------------------------------------------------------------------1k1qA02 A:2-10,A:78-166  [code=3.30.70.270, no name defined]                             1k1qA03 A:167-233 5' to 3' exonuclease, C-terminal subdomain       ----------1k1qA04 A:244-341  [code=3.30.1490.100, no name defined]                                          --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhh..............-----------.hhhhhh.......hhhhhh...........hhhhhhhhhhhhhhhhhh...eeee....eeeee........hhhhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhh.....eee.hhhhhhhhhhh.........hhhhhhhhh.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhh........ee...eeeee............hhhhhhhhhhhhhh....eeeeeeeeee....eeeeeee.....hhhhhhhhhhhhhhhhh.......eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --UMUC  PDB: A:3-188 UniProt: 3-188                                                                                                                                                         ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k1q A   1 MIVIFVDFDYFFAQVEEVLNPQYKGKPLVVSVYS-----------ANYEARKLGVKAGMPIIKAMQIAPSAIYVPMRKPIYEAFSNRIMNLLNKHADKIEVASIDEAYLDVTNKVEGNFENGIELARKIKQEILEKEKITVTVGVAPNKILAKIIADKSKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEKITGKAKALYLLKLAQNKYSEPVENKSKIPHGRYLTLPYNTRDVKVILPYLKKAINEAYNKVNGIPMRITVIAIMEDLDILSKGKKFKHGISIDNAYKVAEDLLRELLVRDKRRNVRRIGVKLDNIIIN 344
                                    10        20        30   |     -     |  50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340    
                                                            34          46                                                                                                                                                                                                                                                                                                          

Chain B from PDB  Type:PROTEIN  Length:341
 aligned with DPO4_SULSF | P96022 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:344
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340    
           DPO4_SULSF     1 MIVIFVDFDYFFAQVEEVLNPQYKGKPLVVCVYSGRTKTSGAVATANYEARKLGVKAGMPIIKAMQIAPSAIYVPMRKPIYEAFSNRIMNLLNKHADKIEVASIDEAYLDVTNKVEGNFENGIELARKIKQEILEKEKITVTVGVAPNKILAKIIADKSKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEKITGKAKALYLLKLAQNKYSEPVENKSKIPHGRYLTLPYNTRDVKVILPYLKKAINEAYNKVNGIPMRITVIAIMEDLDILSKGKKFKHGISIDNAYKVAEDLLRELLVRDKRRNVRRIGVKLDNIIIN 344
               SCOP domains d1k1qb2 B:1-239 DinB homolog (DBH)                                                                                                                                                                                                             d1k1qb1 B:240-344 DinB homolog (DBH)                                                                      SCOP domains
               CATH domains -1k1qB02  -------------------------------------------------------------------1k1qB02 B:2-10,B:78-166  [code=3.30.70.270, no name defined]                             1k1qB03 B:167-233 5' to 3' exonuclease, C-terminal subdomain       ----------1k1qB04 B:244-341  [code=3.30.1490.100, no name defined]                                          --- CATH domains
           Pfam domains (1) -----IMS-1k1qB03 B:6-157                                                                                                                                     -----------IMS_HHH-1k1qB01 B:169-200       ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) -----IMS-1k1qB04 B:6-157                                                                                                                                     -----------IMS_HHH-1k1qB02 B:169-200       ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhh...eeeeee..---..eeeeeehhhhhhh.......hhhhhhh....eeee.hhhhhhhhhhhhhhhhhh...eeeeee..eeeee.hhhhh.hhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh...eee....hhhhhhhhhhhhhh...hhhhhhhhhhh....hhhhh......hhhhhhhhhhhhhhhhhh.........ee...eeeee............hhhhhhhhhhhhhh......eeeeeeee.....eeeeee.....hhhhhhhhhhhhhhhhhh......eeeeeeee..ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --UMUC  PDB: B:3-188 UniProt: 3-188                                                                                                                                                         ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k1q B   1 MIVIFVDFDYFFAQVEEVLNPQYKGKPLVVSVYSG---TSGAVATANYEARKLGVKAGMPIIKAMQIAPSAIYVPMRKPIYEAFSNRIMNLLNKHADKIEVASIDEAYLDVTNKVEGNFENGIELARKIKQEILEKEKITVTVGVAPNKILAKIIADKSKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEKITGKAKALYLLKLAQNKYSEPVENKSKIPHGRYLTLPYNTRDVKVILPYLKKAINEAYNKVNGIPMRITVIAIMEDLDILSKGKKFKHGISIDNAYKVAEDLLRELLVRDKRRNVRRIGVKLDNIIIN 344
                                    10        20        30    |   40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340    
                                                             35  39                                                                                                                                                                                                                                                                                                                 

   Legend:   → Mismatch (orange background)
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    → 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  (3, 6)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: HHH (112)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DPO4_SULSF | P96022)
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:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    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.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DPO4_SULSF | P960221im4 1k1s

(-) Related Entries Specified in the PDB File

1k1s CRYSTAL STRUCTURE OF DINB FROM SULFOLOBUS SOLFATARICUS