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(-) Description

Title :  Y-FAMILY DNA POLYMERASE CHIMERA DBH-DPO4-DBH
 
Authors :  J. D. Pata, R. C. Wilson
Date :  11 May 12  (Deposition) - 02 Jan 13  (Release) - 13 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.34
Chains :  Asym. Unit :  A,B,C,D,P,T
Biol. Unit 1:  A,P,T  (1x)
Biol. Unit 2:  B,C,D  (1x)
Keywords :  Y-Family Polymerase, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. C. Wilson, M. A. Jackson, J. D. Pata
Y-Family Polymerase Conformation Is A Major Determinant Of Fidelity And Translesion Specificity.
Structure V. 21 20 2013
PubMed-ID: 23245850  |  Reference-DOI: 10.1016/J.STR.2012.11.005

(-) Compounds

Molecule 1 - DNA POLYMERASE IV
    Chains: A, B
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BLR(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PKKT7-H
    Gene: DBH, DPO4 (S. SOLFATARICUS) AND DBH (S. ACIDOCALDARIUS), SACI_0554, DPO4, SSO2448
    Organism Scientific: SULFOLOBUS ACIDOCALDARIUS, SULFOLOBUS SOLFATARICUS
    Organism Taxid: 330779, 273057
    Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
    Synonym: POL IV
 
Molecule 2 - DNA (5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*GP*CP*CP*C)- 3')
    Chains: C, P
    Engineered: YES
    Organism Taxid: 32630
    Other Details: PRIMER DNA
    Other Details - Source: CHEMICALLY SYNTHESIZED
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*TP*TP*AP*CP*GP*CP*CP*CP*TP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3')
    Chains: D, T
    Engineered: YES
    Organism Taxid: 32630
    Other Details: TEMPLATE DNA
    Other Details - Source: CHEMICALLY SYNTHESIZED
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDPT
Biological Unit 1 (1x): A   PT
Biological Unit 2 (1x):  BCD  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2DCP2Ligand/Ion2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2DCP1Ligand/Ion2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2DCP1Ligand/Ion2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:10 , PHE A:11 , PHE A:12 , ALA A:44 , THR A:45 , ARG A:51 , GLY A:58 , ASP A:105 , CA A:402 , CA A:403 , HOH A:504 , HOH A:507 , HOH A:521 , HOH A:541 , HOH A:560 , HOH A:564 , HOH A:570 , DG P:13 , DC P:14 , DG T:5BINDING SITE FOR RESIDUE DCP A 401
2AC2SOFTWAREASP A:7 , PHE A:8 , ASP A:105 , DCP A:401 , HOH A:507BINDING SITE FOR RESIDUE CA A 402
3AC3SOFTWAREASP A:7 , ASP A:105 , GLU A:106 , DCP A:401 , DC P:14BINDING SITE FOR RESIDUE CA A 403
4AC4SOFTWAREASP B:7 , PHE B:8 , ASP B:105 , DCP C:101BINDING SITE FOR RESIDUE CA B 401
5AC5SOFTWAREASP B:7 , ASP B:105 , GLU B:106 , DC C:14 , DCP C:101BINDING SITE FOR RESIDUE CA B 402
6AC6SOFTWAREPHE B:8 , TYR B:10 , PHE B:11 , PHE B:12 , ALA B:44 , THR B:45 , ARG B:51 , ASP B:105 , CA B:401 , CA B:402 , DG C:13 , DC C:14 , HOH C:209 , HOH C:210 , HOH C:211 , DG D:5BINDING SITE FOR RESIDUE DCP C 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F4Y)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:160 -Pro A:161
2Lys B:160 -Pro B:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F4Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F4Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4F4Y)

(-) 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:343
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhh...eeeeee.......eeeeeehhhhhhh......hhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh...eeeeee..eeeee.......hhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhh.....eee....hhhhhhhh............hhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhhhhh.............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeeeeee.....hhhhhhhhhhhhhhhhh.......eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f4y A   1 MIVIFVDFDYFFAQVEEVLNPQYKGKPLVVCVYSGRTKTSGAVATANYEARKLGVKAGMPIIKAMQIAPSAIYVPMRKPIYEAFSNRIMNLLNKHADKIEVASIDEAYLDVTNKVEGNFENGIELARKIKQEILEKEKITVTVGVAPNKILAKIIADKSKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEKITGKAKALYLLKLAQDEYNEPIRTRVRKSIGRYLTLPYNTRDVKVILPYLKKAINEAYNKVNGIPMRITVIAIMEDLDILSKGKKFKHGISIDNAYKVAEDLLRELLVRDKRRNVRRIGVKLDNIII 343
                                    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   


Chain B from PDB  Type:PROTEIN  Length:343
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhh...eeeeee.......eeeeeehhhhhhh......hhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhh..eeee....eeeee.......hhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhh...hhhhhhhhhh.....hhhhh..hhhhhhhhhhhhhhhhhhhhhh.............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeeeeee.....hhhhhhhhhhhhhhhhhhhh....eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f4y B   1 MIVIFVDFDYFFAQVEEVLNPQYKGKPLVVCVYSGRTKTSGAVATANYEARKLGVKAGMPIIKAMQIAPSAIYVPMRKPIYEAFSNRIMNLLNKHADKIEVASIDEAYLDVTNKVEGNFENGIELARKIKQEILEKEKITVTVGVAPNKILAKIIADKSKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEKITGKAKALYLLKLAQDEYNEPIRTRVRKSIGRYLTLPYNTRDVKVILPYLKKAINEAYNKVNGIPMRITVIAIMEDLDILSKGKKFKHGISIDNAYKVAEDLLRELLVRDKRRNVRRIGVKLDNIII 343
                                    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   


Chain C from PDB  Type:DNA  Length:16
                                                
                 4f4y C   1 GGCACTGATCGGGCCC  16
                                    10      


Chain D from PDB  Type:DNA  Length:18
                                                  
                 4f4y D   2 TACGCCCTGATCAGTGCC  19
                                    11        


Chain P from PDB  Type:DNA  Length:16
                                                
                 4f4y P   1 GGCACTGATCGGGCCC  16
                                    10      


Chain T from PDB  Type:DNA  Length:18
                                                  
                 4f4y T   2 TACGCCCTGATCAGTGCC  19
                                    11
   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 4F4Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F4Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F4Y)

(-) Gene Ontology  (13, 26)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DPO4_SULAC | Q4JB80: 3bq0 3bq1 3bq2 4f4w 4f4x 4f4z 4f50 4hyk 4nlg
        DPO4_SULSO | Q97W02: 1jx4 1jxl 1n48 1n56 1ryr 1rys 1s0m 1s0n 1s0o 1s10 1s97 1s9f 2ago 2agp 2agq 2asd 2asj 2asl 2atl 2au0 2bq3 2bqr 2bqu 2br0 2c22 2c28 2c2d 2c2e 2c2r 2ia6 2ibk 2imw 2j6s 2j6t 2j6u 2jef 2jeg 2jei 2jej 2r8g 2r8h 2r8i 2rdi 2rdj 2uvr 2uvu 2uvv 2uvw 2v4q 2v4r 2v9w 2va2 2va3 2w8k 2w8l 2w9a 2w9b 2w9c 2xc9 2xca 2xcp 3fds 3gii 3gij 3gik 3gil 3gim 3khg 3khh 3khl 3khr 3m9m 3m9n 3m9o 3pr4 3pr5 3pvx 3pw0 3pw2 3pw4 3pw5 3pw7 3qz7 3qz8 3raq 3rax 3rb0 3rb3 3rb4 3rb6 3rbd 3rbe 3t5h 3t5j 3t5k 3t5l 3v6h 3v6j 3v6k 4f4w 4f4x 4f4z 4f50 4fbt 4fbu 4g3i 4gc6 4gc7 4juz 4jv0 4jv1 4jv2 4qw8 4qw9 4qwa 4qwb 4qwc 4qwd 4qwe 4rua 4ruc 4rzr 4tqr 4tqs 5edw

(-) Related Entries Specified in the PDB File

4f4w 4f4x 4f4z 4f50