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(-) Description

Title :  CRYSTAL STRUCTURE OF DPO4 LINKER REGION P236A MUTANT WITH AN INCOMING D-DCDP
 
Authors :  R. Vyas, Z. Suo
Date :  16 Jul 14  (Deposition) - 27 Aug 14  (Release) - 17 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dbh, Dpo4, Polymerase, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Gaur, R. Vyas, J. D. Fowler, G. Efthimiopoulos, J. Y. Feng, Z. Suo
Structural And Kinetic Insights Into Binding And Incorporation Of L-Nucleotide Analogs By A Y-Family Dna Polymerase.
Nucleic Acids Res. V. 42 9984 2014
PubMed-ID: 25104018  |  Reference-DOI: 10.1093/NAR/GKU709

(-) Compounds

Molecule 1 - DNA POLYMERASE IV
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Taxid: 562
    Fragment: DPO4
    Gene: DBH, DPO4, SSO2448
    Mutation: YES
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 273057
    Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2
    Synonym: POL IV
 
Molecule 2 - DNA (5'-D(*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*(DOC))-3')
    Chains: B
    Engineered: YES
    Other Details: POLYDEOXYRIBONUCLEOTIDE
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*TP*TP*CP*AP*GP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3')
    Chains: C
    Engineered: YES
    Other Details: POLYDEOXYRIBONUCLEOTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric/Biological Unit (5, 13)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2CA4Ligand/IonCALCIUM ION
3DOC1Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
4GOL3Ligand/IonGLYCEROL
5YYY1Ligand/IonDEOXYCYTIDINE DIPHOSPHATE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:7 , PHE A:8 , TYR A:10 , PHE A:11 , TYR A:12 , ALA A:44 , THR A:45 , ARG A:51 , ASP A:105 , CA A:402 , HOH A:502 , HOH A:504 , HOH A:505 , HOH A:527 , HOH A:539 , HOH A:540 , HOH A:547 , HOH A:548 , DOC B:13 , DG C:5BINDING SITE FOR RESIDUE YYY A 401
02AC2SOFTWAREASP A:7 , PHE A:8 , ASP A:105 , YYY A:401 , HOH A:501BINDING SITE FOR RESIDUE CA A 402
03AC3SOFTWAREASP A:7 , GLU A:106 , HOH A:504 , HOH A:505 , DOC B:13 , HOH B:201BINDING SITE FOR RESIDUE CA A 403
04AC4SOFTWAREALA A:181 , ILE A:186 , HOH A:520 , HOH A:541 , HOH A:542 , HOH B:204BINDING SITE FOR RESIDUE CA A 404
05AC5SOFTWAREARG A:77 , LYS A:78 , GLU A:79BINDING SITE FOR RESIDUE ACT A 405
06AC6SOFTWAREGLY A:246 , ARG A:247 , LYS A:275 , DA C:7 , DG C:8BINDING SITE FOR RESIDUE ACT A 406
07AC7SOFTWAREILE A:99 , GLU A:100 , ILE A:101 , THR A:239 , ARG A:240BINDING SITE FOR RESIDUE ACT A 407
08AC8SOFTWARELYS A:172 , ILE A:175 , ARG A:176 , VAL A:203BINDING SITE FOR RESIDUE ACT A 408
09AC9SOFTWARECYS A:31 , VAL A:32 , PHE A:33 , MET A:76 , HOH A:523 , HOH A:576 , HOH A:602BINDING SITE FOR RESIDUE GOL A 409
10BC1SOFTWARELYS A:221 , TYR A:224 , DC C:11 , HOH C:223BINDING SITE FOR RESIDUE GOL A 410
11BC2SOFTWAREHOH A:637 , DG B:1 , DG B:2 , HOH B:223BINDING SITE FOR RESIDUE CA B 101
12BC3SOFTWAREDG C:5 , HOH C:219BINDING SITE FOR RESIDUE GOL C 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:159 -Pro A:160

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QWB)

(-) Sequences/Alignments

Asymmetric/Biological 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 ..eeeeee.hhhhhhhhhhhhhhh...eeeeee.......eeeeeehhhhhh.......hhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh....eeeee..eeeee......hhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee....eeeeeee.....hhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qwb A   1 MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEAIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFIEA 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:DNA  Length:13
                                             
                 4qwb B   1 GGCTACAGGACTc  13
                                    10  |
                                       13-DOC


Chain C from PDB  Type:DNA  Length:15
                                               
                 4qwb C   4 AGGAGTCCTGTAGCC  18
                                    13
   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  (0, 0)

(no "SCOP Domain" information available for 4QWB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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    Lys A:159 - Pro A:160   [ RasMol ]  
 

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  4qwb
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  DPO4_SULSO | Q97W02
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  2.7.7.7
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 Related Entries

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

UniProtKB/Swiss-Prot
        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 4f4y 4f4z 4f50 4fbt 4fbu 4g3i 4gc6 4gc7 4juz 4jv0 4jv1 4jv2 4qw8 4qw9 4qwa 4qwc 4qwd 4qwe 4rua 4ruc 4rzr 4tqr 4tqs 5edw

(-) Related Entries Specified in the PDB File

4qw8 4qw9 4qwa 4qwc 4qwd 4qwe