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(-) Description

Title :  TERNARY COMPLEX OF RB69 MUTANT L415F WITH RIBONUCLEOTIDE AT -3 POSITION
 
Authors :  A. R. Clausen, L. C. Pedersen
Date :  01 May 13  (Deposition) - 09 Oct 13  (Release) - 30 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,P,T
Keywords :  Ribonucleotide, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. R. Clausen, M. S. Murray, A. R. Passer, L. C. Pedersen, T. A. Kunkel
Structure-Function Analysis Of Ribonucleotide Bypass By B Family Dna Replicases.
Proc. Natl. Acad. Sci. Usa V. 110 16802 2013
PubMed-ID: 24082122  |  Reference-DOI: 10.1073/PNAS.1309119110

(-) Compounds

Molecule 1 - DNA POLYMERASE
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: 43
    Mutation: YES
    Organism Scientific: ENTEROBACTERIA PHAGE RB69
    Organism Taxid: 12353
    Synonym: GP43
 
Molecule 2 - DNA/RNA (5'-D(*AP*CP*AP*GP*G)-R(P*U)- D(P*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
    Chains: T
    Engineered: YES
    Other Details: TEMPLATE STRAND
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*C)-3')
    Chains: P
    Engineered: YES
    Other Details: PRIMER STRAND
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : APT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric/Biological Unit (3, 13)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2NA6Ligand/IonSODIUM ION
3TTP1Ligand/IonTHYMIDINE-5'-TRIPHOSPHATE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:411 , LEU A:412 , SER A:414 , PHE A:415 , TYR A:416 , ARG A:482 , LYS A:560 , ASN A:564 , ASP A:623 , CA A:1002 , NA A:1013 , HOH A:1108 , HOH A:1167 , HOH A:1265 , DC P:115 , DA T:3 , DG T:4BINDING SITE FOR RESIDUE TTP A 1001
02AC2SOFTWAREASP A:411 , LEU A:412 , ASP A:623 , TTP A:1001 , NA A:1013BINDING SITE FOR RESIDUE CA A 1002
03AC3SOFTWAREGLU A:686 , GLU A:716BINDING SITE FOR RESIDUE CA A 1003
04AC4SOFTWAREGLU A:660 , ASP A:684 , HOH A:1404 , HOH A:1405BINDING SITE FOR RESIDUE CA A 1005
05AC5SOFTWAREGLU A:172 , GLU A:177 , HOH A:1441 , HOH A:1467BINDING SITE FOR RESIDUE NA A 1006
06AC6SOFTWAREASP A:192 , GLU A:196 , ASP A:860 , HOH A:1383BINDING SITE FOR RESIDUE CA A 1009
07AC7SOFTWAREASN A:505 , ASN A:507 , LYS A:531BINDING SITE FOR RESIDUE CA A 1010
08AC8SOFTWAREASN A:232 , HOH A:1399 , HOH A:1400 , HOH A:1401BINDING SITE FOR RESIDUE NA A 1011
09AC9SOFTWAREASP A:114 , ILE A:115 , GLU A:116 , HOH A:1437 , HOH A:1438 , HOH A:1439 , HOH A:1471BINDING SITE FOR RESIDUE NA A 1012
10BC1SOFTWAREASP A:411 , ASP A:623 , TTP A:1001 , CA A:1002 , HOH A:1141 , HOH A:1424BINDING SITE FOR RESIDUE NA A 1013

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4KHY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KHY)

(-) 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:899
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4khya1 A:1-375 Exonuclease domain of family B DNA polymerases                                                                                                                                                                                                                                                                                                                      d4khya2 A:376-902 Family B DNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee..eeeeeee.....eeeeee....eeeee.........ee.....eeeee..hhhhhhhhhhhhhhhh.......hhhhhhhhhhh......hhhhh.eeeeeeee...............eeeeeeee....eeeeeee.ee..ee....hhhhhhhhhhhh....hhhhhh.eeeeee.hhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhhhhhhhh....eeeeee...eeeeee...ee.hhhhhhhhhh.......hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..ee......................ee...eeeeee.hhhhhhhhhhh.....eeee....hhhhhhh..........ee....eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee...eeeeehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee..........eeeee..eeeeeeeee..eeeeeeeeeee.hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeee...hhh.ee..ee....hhhhhhhhhhhhhhh............eeeeee..........eeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4khy A   1 MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYFDIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYEIKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFDLLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRVKVIENSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNRYKYVMSFDLTSFYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMFD 902
                                    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    || 263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893         
                                                                                                                                                                                                                                                                                        255|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
                                                                                                                                                                                                                                                                                         259                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   


Chain P from PDB  Type:DNA  Length:14
                                              
                 4khy P 102 GCGGACTGCTTACC 115
                                   111    


Chain T from PDB  Type:DNA/RNA  Length:18
                                                  
                 4khy T   1 ACAGGUAAGCAGTCCGCG  18
                                    10
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  4khy
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  DPOL_BPR69 | Q38087
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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
        DPOL_BPR69 | Q38087: 1b1f 1b8h 1clq 1ig9 1ih7 1q9x 1q9y 1qe4 1waf 1wag 1wah 1wai 1waj 2atq 2dtu 2dy4 2oyq 2ozm 2ozs 2p5g 2p5o 3cfo 3cfp 3cfr 3cq8 3kd1 3kd5 3l8b 3lds 3lzi 3lzj 3nae 3nci 3ndk 3ne6 3ngi 3nhg 3qei 3qep 3qer 3qes 3qet 3qev 3qew 3qex 3qnn 3qno 3rma 3rmb 3rmc 3rmd 3rwu 3s9h 3scx 3si6 3sjj 3snn 3spy 3spz 3sq0 3sq1 3sq2 3sq4 3sun 3suo 3sup 3suq 3tab 3tae 3taf 3tag 3uiq 4dtj 4dtm 4dtn 4dto 4dtp 4dtr 4dts 4dtu 4dtx 4du1 4du3 4du4 4e3s 4fj5 4fj7 4fj8 4fj9 4fjg 4fjh 4fji 4fjj 4fjk 4fjl 4fjm 4fjn 4fjx 4fk0 4fk2 4fk4 4i9l 4i9q 4j2a 4j2b 4j2d 4j2e 4khn 4khq 4khs 4khu 4khw 4ki4 4ki6 4m3r 4m3t 4m3u 4m3w 4m3x 4m3y 4m3z 4m41 4m42 4m45

(-) Related Entries Specified in the PDB File

4khq 4khs 4khu 4khw 4ki4 4ki6