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(-) Description

Title :  INSIGHTS INTO THE REPLISOME FROM THE CRYSTRAL STRUCTURE OF THE TERNARY COMPLEX OF THE EUBACTERIAL DNA POLYMERASE III ALPHA-SUBUNIT
 
Authors :  R. A. Wing, S. Bailey, T. A. Steitz
Date :  31 Jul 08  (Deposition) - 23 Sep 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.60
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  Ob Fold, Nucleotidyl Transferase, Polymerase, Beta Barrel, Cytoplasm, Dna Replication, Dna-Directed Dna Polymerase, Nucleotidyltransferase, Transferase, Transferase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. A. Wing, S. Bailey, T. A. Steitz
Insights Into The Replisome From The Structure Of A Ternary Complex Of The Dna Polymerase Iii Alpha-Subunit.
J. Mol. Biol. V. 382 859 2008
PubMed-ID: 18691598  |  Reference-DOI: 10.1016/J.JMB.2008.07.058
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA SUBSTRATE TEMPLATE STRAND
    Chains: C, E
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA SUBSTRATE PRIMER STRAND
    Chains: D, F
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA POLYMERASE III SUBUNIT ALPHA
    Chains: A, B
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DNAE
    Mutation: YES
    Organism Scientific: THERMUS AQUATICUS
    Organism Taxid: 271

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A CD  
Biological Unit 2 (1x):  B  EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2DOC2Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3DTP2Ligand/Ion2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2DOC1Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3DTP1Ligand/Ion2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2DOC1Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3DTP1Ligand/Ion2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:463BINDING SITE FOR RESIDUE CA A 1221
2AC2SOFTWAREASP B:463 , ASP B:465BINDING SITE FOR RESIDUE CA B 1221
3AC3SOFTWAREARG A:424 , GLY A:425 , SER A:426 , ARG A:452 , ASP A:465 , HIS A:817 , DT C:6 , DG C:7BINDING SITE FOR RESIDUE DTP A 1222
4AC4SOFTWAREARG B:424 , GLY B:425 , SER B:426 , ASP B:465 , HIS B:817 , DT E:6 , DG E:7BINDING SITE FOR RESIDUE DTP B 1222

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E0D)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asp A:238 -Pro A:239
2Asp B:238 -Pro B:239
3Pro B:1128 -Lys B:1129

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E0D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3E0D)

(-) Exons   (0, 0)

(no "Exon" information available for 3E0D)

(-) 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:1148
 aligned with DPO3A_THEAQ | Q9XDH5 from UniProtKB/Swiss-Prot  Length:1220

    Alignment length:1201
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204 
         DPO3A_THEAQ      5 LKFAHLHQHTQFSLLDGAAKLQDLLKWVKETTPEDPALAMTDHGNLFGAVEFYKKATAMGVKPIIGYEAYVAAESRFDRKRGKGLDGGYFHLTLLAKDFTGYQNLVRLASRAYLEGFYEKPRIDREILREHAQGLIALSGCLGAEIPQFILQDRLDLAEARLNEDLSIFGDRFFIEIQNHGLPEQKKVNQVLKEFARKYGLGMVATNDGHYVRKEDARAHEVLLAIQSKTTLDDPERWRFPCDEFYVKTPEEMRAMLPEAEWGDEPFDNTVEIARMCDVDLPIGDKMVYRIPRFPLPEGRTEAQYLRELTFLGLLRRYPDRITEAFYREVLRLLGTMPPHGDERALAEALARVEEKAWEELRKRLPPLEGVREWTAEAILHRALYELSVIERMGFPGYFLIVQDYINWARGHGVSVGPGRGSAAGSLVAYAVGITNIDPLRFGLLFERFLNPERVSMPDIDTDFSDRERDRVIQYVRERYGEDKVAQIGTFGSLASKAALKDVARVYGIPHKKAEELAKLIPVQFGKPKPLQEAIQVVPELRAEMEKDERIRQVIEVAMRLEGLNRHASVHAAGVVIAAEPLTDLVPLMRDQEGRPVTQYDMGAVEALGLLKMDFLGLRTLTFLDEARRIVKESKGVELDYDRLPLDDPKTFELLSRGETKGVFQLESGGMTATVRGLKPRRLEDIIALVSLYRPGPMEHIPTYIRRHHGQEPVSYAEFPHAEKYLRPILDETYGIPVYQEQIMQIASQVAGYSLGEADLLRRAMGKKRVEEMQKHRERFVRGAKERGVPEEEANRLFDMLEAFANYGFNKSHAAAYSLLSYQTAYVKAHYPVEFMAALLSVERHDSDKVAEYIRDARALGIPVLPPDVNRSGFDFKVVGEEILFGLSAVKNVGEMAARAILEERERGGPFKSLGDFLKRLPEQVVNKRALESLVKAGALDAFGDRARLLASLEPLLRWAAETRERGRSGLVGLFAEVEEPPLVEASPLDEITMLRYEKEALGIYVSGHPVLRYPGLREVASCTIEELSEFVRELPGKPKVLLSGMVEEVVRKPTRSGGMMARFTLSDETGALEVVVFGRAYEGVSPKLKEDIPLLVLAEVEKGEELRVLAQAVWTLEEVLEAPKALEVEVDHALLDEKGVARLKSLLDEHPGSLPVYLRVLGPFGEALFALREVRVGEEALGLLEAEGYRAYLVPDREVF 1205
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhh...eeeeeeeeeee.........-----..eeeeeeee.hhhhhhhhhhhhhhhhhh......eehhhhhhhh...eeee.....hhhhhhhhh.hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhh....................--..hhhhhhhhhhhhhhhhhh....hhhhhhhhhh..-------hhhhhhhhhhhhhhhhhh.....--------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh............hhhhhh..........eee....hhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhh..hhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhh......eee...eeee...hhhhh..eee.....eeeeeehhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhh..........hhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhh............hhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh....ee...........eee..eee.........hhhhhhhhhhhhhhh....hhhhhhhhh.....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhh......eeeeeeee...------------.eeeee..eeeee.-------------....eeeeeee..-----..eeeee.hhhhhh.....eeeee.........-hhhhhhhhh.eeeeeeeeeee....eeeeeeeeeee..hhhhhhh....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3e0d A    5 LKFAHLHQHTQFSLLNGAAKLQDLLKWVKETTPEDPALAMTDHGNLFGAVEFYKKATAMGVKPIIGYEAYVAAESRFDRKR-----GGYFHLTLLAKDFTGYQNLVRLASRAYLEGFYEKPRIDREILREHAQGLIALSGCLGAEIPQFILQDRLDLAEARLNEDLSIFGDRFFIEIQNHGLPEQKKVNQVLKEFARKYGLGMVATNNGHYVRKEDARAHEVLLAIQSKTTLDDPERWRFPCDEFYVKTPEEMRAMLPEAEWGDEPFDNTVEIARMCDVDLPIGDKMVYRIPRFPL--GRTEAQYLRELTFLGLLRRYPDRITEAFYREVLRLL-------DERALAEALARVEEKAWEELRKR--------EWTAEAILHRALYELSVIERMGFPGYFLIVQDYINWARGHGVSVGPGRGSAAGSLVAYAVGITNIDPLRFGLLFERFLNPERVSMPDIDTDFSDRERDRVIQYVRERYGEDKVAQIGTFGSLASKAALKDVARVYGIPHKKAEELAKLIPVQFGKPKPLQEAFEAEPELRAEMEKDERIRQVIEVAMRLEGLNRHASVHAAGVVIAAEPLTDLVPLMRDQEGRPVTQYDMGAVEALGLLKMDFLGLRTLTFLDEARRIVKESKGVELDYDRLPLDDPKTFELLSRGETKGVFQLESGGMTATVRGLKPRRLEDIIALVSLYRPGPMEHIPTYIRRHHGQEPVSYAEFPHAEKYLRPILDETYGIPVYQEQIMQIASQVAGYSLGEADLLRRAMGKKRVEEMQKHRERFVRGAKERGVPEEEANRLFDMLEAFANYGFNKSHAAAYSLLSYQTAYVKAHYPVEFMAALLSVERHDSDKVAEYIRDARALGIPVLPPDVNRSGFDFKVVGEEILFGLSAVKNVGEMAARAILEERERGGPFKSLGDFLKRLPEQVVNKRALESLVKAGALDAFGDRARLLASLEPLLRWAAETRERGRSGLVGLFAEVEEPPLVEASPLDEITMLRYEKEALGIYVSGHPVLRYPGLREVASCTIEELSEFVRELPGKPKVLLSGMVEEV------------RFTLSDETGALEVV-------------KEDIPLLVLAEVE-----RVLAQAVWTLEEVLEAPKALEVEVDHALLDEKG-ARLKSLLDEHPGSLPVYLRVLGPFGEALFALREVRVGEEALGLLEAEGYRAYLVPDREVF 1205
                                    14        24        34        44        54        64        74        84|     | 94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294     | 304       314       324       334   |     - |     354       364   |     -  |    384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054         -  |   1074     |   -      1094      1104 |    1114      1124      1134      1144 |    1154      1164      1174      1184      1194      1204 
                                                                                                           85    91                                                                                                                                                                                                              300  |                                338     346                   368      377                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 1054         1067         1080          1094        1106  1112                            1144 |                                                           
                                                                                                                                                                                                                                                                                                                                    303                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       1146                                                           


Chain B from PDB  Type:PROTEIN  Length:1148
 aligned with DPO3A_THEAQ | Q9XDH5 from UniProtKB/Swiss-Prot  Length:1220

    Alignment length:1201
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204 
         DPO3A_THEAQ      5 LKFAHLHQHTQFSLLDGAAKLQDLLKWVKETTPEDPALAMTDHGNLFGAVEFYKKATAMGVKPIIGYEAYVAAESRFDRKRGKGLDGGYFHLTLLAKDFTGYQNLVRLASRAYLEGFYEKPRIDREILREHAQGLIALSGCLGAEIPQFILQDRLDLAEARLNEDLSIFGDRFFIEIQNHGLPEQKKVNQVLKEFARKYGLGMVATNDGHYVRKEDARAHEVLLAIQSKTTLDDPERWRFPCDEFYVKTPEEMRAMLPEAEWGDEPFDNTVEIARMCDVDLPIGDKMVYRIPRFPLPEGRTEAQYLRELTFLGLLRRYPDRITEAFYREVLRLLGTMPPHGDERALAEALARVEEKAWEELRKRLPPLEGVREWTAEAILHRALYELSVIERMGFPGYFLIVQDYINWARGHGVSVGPGRGSAAGSLVAYAVGITNIDPLRFGLLFERFLNPERVSMPDIDTDFSDRERDRVIQYVRERYGEDKVAQIGTFGSLASKAALKDVARVYGIPHKKAEELAKLIPVQFGKPKPLQEAIQVVPELRAEMEKDERIRQVIEVAMRLEGLNRHASVHAAGVVIAAEPLTDLVPLMRDQEGRPVTQYDMGAVEALGLLKMDFLGLRTLTFLDEARRIVKESKGVELDYDRLPLDDPKTFELLSRGETKGVFQLESGGMTATVRGLKPRRLEDIIALVSLYRPGPMEHIPTYIRRHHGQEPVSYAEFPHAEKYLRPILDETYGIPVYQEQIMQIASQVAGYSLGEADLLRRAMGKKRVEEMQKHRERFVRGAKERGVPEEEANRLFDMLEAFANYGFNKSHAAAYSLLSYQTAYVKAHYPVEFMAALLSVERHDSDKVAEYIRDARALGIPVLPPDVNRSGFDFKVVGEEILFGLSAVKNVGEMAARAILEERERGGPFKSLGDFLKRLPEQVVNKRALESLVKAGALDAFGDRARLLASLEPLLRWAAETRERGRSGLVGLFAEVEEPPLVEASPLDEITMLRYEKEALGIYVSGHPVLRYPGLREVASCTIEELSEFVRELPGKPKVLLSGMVEEVVRKPTRSGGMMARFTLSDETGALEVVVFGRAYEGVSPKLKEDIPLLVLAEVEKGEELRVLAQAVWTLEEVLEAPKALEVEVDHALLDEKGVARLKSLLDEHPGSLPVYLRVLGPFGEALFALREVRVGEEALGLLEAEGYRAYLVPDREVF 1205
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhh...eeeeeeeeeee.........-----..eeeeeeee.hhhhhhhhhhhhhhhhhh......eehhhhhhhh...eeee.....hhhhhhhhh.hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhh....................--..hhhhhhhhhhhhhhhhhh....hhhhhhhhhh..-------hhhhhhhhhhhhhhhhhh.....--------..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh............hhhhhh..........eee....hhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhh..hhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhh.......ee...eeee...hhhhh..eee.....eee..hhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhh..........hhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhh............hhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh....ee...........eee..eee.........hhhhhhhhhhhhhhh....hhhhhhhhh.....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhh.....hhhhhhhhhhhhh.....hhhhhhh......eeeeeeee...------------.eeeee..eeeee.-------------....eeeeeee..-----..eeeeeeehhhhh....eeeeee.........-hhhhhhhhh.eeeeeeeeeee....eeeeeeeeeee..hhhhhhh....eeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3e0d B    5 LKFAHLHQHTQFSLLNGAAKLQDLLKWVKETTPEDPALAMTDHGNLFGAVEFYKKATAMGVKPIIGYEAYVAAESRFDRKR-----GGYFHLTLLAKDFTGYQNLVRLASRAYLEGFYEKPRIDREILREHAQGLIALSGCLGAEIPQFILQDRLDLAEARLNEDLSIFGDRFFIEIQNHGLPEQKKVNQVLKEFARKYGLGMVATNNGHYVRKEDARAHEVLLAIQSKTTLDDPERWRFPCDEFYVKTPEEMRAMLPEAEWGDEPFDNTVEIARMCDVDLPIGDKMVYRIPRFPL--GRTEAQYLRELTFLGLLRRYPDRITEAFYREVLRLL-------DERALAEALARVEEKAWEELRKR--------EWTAEAILHRALYELSVIERMGFPGYFLIVQDYINWARGHGVSVGPGRGSAAGSLVAYAVGITNIDPLRFGLLFERFLNPERVSMPDIDTDFSDRERDRVIQYVRERYGEDKVAQIGTFGSLASKAALKDVARVYGIPHKKAEELAKLIPVQFGKPKPLQEAFEAEPELRAEMEKDERIRQVIEVAMRLEGLNRHASVHAAGVVIAAEPLTDLVPLMRDQEGRPVTQYDMGAVEALGLLKMDFLGLRTLTFLDEARRIVKESKGVELDYDRLPLDDPKTFELLSRGETKGVFQLESGGMTATVRGLKPRRLEDIIALVSLYRPGPMEHIPTYIRRHHGQEPVSYAEFPHAEKYLRPILDETYGIPVYQEQIMQIASQVAGYSLGEADLLRRAMGKKRVEEMQKHRERFVRGAKERGVPEEEANRLFDMLEAFANYGFNKSHAAAYSLLSYQTAYVKAHYPVEFMAALLSVERHDSDKVAEYIRDARALGIPVLPPDVNRSGFDFKVVGEEILFGLSAVKNVGEMAARAILEERERGGPFKSLGDFLKRLPEQVVNKRALESLVKAGALDAFGDRARLLASLEPLLRWAAETRERGRSGLVGLFAEVEEPPLVEASPLDEITMLRYEKEALGIYVSGHPVLRYPGLREVASCTIEELSEFVRELPGKPKVLLSGMVEEV------------RFTLSDETGALEVV-------------KEDIPLLVLAEVE-----RVLAQAVWTLEEVLEAPKALEVEVDHALLDEKG-ARLKSLLDEHPGSLPVYLRVLGPFGEALFALREVRVGEEALGLLEAEGYRAYLVPDREVF 1205
                                    14        24        34        44        54        64        74        84|     | 94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294     | 304       314       324       334   |     - |     354       364   |     -  |    384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054         -  |   1074     |   -      1094      1104 |    1114      1124      1134      1144 |    1154      1164      1174      1184      1194      1204 
                                                                                                           85    91                                                                                                                                                                                                              300  |                                338     346                   368      377                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 1054         1067         1080          1094        1106  1112                            1144 |                                                           
                                                                                                                                                                                                                                                                                                                                    303                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       1146                                                           


Chain C from PDB  Type:DNA  Length:20
                                                     
                3e0d C    6 TGTGGCACTGGCCGTCGTTT   25
                                    15        25


Chain D from PDB  Type:DNA  Length:19
                                                    
                3e0d D    3 AAACGACGGCCAGTGCCAc   21
                                    12        |
                                             21-DOC


Chain E from PDB  Type:DNA  Length:20
                                                     
                3e0d E    6 TGTGGCACTGGCCGTCGTTT   25
                                    15        25


Chain F from PDB  Type:DNA  Length:19
                                                    
                3e0d F    3 AAACGACGGCCAGTGCCAc   21
                                    12        |
                                             21-DOC
   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 3E0D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3E0D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E0D)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DPO3A_THEAQ | Q9XDH5)
molecular function
    GO:0008408    3'-5' exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
    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:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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: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:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 Visualization

(-) Interactive Views

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        DPO3A_THEAQ | Q9XDH5: 2hpi 2hpm 4iqj

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