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(-) Description

Title :  PHI29 DNA POLYMERASE COMPLEXED WITH PRIMER-TEMPLATE DNA AND INCOMING NUCLEOTIDE SUBSTRATES (TERNARY COMPLEX)
 
Authors :  A. J. Berman, S. Kamtekar, J. L. Goodman, J. M. Lazaro, M. De Vega, L. Blanco, M. Salas, T. A. Steitz
Date :  16 May 07  (Deposition) - 17 Jul 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.03
Chains :  Asym. Unit :  A,B,J,K,Q,R,X,Y
Biol. Unit 1:  A,X,Y  (1x)
Biol. Unit 2:  B,Q,R  (1x)
Biol. Unit 3:  J,K  (1x)
Keywords :  Protein-Dna Complex, Replication, Transferase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Berman, S. Kamtekar, J. L. Goodman, J. M. Lazaro, M. De Vega, L. Blanco, M. Salas, T. A. Steitz
Structures Of Phi29 Dna Polymerase Complexed With Substrate: The Mechanism Of Translocation In B-Family Polymerases
Embo J. V. 26 3494 2007
PubMed-ID: 17611604  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601780
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(GACTGCTTA(DOC)-3'
    Chains: X, Q, J
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-D(ACACGTAAGCAGTC)-3'
    Chains: Y, R, K
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA POLYMERASE
    Chains: A, B
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: 2, GP2
    Mutation: YES
    Organism Scientific: BACILLUS PHAGE PHI29
    Organism Taxid: 10756
    Synonym: EARLY PROTEIN GP2

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABJKQRXY
Biological Unit 1 (1x): A     XY
Biological Unit 2 (1x):  B  QR  
Biological Unit 3 (1x):   JK    

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 50)

Asymmetric Unit (5, 50)
No.NameCountTypeFull Name
1DGT2Ligand/Ion2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2DOC3Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3EDO41Ligand/Ion1,2-ETHANEDIOL
4MG2Ligand/IonMAGNESIUM ION
5MN2Ligand/IonMANGANESE (II) ION
Biological Unit 1 (3, 23)
No.NameCountTypeFull Name
1DGT1Ligand/Ion2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2DOC1Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3EDO21Ligand/Ion1,2-ETHANEDIOL
4MG-1Ligand/IonMAGNESIUM ION
5MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (3, 19)
No.NameCountTypeFull Name
1DGT1Ligand/Ion2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2DOC1Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3EDO17Ligand/Ion1,2-ETHANEDIOL
4MG-1Ligand/IonMAGNESIUM ION
5MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1DGT-1Ligand/Ion2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2DOC1Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3EDO3Ligand/Ion1,2-ETHANEDIOL
4MG-1Ligand/IonMAGNESIUM ION
5MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (47, 47)

Asymmetric Unit (47, 47)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP B:249 , VAL B:250 , ASP B:458 , DGT B:1589 , MG B:9002BINDING SITE FOR RESIDUE MN B 9001
02AC2SOFTWAREASP B:249 , ASP B:458 , DGT B:1589 , MN B:9001 , HOH B:9084 , HOH B:9130 , DOC Q:10BINDING SITE FOR RESIDUE MG B 9002
03AC3SOFTWAREASP A:249 , VAL A:250 , ASP A:458 , DGT A:1588 , MG A:9004BINDING SITE FOR RESIDUE MN A 9003
04AC4SOFTWAREASP A:249 , ASP A:458 , DGT A:1588 , MN A:9003 , HOH A:9158 , HOH A:9326 , DOC X:10BINDING SITE FOR RESIDUE MG A 9004
05AC5SOFTWAREASP A:249 , VAL A:250 , ASN A:251 , SER A:252 , LEU A:253 , TYR A:254 , LYS A:371 , LYS A:383 , ASN A:387 , TYR A:390 , ASP A:458 , MN A:9003 , MG A:9004 , HOH A:9018 , HOH A:9042 , HOH A:9090 , HOH A:9155 , HOH A:9236 , HOH A:9326 , HOH A:9435 , DOC X:10 , DC Y:6 , DG Y:7BINDING SITE FOR RESIDUE DGT A 1588
06AC6SOFTWAREASP B:249 , VAL B:250 , ASN B:251 , SER B:252 , LEU B:253 , TYR B:254 , LYS B:371 , LYS B:383 , ASN B:387 , TYR B:390 , THR B:457 , ASP B:458 , EDO B:2775 , MN B:9001 , MG B:9002 , HOH B:9013 , HOH B:9017 , HOH B:9047 , HOH B:9048 , HOH B:9065 , HOH B:9130 , HOH B:9150 , DOC Q:10 , DC R:6 , DG R:7BINDING SITE FOR RESIDUE DGT B 1589
07AC7SOFTWAREARG B:491 , ASP B:503 , THR B:542 , PHE B:543 , HOH B:9125BINDING SITE FOR RESIDUE EDO B 2762
08AC8SOFTWAREILE B:504 , MET B:506 , GLU B:515 , LYS B:525 , HOH B:9266BINDING SITE FOR RESIDUE EDO B 2763
09AC9SOFTWARETYR B:265 , THR B:356BINDING SITE FOR RESIDUE EDO B 2764
10BC1SOFTWAREDA K:6 , DA K:10 , HOH K:1218BINDING SITE FOR RESIDUE EDO K 2765
11BC2SOFTWAREDA K:6 , EDO K:2767 , DC R:4BINDING SITE FOR RESIDUE EDO K 2766
12BC3SOFTWAREASP B:104 , LYS B:114 , HIS B:116 , DC K:5 , DA K:6 , EDO K:2766 , DC R:4BINDING SITE FOR RESIDUE EDO K 2767
13BC4SOFTWAREPHE A:309 , THR B:368 , THR B:372 , LYS B:478 , LYS B:479 , LEU B:480 , HOH B:9026 , HOH B:9217 , HOH B:9296BINDING SITE FOR RESIDUE EDO B 2769
14BC5SOFTWAREGLY A:481 , TYR A:482BINDING SITE FOR RESIDUE EDO A 2770
15BC6SOFTWARELYS A:274 , HIS A:284 , GLN A:286 , LEU A:333 , LYS A:337 , TYR A:347BINDING SITE FOR RESIDUE EDO A 2771
16BC7SOFTWARELYS A:305 , DA Y:9 , HOH Y:1029 , HOH Y:1030BINDING SITE FOR RESIDUE EDO Y 2772
17BC8SOFTWAREARG A:308 , EDO A:2774 , ASP B:365BINDING SITE FOR RESIDUE EDO A 2773
18BC9SOFTWAREEDO A:2773 , HOH A:9397 , TYR B:369BINDING SITE FOR RESIDUE EDO A 2774
19CC1SOFTWAREASN B:251 , LYS B:371 , LYS B:379 , PRO B:477 , DGT B:1589 , HOH B:9008BINDING SITE FOR RESIDUE EDO B 2775
20CC2SOFTWAREGLY B:376 , LYS B:379BINDING SITE FOR RESIDUE EDO B 2776
21CC3SOFTWAREHIS A:149 , LYS A:150 , GLU A:151 , GLU B:334 , GLU B:338 , TRP B:436 , TYR B:439BINDING SITE FOR RESIDUE EDO B 2777
22CC4SOFTWAREARG B:227 , THR B:301 , ILE B:302 , GLN B:303 , ASP B:332 , ARG B:438 , HOH B:9097 , HOH B:9122BINDING SITE FOR RESIDUE EDO B 2778
23CC5SOFTWAREGLU A:151 , PRO A:153 , PRO B:282 , HOH B:9287BINDING SITE FOR RESIDUE EDO B 2779
24CC6SOFTWAREASN A:62 , PRO A:558 , HOH A:9262BINDING SITE FOR RESIDUE EDO A 2780
25CC7SOFTWAREASN A:62 , PRO A:129 , HOH A:9245BINDING SITE FOR RESIDUE EDO A 2781
26CC8SOFTWAREPHE A:414 , ARG A:415 , LEU A:416 , DT X:4 , DG X:5 , HOH X:834BINDING SITE FOR RESIDUE EDO X 2782
27CC9SOFTWARELYS A:206 , LEU A:359 , HOH A:9377BINDING SITE FOR RESIDUE EDO A 2784
28DC1SOFTWAREDT Q:8 , DA Q:9 , DOC Q:10 , HOH Q:2791 , HOH Q:2796 , HOH Q:2799 , HOH Q:2800BINDING SITE FOR RESIDUE EDO Q 2785
29DC2SOFTWAREGLN A:380 , LYS A:383 , HOH A:9229 , HOH A:9317BINDING SITE FOR RESIDUE EDO A 2786
30DC3SOFTWAREMET B:4 , GLU B:291 , HOH B:9324BINDING SITE FOR RESIDUE EDO B 2787
31DC4SOFTWAREDG Y:14BINDING SITE FOR RESIDUE EDO Y 2788
32DC5SOFTWARESER A:551 , GLU B:33 , LYS B:182 , GLU B:296 , HOH B:9277BINDING SITE FOR RESIDUE EDO B 2789
33DC6SOFTWAREARG A:552 , MET A:554 , EDO A:2803 , ASP B:34 , GLU B:296BINDING SITE FOR RESIDUE EDO A 2790
34DC7SOFTWARETYR B:29 , SER B:36 , TYR B:38BINDING SITE FOR RESIDUE EDO B 2791
35DC8SOFTWARELYS A:143 , ILE A:323 , HOH A:9123 , HOH A:9291BINDING SITE FOR RESIDUE EDO A 2792
36DC9SOFTWAREGLN A:183 , LYS A:366BINDING SITE FOR RESIDUE EDO A 2793
37EC1SOFTWAREGLN A:257 , THR A:440 , GLY A:481 , HOH A:9110 , HOH A:9142BINDING SITE FOR RESIDUE EDO A 2794
38EC2SOFTWAREHOH B:9202BINDING SITE FOR RESIDUE EDO B 2795
39EC3SOFTWAREARG B:496 , LYS B:575 , DG R:11 , DC R:12BINDING SITE FOR RESIDUE EDO R 2796
40EC4SOFTWARELYS A:64 , GLY A:98 , TRP A:100 , LYS A:402 , PHE A:414 , HOH A:9197 , DG X:5 , DC X:6BINDING SITE FOR RESIDUE EDO A 2797
41EC5SOFTWAREPHE A:414 , GLN A:560 , HOH A:9306 , DG X:5 , DC X:6 , HOH X:1053BINDING SITE FOR RESIDUE EDO X 2798
42EC6SOFTWARELYS A:64 , MET A:97 , DC X:6 , DT X:7BINDING SITE FOR RESIDUE EDO A 2800
43EC7SOFTWAREGLY A:41 , ASN A:42 , GLU A:46BINDING SITE FOR RESIDUE EDO A 2801
44EC8SOFTWAREPHE A:309 , TYR A:310 , SER A:319 , GLY A:320 , THR B:372 , LYS B:478BINDING SITE FOR RESIDUE EDO B 2802
45EC9SOFTWAREGLY A:549 , PHE A:550 , SER A:551 , ARG A:552 , EDO A:2790 , HOH A:9198 , GLU B:33 , ASP B:34 , HIS B:35BINDING SITE FOR RESIDUE EDO A 2803
46FC1SOFTWARETHR A:92 , ILE A:93 , ILE A:94 , GLY A:401 , LYS A:402 , HOH A:9271BINDING SITE FOR RESIDUE EDO A 2804
47FC2SOFTWARELYS A:150 , SER B:260 , ARG B:261 , HOH B:9037BINDING SITE FOR RESIDUE EDO B 2805

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PYJ)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys B:110 -Gly B:111
2Tyr B:148 -His B:149
3Pro B:562 -Gly B:563
4Gly B:563 -Gly B:564

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_DPOL_BPPH2_001 *A176RDPOL_BPPH2  ---  ---A/BA176R
2UniProtVAR_DPOL_BPPH2_002 *A355VDPOL_BPPH2  ---  ---A/BA355V
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_DPOL_BPPH2_001 *A176RDPOL_BPPH2  ---  ---AA176R
2UniProtVAR_DPOL_BPPH2_002 *A355VDPOL_BPPH2  ---  ---AA355V
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_DPOL_BPPH2_001 *A176RDPOL_BPPH2  ---  ---BA176R
2UniProtVAR_DPOL_BPPH2_002 *A355VDPOL_BPPH2  ---  ---BA355V
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (0, 0)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNA_POLYMERASE_BPS00116 DNA polymerase family B signature.DPOL_BPPH2454-462
 		  2A:454-462
B:454-462
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNA_POLYMERASE_BPS00116 DNA polymerase family B signature.DPOL_BPPH2454-462
 		  1A:454-462
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNA_POLYMERASE_BPS00116 DNA polymerase family B signature.DPOL_BPPH2454-462
 		  1-
B:454-462
Biological Unit 3 (, 0)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNA_POLYMERASE_BPS00116 DNA polymerase family B signature.DPOL_BPPH2454-462
 		  0-
-

(-) Exons   (0, 0)

(no "Exon" information available for 2PYJ)

(-) 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:567
 aligned with DPOL_BPPH2 | P03680 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:571
                                    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 
           DPOL_BPPH2     5 PRKMYSCDFETTTKVEDCRVWAYGYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFIINWLERNGFKWSADGLPNTYNTIISRMGQWYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLKGDIDYHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLDKEVRYAYRGGFTWLNDRFKEKEIGEGMVFDVNSLYPAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDKWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDPKKLGYWAHESTFKRAKYLRQKTYIQDIYMKEVDGKLVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKVGFSRKMKPKPVQVPGGVVLVDDTFTIK 575
               SCOP domains d2pyja1 A:5-187 Exonuclease domain of phi29 DNA polymerase                                                                                                                             d2pyja2 A:188-575 phi29 DNA polymerase                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2pyjA01 A:5-188  [code=3.30.420.10, no name defined]                                                                                                                                    2pyjA02 A:189-261,A:426-531 Palm domain of DNA polymerase                2pyjA03 A:262-359 TPR 1 domain of DNA polymerase                                                  2pyjA04 A:360-395 Helix hairpin bin 2pyjA05 A:396-425             2pyjA02 A:189-261,A:426-531 Palm domain of DNA polymerase                                                 2pyjA06 A:532-575 DNA polymerase; domain 6   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee........eeeeeeee..eeeeeeee.hhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhh..ee.......eeeeee.....eeeeeeeeeee..eeeeeeeee.hhh...hhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh......eee.......ee..eeeeee.hhhhhhhhhh.eeeeeeeeee..........eeeeeeeeeeee.............................eeeeeehhhhhhhhhheeeeeeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee.....eeeee.........hhhhhhhhhhhhhhhhhhhhhhh...eeeee..eeeee...................eeeeeeeeeeeeee..eeeeeeee...----.........eeeeeeee...hhhhhh...........eeeeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYM----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pyj A   5 PRKMYSCAFETTTKVEDCRVWAYGYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHNLKFAGAFIINWLERNGFKWSADGLPNTYNTIISRMGQWYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLKGDIDYHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLDKEVRYAYRGGFTWLNDRFKEKEIGEGMVFDVNSLYPAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDKWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDPKKLGYWAHESTFKRAKYLRQKTYIQDIYMKEV----VEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKVGFSRKMKPKPVQVPGGVVLVDDTFTIK 575
                                    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 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  509  514                                                             


Chain B from PDB  Type:PROTEIN  Length:572
 aligned with DPOL_BPPH2 | P03680 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:573
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572   
           DPOL_BPPH2     3 HMPRKMYSCDFETTTKVEDCRVWAYGYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFIINWLERNGFKWSADGLPNTYNTIISRMGQWYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLKGDIDYHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLDKEVRYAYRGGFTWLNDRFKEKEIGEGMVFDVNSLYPAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDKWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDPKKLGYWAHESTFKRAKYLRQKTYIQDIYMKEVDGKLVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKVGFSRKMKPKPVQVPGGVVLVDDTFTIK 575
               SCOP domains d2pyjb1 B:3-187 Exonuclease domain of phi29 DNA polymerase                                                                                                                               d2pyjb2 B:188-575 phi29 DNA polymerase                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2pyjB01 B:3-188  [code=3.30.420.10, no name defined]                                                                                                                                      2pyjB02 B:189-261,B:426-531 Palm domain of DNA polymerase                2pyjB03 B:262-359 TPR 1 domain of DNA polymerase                                                  2pyjB04 B:360-395 Helix hairpin bin 2pyjB05 B:396-425             2pyjB02 B:189-261,B:426-531 Palm domain of DNA polymerase                                                 2pyjB06 B:532-575 DNA polymerase; domain 6   CATH domains
           Pfam domains (1) ----------------------------------------------DNA_pol_B_2-2pyjB01 B:49-488                                                                                                                                                                                                                                                                                                                                                                                                                            --------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------DNA_pol_B_2-2pyjB02 B:49-488                                                                                                                                                                                                                                                                                                                                                                                                                            --------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .....eeeeeeee..hhhhh.eeeeeeee..eeeeeeee.hhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhh..ee.......eeeeee.....eeeeeeeeee....eeeeeeee.hhh...hhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh......eee.hhhh..ee..eeeeee.hhhhhhhhhh.eeeeeeeeee..........eeeeeeeeeeee.............................eeeeeehhhhhhhhhheeeeeeeeeeeeeeeee...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.......eeeee.....eeeee.........hhhhhhhhhhhhhhhhhhhhhhh...eeeee..eeeee....hhhhhhhh.......eeeeeeeeeeeeee..eeeeeeeeee.-..eee.......eeeeeeee...hhhhhh...........ee...eeee......eeee..ee.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYM----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pyj B   3 HMPRKMYSCAFETTTKVEDCRVWAYGYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHNLKFAGAFIINWLERNGFKWSADGLPNTYNTIISRMGQWYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLKGDIDYHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLDKEVRYAYRGGFTWLNDRFKEKEIGEGMVFDVNSLYPAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDKWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDPKKLGYWAHESTFKRAKYLRQKTYIQDIYMKEV-GKLVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKVGFSRKMKPKPVQVPGGVVLVDDTFTIK 575
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502      |512       522       532       542       552       562       572   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    509 |                                                                
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      511                                                                


Chain J from PDB  Type:DNA  Length:10
                                          
                 2pyj J   1 GACTGCTTAc  10
                                    10
                                    10-DOC


Chain K from PDB  Type:DNA  Length:14
                                              
                 2pyj K   4 ACACGTAAGCAGTC  17
                                    13    


Chain Q from PDB  Type:DNA  Length:10
                                          
                 2pyj Q   1 GACTGCTTAc  10
                                    10
                                    10-DOC


Chain R from PDB  Type:DNA  Length:13
                                             
                 2pyj R   4 CACGTAAGCAGTC  16
                                    13   


Chain X from PDB  Type:DNA  Length:10
                                          
                 2pyj X   1 GACTGCTTAc  10
                                    10
                                    10-DOC


Chain Y from PDB  Type:DNA  Length:14
                                              
                 2pyj Y   3 ACACGTAAGCAGTC  16
                                    12
   Legend:   → Mismatch (orange background)
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 Classification and Annotation

(-) SCOP Domains  (2, 4)

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

(-) CATH Domains  (6, 12)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Few Secondary Structures (1120)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: DNA_pol_B-like (44)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DPOL_BPPH2 | P03680)
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:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0001882    nucleoside binding    Interacting selectively and non-covalently with a nucleoside, a compound consisting of a purine or pyrimidine nitrogenous base linked either to ribose or deoxyribose.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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.
    GO:0039693    viral DNA genome replication    The replication of a viral DNA genome.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DPOL_BPPH2 | P03680: 1xhx 1xhz 1xi1 2ex3 2py5 2pyl 2pzs

(-) Related Entries Specified in the PDB File

2py5 PHI29 DNA POLYMERASE COMPLEXED WITH SINGLE-STRANDED DNA
2pyl PHI29 DNA POLYMERASE COMPLEXED WITH PRIMER-TEMPLATE AND INCOMING NUCLEOTIDE SUBSTRATES (PRE-TRANSLOCATED TERNARY COMPLEX)
2pzs PHI29 DNA POLYMERASE COMPLEXED WITH PRIMER-TEMPLATE AND INCOMING NUCLEOTIDE SUBSTRATES (PRE-TRANSLOCATED TERNARY COMPLEX)