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(-) Description

Title :  PHI29 DNA POLYMERASE COMPLEXED WITH SINGLE-STRANDED DNA
 
Authors :  A. J. Berman, S. Kamtekar, J. L. Goodman, J. M. Lazaro, M. De Vega, L. Blanco, M. Salas, T. A. Steitz
Date :  15 May 07  (Deposition) - 17 Jul 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,D,E,J,L,Y
Biol. Unit 1:  A,D,J,Y  (1x)
Biol. Unit 2:  B,E,L  (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(GGACTTT)-3'
    Chains: J, Y, D, E, L
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 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

  1234567
Asymmetric Unit : ABDEJLY
Biological Unit 1 (1x): A D J Y
Biological Unit 2 (1x):  B E L 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 27)

Asymmetric Unit (1, 27)
No.NameCountTypeFull Name
1EDO27Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 18)
No.NameCountTypeFull Name
1EDO18Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 9)
No.NameCountTypeFull Name
1EDO9Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (27, 27)

Asymmetric Unit (27, 27)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:252 , LYS A:371 , LYS A:383 , ASN A:387 , HOH A:9362BINDING SITE FOR RESIDUE EDO A 8001
02AC2SOFTWARELYS B:238 , GLN B:497 , HOH B:9134BINDING SITE FOR RESIDUE EDO B 8002
03AC3SOFTWAREARG B:261 , HOH B:9103 , HOH B:9369 , HOH B:9476BINDING SITE FOR RESIDUE EDO B 8003
04AC4SOFTWARESER A:260 , THR A:357 , HOH A:9038BINDING SITE FOR RESIDUE EDO A 8004
05AC5SOFTWAREILE B:474 , LEU B:480 , TYR B:482 , HOH B:9084 , HOH B:9273BINDING SITE FOR RESIDUE EDO B 8005
06AC6SOFTWARELEU B:216 , ASP B:219 , LYS B:220 , ARG B:223 , PRO B:397BINDING SITE FOR RESIDUE EDO B 8006
07AC7SOFTWAREGLU B:241 , ILE B:242 , GLY B:243 , ARG B:491 , HOH B:9146BINDING SITE FOR RESIDUE EDO B 8007
08AC8SOFTWARELEU A:294 , LYS A:295 , GLU A:296 , GLY A:297 , TYR A:298 , LYS A:317 , TYR A:449BINDING SITE FOR RESIDUE EDO A 8008
09AC9SOFTWAREASN A:234 , ARG A:236 , TYR A:449 , HOH A:9573BINDING SITE FOR RESIDUE EDO A 8009
10BC1SOFTWARELYS A:490 , ARG A:491 , HOH A:9164BINDING SITE FOR RESIDUE EDO A 8010
11BC2SOFTWARELYS A:208 , PHE A:211 , THR A:213 , HOH A:9143 , HOH A:9515 , HOH A:9558BINDING SITE FOR RESIDUE EDO A 8011
12BC3SOFTWARETYR A:259 , ASP A:365 , THR A:368 , LEU A:480 , HOH A:9177 , HOH A:9780BINDING SITE FOR RESIDUE EDO A 8012
13BC4SOFTWARETYR A:405 , ARG A:415BINDING SITE FOR RESIDUE EDO A 8013
14BC5SOFTWARESER A:43 , ASP A:45 , TRP A:277 , HOH A:9124BINDING SITE FOR RESIDUE EDO A 9001
15BC6SOFTWARETYR B:259 , ASP B:365 , THR B:368 , HOH B:9397 , HOH B:9621BINDING SITE FOR RESIDUE EDO B 9002
16BC7SOFTWAREHIS B:485 , THR B:488 , GLY B:516BINDING SITE FOR RESIDUE EDO B 9003
17BC8SOFTWAREGLU B:33 , HIS B:35 , LEU B:178 , LYS B:182 , GLU B:296BINDING SITE FOR RESIDUE EDO B 9004
18BC9SOFTWAREVAL A:210 , TYR A:265 , EDO A:9006BINDING SITE FOR RESIDUE EDO A 9005
19CC1SOFTWARELYS A:206 , THR A:357 , GLY A:358 , LEU A:359 , EDO A:9005BINDING SITE FOR RESIDUE EDO A 9006
20CC2SOFTWAREGLU A:334 , TYR A:439 , HOH A:9126 , HOH A:9753 , HOH A:9773BINDING SITE FOR RESIDUE EDO A 9007
21CC3SOFTWAREGLN A:257 , SER A:260 , ARG A:261 , THR A:440 , GLY A:481 , HOH A:9171BINDING SITE FOR RESIDUE EDO A 9008
22CC4SOFTWAREVAL B:528 , LYS B:529 , CYS B:530 , LYS B:538 , HOH B:9446BINDING SITE FOR RESIDUE EDO B 9009
23CC5SOFTWAREASP A:456 , THR A:457 , ASP A:458 , SER A:459BINDING SITE FOR RESIDUE EDO A 9010
24CC6SOFTWAREILE A:269 , ASP A:278 , HOH A:9370 , HOH A:9518 , GLY B:111BINDING SITE FOR RESIDUE EDO A 9011
25CC7SOFTWAREHIS A:485 , GLU A:486 , GLY A:516BINDING SITE FOR RESIDUE EDO A 9012
26CC8SOFTWAREGLU A:338 , THR A:443 , ALA A:447 , HOH A:9089 , HOH A:9669 , HOH A:9672 , HOH A:9674BINDING SITE FOR RESIDUE EDO A 9013
27CC9SOFTWAREILE A:504 , GLU A:515 , LYS A:525 , HOH A:9320BINDING SITE FOR RESIDUE EDO A 9014

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PY5)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:312 -Asn A:313
2Lys B:143 -Gly B:144
3Gly B:144 -Asp B:145

 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)

(-) 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

(-) Exons   (0, 0)

(no "Exon" information available for 2PY5)

(-) 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:564
 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 d2py5a1 A:5-187 Exonuclease domain of phi29 DNA polymerase                                                                                                                             d2py5a2 A:188-575 phi29 DNA polymerase                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2py5A01 A:5-188  [code=3.30.420.10, no name defined]                                                                                                                                    2py5A02 A:189-261,A:426-531 Palm domain of DNA polymerase                2py5A03 A:262-359 TPR 1 domain of DNA polym       erase                                           2py5A04 A:360-395 Helix hairpin bin 2py5A05 A:396-425             2py5A02 A:189-261,A:426-531 Palm domain of DNA polymerase                                                 2py5A06 A:532-575 DNA polymerase; domain 6   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee........eeeeeeee......eeee.hhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhh..ee.......eeeeee.....eeeeeeeeeee..eeeeeeeeehhhhh..hhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh......eee.hhhh..ee..eeeeee.hhhhhhhhhh.eeeeeeeeee..........eeeeeeeeeeee..........-------............eeeeeehhhhhhhhhheeeeeeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee.....eeeee.........hhhhhhhhhhhhhhhhhhhhhhh...eeeee..eeeee....hhhhhhhh.......eeeeeeeeeeeeee..eeeeeeeeeee..eeee.......eeeeeeee...hhhhhh...........eeeeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYM----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2py5 A   5 PRKMYSCAFETTTKVEDCRVWAYGYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHNLKFAGAFIINWLERNGFKWSADGLPNTYNTIISRMGQWYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLKGDIDYHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLDKEVRYAYRGGFTWLNDRFKEKEIGEGMVFDVNSLYPAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPTIQI-------GNEYLKSSGGEIADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDKWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDPKKLGYWAHESTFKRAKYLRQKTYIQDIYMKEVDGKLVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKVGFSRKMKPKPVQVPGGVVLVDDTFTIK 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 
                                                                                                                                                                                                                                                                                                                                     304     312                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:562
 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 d2py5b1 B:5-187 Exonuclease domain of phi29 DNA polymerase                                                                                                                             d2py5b2 B:188-575 phi29 DNA polymerase                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2py5B01 B:5-188  [code=3.30.420.10, no name defined]                                                                                                                                    2py5B02 B:189-261,B:426-531 Palm domain of DNA polymerase                2py5B03 B:262-359 TPR 1 domain of DNA polym         erase                                         2py5B04 B:360-395 Helix hairpin bin 2py5B05 B:396-425             2py5B02 B:189-261,B:426-531 Palm domain of DNA polymerase                                                 2py5B06 B:532-575 DNA polymerase; domain 6   CATH domains
           Pfam domains (1) --------------------------------------------DNA_pol_B_2-2py5B01 B:49-488                                                                                                                                                                                                                                                                                                                                                                                                                            --------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------DNA_pol_B_2-2py5B02 B:49-488                                                                                                                                                                                                                                                                                                                                                                                                                            --------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeeeeee........eeeeeeee......eeee.hhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhh..ee.......eeeeee.....eeeeeeeeeee..eeeeeeeeehhhhh..hhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.....eee.hhhh..ee..eeeeee.hhhhhhhhhh.eeeeeeeeee..........eeeeeeeeeeee..........---------..........eeeeeehhhhhhhhhheeeeeeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.....eeeee.........hhhhhhhhhhhhhhhhhhhhhhh...eeeee..eeeee....hhhhhhhh.......eeeeeeeeeeeeee..eeeeeeeeeee..eeee.......eeeeeeee...hhhhhh...........eeeeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYM----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2py5 B   5 PRKMYSCAFETTTKVEDCRVWAYGYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHNLKFAGAFIINWLERNGFKWSADGLPNTYNTIISRMGQWYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLKGDIDYHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLDKEVRYAYRGGFTWLNDRFKEKEIGEGMVFDVNSLYPAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPTIQI---------EYLKSSGGEIADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDKWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDPKKLGYWAHESTFKRAKYLRQKTYIQDIYMKEVDGKLVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKVGFSRKMKPKPVQVPGGVVLVDDTFTIK 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 
                                                                                                                                                                                                                                                                                                                                     304       314                                                                                                                                                                                                                                                                     


Chain D from PDB  Type:DNA  Length:6
                                      
                 2py5 D   1 GGACTT   6


Chain E from PDB  Type:DNA  Length:6
                                      
                 2py5 E   1 GGACTT   6


Chain J from PDB  Type:DNA  Length:6
                                      
                 2py5 J   2 GACTTT   7


Chain L from PDB  Type:DNA  Length:4
                                    
                 2py5 L   4 CTTT   7


Chain Y from PDB  Type:DNA  Length:6
                                      
                 2py5 Y   1 GGACTT   6
   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, 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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  DPOL_BPPH2 | P03680
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        DPOL_BPPH2 | P03680: 1xhx 1xhz 1xi1 2ex3 2pyj 2pyl 2pzs

(-) Related Entries Specified in the PDB File

2pyj PHI29 DNA POLYMERASE COMPLEXED WITH PRIMER-TEMPLATE SUBSTRATE (POST-TRANSLOCATED BINARY COMPLEX)
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)