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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 :   2.20

Chains :   Asym./Biol. Unit : A,X,Y

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)

Molecule 1 - 5'-D(GACTGCTTAC(2DA))-3'
	Chains	:	X
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - 5'-D(CTGACGAATGTACA)-3'
	Chains	:	Y
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - DNA POLYMERASE
	Chains	:	A
	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

		1	2	3
Asymmetric/Biological Unit	:	A	X	Y

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 10)

No.	Name	Count	Type	Full Name
1	2DA	1	Mod. Nucleotide	2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE
2	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
3	MG	2	Ligand/Ion	MAGNESIUM ION
4	TTP	1	Ligand/Ion	THYMIDINE-5'-TRIPHOSPHATE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:249 , VAL A:250 , ASP A:458 , MG A:3203 , TTP A:3204 , HOH A:3274 , HOH A:3523 , HOH A:3525	BINDING SITE FOR RESIDUE MG A 3202
2	AC2	SOFTWARE	ASP A:249 , ASP A:458 , MG A:3202 , TTP A:3204 , HOH A:3525	BINDING SITE FOR RESIDUE MG A 3203
3	AC3	SOFTWARE	LEU A:253 , TYR A:254 , LYS A:371 , LYS A:383 , ASN A:387 , ASP A:458 , MG A:3202 , MG A:3203 , HOH A:3233 , HOH A:3235 , HOH A:3265 , HOH A:3274 , HOH A:3300 , HOH A:3501 , HOH A:3523 , HOH A:3524 , HOH A:3525 , HOH A:3527 , 2DA X:11 , DA Y:6 , DT Y:7	BINDING SITE FOR RESIDUE TTP A 3204
4	AC4	SOFTWARE	ILE A:158 , GLU A:291 , EDO A:1004	BINDING SITE FOR RESIDUE EDO A 1001
5	AC5	SOFTWARE	GLN A:257 , SER A:260 , THR A:440 , GLY A:481 , HOH A:3504	BINDING SITE FOR RESIDUE EDO A 1002
6	AC6	SOFTWARE	LYS A:80 , PRO A:87 , ASN A:88	BINDING SITE FOR RESIDUE EDO A 1003
7	AC7	SOFTWARE	ILE A:40 , ASN A:42 , ILE A:158 , ASN A:344 , EDO A:1001	BINDING SITE FOR RESIDUE EDO A 1004
8	AC8	SOFTWARE	TYR A:59 , ASP A:186 , ARG A:187 , MET A:188	BINDING SITE FOR RESIDUE EDO A 1005
9	AC9	SOFTWARE	LYS A:124 , THR A:189 , GLY A:191 , HOH A:3318 , DA Y:6	BINDING SITE FOR RESIDUE EDO A 1006

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

(no "Cis Peptide Bond" information available for 2PYL)

Asymmetric/Biological Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_DPOL_BPPH2_001 *	A	176	R	DPOL_BPPH2	---	---	A	A	176	R
2	UniProt	VAR_DPOL_BPPH2_002 *	A	355	V	DPOL_BPPH2	---	---	A	A	355	V
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_POLYMERASE_B	PS00116	DNA polymerase family B signature.	DPOL_BPPH2	454-462	1	A:454-462

(no "Exon" information available for 2PYL)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:571
 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 d2pyla1 A:5-187 Exonuclease domain of phi29 DNA polymerase                                                                                                                             d2pyla2 A:188-575 phi29 DNA polymerase                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2pylA01 A:5-188  [code=3.30.420.10, no name defined]                                                                                                                                    2pylA02 A:189-261,A:426-531 Palm domain of DNA polymerase                2pylA03 A:262-359 TPR 1 domain of DNA polymerase                                                  2pylA04 A:360-395 Helix hairpin bin 2pylA05 A:396-425             2pylA02 A:189-261,A:426-531 Palm domain of DNA polymerase                                                 2pylA06 A:532-575 DNA polymerase; domain 6   CATH domains
               Pfam domains --------------------------------------------DNA_pol_B_2-2pylA01 A:49-488                                                                                                                                                                                                                                                                                                                                                                                                                            --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee........eeeeeeee..eeeeeeee.hhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhh..ee.......eeeeee.....eeeeeeeeee....eeeeeeee.hhh...hhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh......eee.hhhh..ee..eeeeee.hhhhhhhhhh.eeeeeeeeee..........eeeeeeeeeeee.............................eeeeeehhhhhhhhhheeeeeeeeeeeeeeeee...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.......eeeee.....eeeee.........hhhhhhhhhhhhhhhhhhhhhhh...eeeee..eeeee.......hhhhh.......eeeeeeeeeeeeee..eeeeeeeeee....eee.......eeeeeeee...hhhhhh...........eeeeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYM----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pyl A   5 PRKMYSCAFETTTKVEDCRVWAYGYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHNLKFAGAFIINWLERNGFKWSADGLPNTYNTIISRMGQWYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLKGDIDYHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLDKEVRYAYRGGFTWLNDRFKEKEIGEGMVFDVNSLYPAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDKWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDPKKLGYWAHESTFKRAKYLRQKTYIQDIYMKEVDGKLVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKVGFSRKMKPKPVQVPGGVVLVDDTFTIK 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

Chain X from PDB  Type:DNA  Length:11
                                           
                 2pyl X   1 GACTGCTTACx  11
                                    10|
                                     11-2DA

Chain Y from PDB  Type:DNA  Length:14
                                              
                 2pyl Y   4 ACATGTAAGCAGTC  17
                                    13

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 '\|'

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: DNA_pol_B-like (44)

Family: DNA_pol_B_2 (6)

Bacillus phage phi29 (Bacteriophage phi-29) (6)

DNA_pol_B_2-2pylA01

A:49-488

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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	2pyl
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UniProtKB/Swiss-Prot
	DPOL_BPPH2 \| P03680	:	1xhx 1xhz 1xi1 2ex3 2py5 2pyj 2pzs

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 10)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (1, 1)

Exons (0, 0)

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SCOP Domains (2, 2)

CATH Domains (6, 6)

Pfam Domains (1, 1)

Gene Ontology (16, 16)

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