Structure of PDB 2pyj Chain A

Receptor sequence

>2pyjA (length=567) Species: 10756 (Salasvirus phi29) [Search protein sequence]

PRKMYSCAFETTTKVEDCRVWAYGYMNIEDHSEYKIGNSLDEFMAWVLKV
QADLYFHNLKFAGAFIINWLERNGFKWSADGLPNTYNTIISRMGQWYMID
ICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLKGDIDYHKERPV
GYKITPEEYAYIKNDIQIIAEALLIQFKQGLDRMTAGSDSLKGFKDIITT
KKFKKVFPTLSLGLDKEVRYAYRGGFTWLNDRFKEKEIGEGMVFDVNSLY
PAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPTIQI
KRSRFYKGNEYLKSSGGEIADLWLSNVDLELMKEHYDLYNVEYISGLKFK
ATTGLFKDFIDKWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVTGKVP
YLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITAAQACYDRIIY
CDTDSIHLTGTEIPDVIKDIVDPKKLGYWAHESTFKRAKYLRQKTYIQDI
YMKEVVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKVGFSRKMKPKP
VQVPGGVVLVDDTFTIK

3D structure

PDB

2pyj Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases

Chain

Resolution

2.03 Å

3D
structure

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Enzymatic activity

Enzyme Commision number

2.7.7.7: DNA-directed DNA polymerase.
3.1.11.-

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)
BS01	dna	A	K64 K402 T457 K498 Y500 K529 C530 A531 G532 M533 K538	K60 K398 T453 K494 Y496 K521 C522 A523 G524 M525 K530
BS02	dna	A	I93 Y101 M188 T189 S192 Y226 R227 G228 Q303 K305 N313 S388 G391 K392 K422 R496 Q497 K498 D570 T571 F572 T573 K575	I89 Y97 M184 T185 S188 Y222 R223 G224 Q299 K301 N309 S384 G387 K388 K418 R492 Q493 K494 D562 T563 F564 T565 K567
BS03	MN	A	D249 V250 D458	D245 V246 D454
BS04	MG	A	D249 D458	D245 D454
BS05	DGT	A	D249 V250 S252 L253 Y254 K371 K383 N387 Y390 D458	D245 V246 S248 L249 Y250 K367 K379 N383 Y386 D454

Gene Ontology

	Molecular Function
GO:0000166	nucleotide binding
GO:0001882	nucleoside binding
GO:0003676	nucleic acid binding
GO:0003677	DNA binding
GO:0003887	DNA-directed DNA polymerase activity
GO:0004527	exonuclease activity
GO:0046872	metal ion binding

	Biological Process
GO:0006260	DNA replication
GO:0039693	viral DNA genome replication

View graph for
Molecular Function

View graph for
Biological Process

External links

PDB	RCSB:2pyj, PDBe:2pyj, PDBj:2pyj
PDBsum	2pyj
PubMed	17611604
UniProt	P03680\|DPOL_BPPH2 DNA polymerase (Gene Name=2)

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