Structure of PDB 2pyj Chain B

Receptor sequence

>2pyjB (length=572) Species: 10756 (Salasvirus phi29) [Search protein sequence]

HMPRKMYSCAFETTTKVEDCRVWAYGYMNIEDHSEYKIGNSLDEFMAWVL
KVQADLYFHNLKFAGAFIINWLERNGFKWSADGLPNTYNTIISRMGQWYM
IDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLKGDIDYHKER
PVGYKITPEEYAYIKNDIQIIAEALLIQFKQGLDRMTAGSDSLKGFKDII
TTKKFKKVFPTLSLGLDKEVRYAYRGGFTWLNDRFKEKEIGEGMVFDVNS
LYPAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPTI
QIKRSRFYKGNEYLKSSGGEIADLWLSNVDLELMKEHYDLYNVEYISGLK
FKATTGLFKDFIDKWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVTGK
VPYLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITAAQACYDRI
IYCDTDSIHLTGTEIPDVIKDIVDPKKLGYWAHESTFKRAKYLRQKTYIQ
DIYMKEVGKLVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKVGFSRK
MKPKPVQVPGGVVLVDDTFTIK

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	B	D362 D365 K366	D360 D363 K364
BS02	dna	B	K182 D200 I201	K180 D198 I199
BS03	dna	B	T457 K498 Y500 K529 C530 A531 G532 M533 T534 K538	T455 K496 Y498 K526 C527 A528 G529 M530 T531 K535
BS04	dna	B	I93 Y101 M102 M188 T189 S192 Y226 R227 G228 Q303 K305 N313 L384 S388 G391 K392 A394 S395 N396 R496 Q497 T571 F572 T573 I574 K575	I91 Y99 M100 M186 T187 S190 Y224 R225 G226 Q301 K303 N311 L382 S386 G389 K390 A392 S393 N394 R494 Q495 T568 F569 T570 I571 K572
BS05	dna	B	H3 P5 R6 D84 P87 Y109 G111 K112 R113 K114 H116 D186 R187 T204 K205	H1 P3 R4 D82 P85 Y107 G109 K110 R111 K112 H114 D184 R185 T202 K203
BS06	MN	B	D249 V250 D458	D247 V248 D456
BS07	MG	B	D249 D458	D247 D456
BS08	DGT	B	D249 V250 S252 L253 Y254 K371 K383 N387 Y390 T457 D458	D247 V248 S250 L251 Y252 K369 K381 N385 Y388 T455 D456

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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