Structure of PDB 1zyq Chain A

Receptor sequence

>1zyqA (length=680) Species: 10760 (Escherichia phage T7) [Search protein sequence]

MIVSDIEANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAYLDALEAEV
ARGGLIVFHNGHKYDVPALTKLAKLQLNREFHLPRENCIDTLVLSRLIHS
NLKDTDMGLLRSGKLPGALEAWGYRLGEMKGEYKDDFKRMLEEQGEEYVD
GMEWWNFNEEMMDYNVQDVVVTKALLEKLLSDKHYFPPEIDFTDVGYTTF
WSESLEAVDIEHRAAWLLAKQERNGFPFDTKAIEELYVELAARRSELLRK
LTETFGSWYQPKGGTEMFCHPRTGKPLPKYPRIKTPKVGGLDTREYVAGA
PYTPVEHVVFNPSSRDHIQKKLQEAGWVPTKYTDKGAPVVDDEVLEGVRV
DDPEKQAAIDLIKEYLMIQKRIGQSAEGDKAWLRYVAEDGKIHGSVNPNG
AVTGRATHAFPNLAQIPGVRSPYGEQCRAAFGAEHHLDGITGKPWVQAGI
DASGLELRCLAHFMARFDNGEYAHEILNGDIHTKNQIAAELPTRDNAKTF
IYGFLYGAGDEAIGQIVGAGKERGKELKKKFLENTPAIAALRESIQQTLV
ESSQWVAGEQQVKWKRRWIKGLDGRKVHVRSPHAALNTLLQSAGALICKL
WIIKTEEMLVEKGLKHGWDGDFAYMAWVHDEIQVGCRTEEIAQVVIETAQ
EAMRWVGDHWNFRCLLDTEGKMGPNWAICH

3D structure

PDB

1zyq A lysine residue in the fingers subdomain of t7 DNA polymerase modulates the miscoding potential of 8-oxo-7,8-dihydroguanosine.

Chain

Resolution

2.7 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	R111 R339 T357 V364 D365 D366 K394 A438 Q439 I440 P441 G442 V652 H653	R111 R315 T333 V340 D341 D342 K370 A414 Q415 I416 P417 G418 V628 H629
BS02	dna	A	S337 S338 H341 K404 A425 V426 H432 A433 Q439 Y526 G527 Y530 A532 G533 A536 R604 H607 Q615	S313 S314 H317 K380 A401 V402 H408 A409 Q415 Y502 G503 Y506 A508 G509 A512 R580 H583 Q591
BS03	MG	A	D475 A476 D654	D451 A452 D630
BS04	MG	A	D654 E655	D630 E631
BS05	DAD	A	R429 D475 S477 G478 L479 E480 H506 R518 K522 Y526 D654	R405 D451 S453 G454 L455 E456 H482 R494 K498 Y502 D630

Gene Ontology

	Molecular Function
GO:0000166	nucleotide binding
GO:0003676	nucleic acid binding
GO:0003677	DNA binding
GO:0003887	DNA-directed DNA polymerase activity
GO:0004527	exonuclease activity
GO:0004529	DNA exonuclease activity
GO:0005515	protein binding
GO:0008408	3'-5' exonuclease activity
GO:0046872	metal ion binding

	Biological Process
GO:0006260	DNA replication
GO:0006261	DNA-templated DNA replication
GO:0006302	double-strand break repair
GO:0039693	viral DNA genome replication
GO:0090592	DNA synthesis involved in DNA replication

View graph for
Molecular Function

View graph for
Biological Process

External links

PDB	RCSB:1zyq, PDBe:1zyq, PDBj:1zyq
PDBsum	1zyq
PubMed	16271888
UniProt	P00581\|DPOL_BPT7 DNA-directed DNA polymerase (Gene Name=5)

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