Structure of PDB 1tkd Chain A

Receptor sequence

>1tkdA (length=698) Species: 10760 (Escherichia phage T7) [Search protein sequence]

MIVSDIEANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAYLDALEAEV
ARGGLIVFHNGHKYDVPALTKLAKLQLNREFHLPRENCIDTLVLSRLIHS
NLKDTDMGLLRSGKLPGALEAWGYRLGEMKGEYKDDFKRMLEEQGEEYVD
GMEWWNFNEEMMDYNVQDVVVTKALLEKLLSDKHYFPPEIDFTDVGYTTF
WSESLEAVDIEHRAAWLLAKQERNGFPFDTKAIEELYVELAARRSELLRK
LTETFGSWYQPKGGTEMFCHPRTGKPLPKYPRIKTPKVGGIFKKPKNKAQ
REGREPCELDTREYVAGAPYTPVEHVVFNPSSRDHIQKKLQEAGWVPTKY
TDKGAPVVDDEVLEGVRVDDPEKQAAIDLIKEYLMIQKRIGQSAEGDKAW
LRYVAEDGKIHGSVNPNGAVTGRATHAFPNLAQIPGVRSPYGEQCRAAFG
AEHHLDGITGKPWVQAGIDASGLELRCLAHFMARFDNGEYAHEILNGDIH
TKNQIAAELPTRDNAKTFIYGFLYGAGDEKIGQIVGAGKERGKELKKKFL
ENTPAIAALRESIQQTLVESSQWVAGEQQVKWKRRWIKGLDGRKVHVRSP
HAALNTLLQSAGALICKLWIIKTEEMLVEKGLKHGWDGDFAYMAWVHDEI
QVGCRTEEIAQVVIETAQEAMRWVGDHWNFRCLLDTEGKMGPNWAICH

3D structure

PDB

1tkd Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase.

Chain

Resolution

2.49 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 T357 K359 V363 V364 D365 D366 K394 R429 A438 Q439 I440 G442 V652 H653 H704	R111 T351 K353 V357 V358 D359 D360 K388 R423 A432 Q433 I434 G436 V646 H647 H698
BS02	dna	A	S337 S338 H341 G402 K404 A425 V426 R429 T431 H432 A433 N436 Q439 G527 G531 A532 G533 K536 R604 H607 N611 Q615	S331 S332 H335 G396 K398 A419 V420 R423 T425 H426 A427 N430 Q433 G521 G525 A526 G527 K530 R598 H601 N605 Q609
BS03	MG	A	D475 A476 D654	D469 A470 D648
BS04	MG	A	D475 D654	D469 D648
BS05	D3T	A	R429 D475 A476 G478 E480 H506 R518 K522 Y526 D654	R423 D469 A470 G472 E474 H500 R512 K516 Y520 D648

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:1tkd, PDBe:1tkd, PDBj:1tkd
PDBsum	1tkd
PubMed	15297882
UniProt	P00581\|DPOL_BPT7 DNA-directed DNA polymerase (Gene Name=5)

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