Structure of PDB 3l8b Chain A

Receptor sequence

>3l8bA (length=896) Species: 12353 (Escherichia phage RB69)

MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYF
DIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYE
IKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFD
LLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLME
YLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRV
KVIEIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKLKYDG
PISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQS
VFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNRYKYV
MSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCS
PNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPN
LSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQI
NRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNE
VCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARE
RMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKR
YALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGE
ESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRG
ILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTEITDL
IKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMFDF

3D structure

• PDB: 3l8b Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoin.
• Chain: A
• Resolution: 2.15 Å

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)	Binding affinity
BS01	dna	A	K279 S360 P361 I362 Y391 P392 G393 A394 G568 N572 W574 K705 K706 R707 P799 K800 F803 K844 K874 K878	K272 S353 P354 I355 Y384 P385 G386 A387 G561 N565 W567 K698 K699 R700 P792 K793 F796 K837 K867 K871
BS02	dna	A	N284 D621 T622 D623 K706 Y708 M728 G729 Q733 S735 S783 S784 N786 K790 Y791	N277 D614 T615 D616 K699 Y701 M721 G722 Q726 S728 S776 S777 N779 K783 Y784

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:0008408 3'-5' exonuclease activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006260 DNA replication
• GO:0006261 DNA-templated DNA replication
• GO:0039686 bidirectional double-stranded viral DNA replication
• GO:0039693 viral DNA genome replication

External links

• PDB: RCSB:3l8b, PDBe:3l8b, PDBj:3l8b
• PDBsum: 3l8b
• PubMed: 20166752
• UniProt: Q38087|DPOL_BPR69 DNA-directed DNA polymerase (Gene Name=43)