Structure of PDB 2dy4 Chain B

Receptor sequence

>2dy4B (length=888) Species: 12353 (Escherichia phage RB69)

MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYF
DIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYE
IKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFD
LLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLME
YLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRV
KVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNV
GKLKYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYY
AKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPI
PNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERP
SDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIK
DVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLIN
SLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGE
AFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAID
RGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWD
MEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEESLQEYF
KEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRA
IKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTEITDLIKDDVLH
WMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMFD

3D structure

• PDB: 2dy4 A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol.
• Chain: B
• Resolution: 2.65 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	B	K279 S360 P361 I362 Y391 G393 A394 G571 N572 W574 K705 K706 R707 K800 K844	K279 S360 P361 I362 Y391 G393 A394 G557 N558 W560 K691 K692 R693 K786 K830
BS02	dna	B	N284 D621 K706 Y708 M728 G729 K734 S735 S784 N786 N787 K800 H804	N284 D607 K692 Y694 M714 G715 K720 S721 S770 N772 N773 K786 H790

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:2dy4, PDBe:2dy4, PDBj:2dy4
• PDBsum: 2dy4
• PubMed: 17210917
• UniProt: Q38087|DPOL_BPR69 DNA-directed DNA polymerase (Gene Name=43)