Structure of PDB 2p5g Chain A

Receptor sequence

>2p5gA (length=890) Species: 12353 (Escherichia phage RB69)

MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYF
DIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYE
IKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFD
LLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLME
YLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRV
KVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNV
GKLKYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYY
AKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPI
PNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERP
SDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIK
EALHYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLI
NSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEG
EAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAI
DRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVW
DMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEESLQEY
FKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNR
AIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTEITDLIKDDVL
HWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMFDF

3D structure

• PDB: 2p5g Caught bending the a-rule: crystal structures of translesion DNA synthesis with a non-natural nucleotide.
• Chain: A
• Resolution: 2.8 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	G393 A394 K705 R707 P799 K800 F803 K844 K874 K878	G393 A394 K692 R694 P786 K787 F790 K831 K861 K865
BS02	dna	A	N564 K706 M728 G729 Q733 K734 S735 S783 S784 N786 Y791 K800 H804	N551 K693 M715 G716 Q720 K721 S722 S770 S771 N773 Y778 K787 H791
BS03	dna	A	S36 F38 Y49 R59 G84 M85 D95 F370 K374 K378 V379 I380	S36 F38 Y49 R59 G84 M85 D95 F370 K374 K378 V379 I380
BS04	dna	A	K2 Y99	K2 Y99

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:2p5g, PDBe:2p5g, PDBj:2p5g
• PDBsum: 2p5g
• PubMed: 17718515
• UniProt: Q38087|DPOL_BPR69 DNA-directed DNA polymerase (Gene Name=43)