Structure of PDB 5tyv Chain A

Receptor sequence

>5tyvA (length=327) Species: 9606 (Homo sapiens)

WMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVL
KALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQT
MKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDL
STPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLIT
HPKEGQEAGLLPRVMCRLQDQGLILYHQAFERSFCIFRLPQPGSWKAVRV
DLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQK
TFFQAASEEDIFRHLGLEYLPPEQRNA

3D structure

• PDB: 5tyv Time-lapse crystallography snapshots of a double-strand break repair polymerase in action.
• Chain: A
• Resolution: 1.93 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D330 D332 D418
• Catalytic site (residue number reindexed from 1): D194 D196 D251
• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.

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	L177 F385 E386 R387 R442 R445 R446 R449 K450 L456 N457	L41 F230 E231 R232 R275 R278 R279 R282 K283 L289 N290
BS02	dna	A	G245 V246 G247 T250 D330 D332 F389 R416 D418 G433 W434 T435 G436 K438	G109 V110 G111 T114 D194 D196 F234 R249 D251 G266 W267 T268 G269 K271
BS03	dna	A	G174 R175 T178 F179 H204 G206 H208 S209	G38 R39 T42 F43 H68 G70 H72 S73
BS04	TTP	A	R323 H329 D330 D332 G433 G436 K438	R187 H193 D194 D196 G266 G269 K271
BS05	MN	A	D330 D332	D194 D196
BS06	MN	A	D330 D332 D418	D194 D196 D251
BS07	MN	A	E386 H459	E231 H292
BS08	MN	A	E218 H219	E82 H83

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0016779 nucleotidyltransferase activity
• GO:0034061 DNA polymerase activity

Biological Process

• GO:0006281 DNA repair

Cellular Component

• GO:0005634 nucleus

External links

• PDB: RCSB:5tyv, PDBe:5tyv, PDBj:5tyv
• PDBsum: 5tyv
• PubMed: 28811466
• UniProt: Q9NP87|DPOLM_HUMAN DNA-directed DNA/RNA polymerase mu (Gene Name=POLM)