Structure of PDB 3upq Chain A

Receptor sequence

>3upqA (length=308) Species: 9606 (Homo sapiens)

HNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACS
IPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQM
WYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQK
AAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSL
RQEGFLTDDLVKGETKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYF
TGSAHFNRSMRALAKTKGMSLSEHALSTAVGRVLPTPTEKDVFRLLGLPY
REPAERDW

3D structure

• PDB: 3upq The catalytic cycle for ribonucleotide incorporation by human DNA Pol lambda
• Chain: A
• Resolution: 1.95 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D427 D429 D490
• Catalytic site (residue number reindexed from 1): D176 D178 D234
• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.
  4.2.99.-

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	W274 V462 K463 G464 K472 R514 R517 K521 L527 E529 H530	W23 V211 K212 G213 K216 R258 R261 K265 L271 E273 H274
BS02	dna	A	W342 G343 G345 K347 T348 R488 D490 Y505	W91 G92 G94 K96 T97 R232 D234 Y249
BS03	dna	A	W274 R275 G278 Y279 G304 G306 R308 M309 K312	W23 R24 G27 Y28 G53 G55 R57 M58 K61
BS04	ZAN	A	R386 G416 S417 R420 C425 G426 D427 D429 Y505 F506 T507 G508 N513	R135 G165 S166 R169 C174 G175 D176 D178 Y249 F250 T251 G252 N257
BS05	MN	A	D427 D429	D176 D178
BS06	MN	A	D427 D429 D490	D176 D178 D234
BS07	MN	A	D382 H486	D131 H230

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

External links

• PDB: RCSB:3upq, PDBe:3upq, PDBj:3upq
• PDBsum: 3upq
• PubMed: 22584622
• UniProt: Q9UGP5|DPOLL_HUMAN DNA polymerase lambda (Gene Name=POLL)