Structure of PDB 3cm5 Chain B

Receptor sequence

>3cm5B (length=294) Species: 6239 (Caenorhabditis elegans)

HCPFDTLLILDFETTSDAANQDYPCEVIQFAIVAYDVPNDKIREDISFNK
YVKPVLNRTLTKNCVDFTGIPQRSIDTADTFDVVYEQFQQWLITLGLEEG
KFAFVCDSRQDLWRIAQYQMKLSNIQMPAFFRQYINLYKIFTNEMDRMGP
KELSATTNIGKMNEYYDLPTIGRAHDAMDDCLNIATILQRMINMGAKVTV
NELLTCCASWRRQPLVYNKEWRSSFMDAGKIFERVLPLVVTTIRAGDFRL
EMYGVCRYCRKGMDVCGTSHQQTPHDLYKNEEDPIHFAKIAGYY

3D structure

• PDB: 3cm5 Crystal structure of CRN-4: implications for domain function in apoptotic DNA degradation
• Chain: B
• Resolution: 2.81 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D15 E17 D115 H179 D184
• Catalytic site (residue number reindexed from 1): D11 E13 D111 H175 D180
• Enzyme Commision number: 3.1.-.-

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	ZN	B	C210 C260 C263 C270	C206 C256 C259 C266
BS02	MN	B	D15 E17 D184	D11 E13 D180

Gene Ontology

Molecular Function

• GO:0000175 3'-5'-RNA exonuclease activity
• GO:0003676 nucleic acid binding
• GO:0003697 single-stranded DNA binding
• GO:0004520 DNA endonuclease activity
• GO:0004527 exonuclease activity
• GO:0004536 DNA nuclease activity
• GO:0004540 RNA nuclease activity
• GO:0008408 3'-5' exonuclease activity
• GO:0046872 metal ion binding

Biological Process

• GO:0000467 exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0006308 DNA catabolic process
• GO:0006309 apoptotic DNA fragmentation
• GO:0006401 RNA catabolic process
• GO:0006915 apoptotic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:3cm5, PDBe:3cm5, PDBj:3cm5
• PDBsum: 3cm5
• PubMed: 18981218
• UniProt: Q10905|CRN4_CAEEL 3'-5' exonuclease crn-4 (Gene Name=crn-4)