Structure of PDB 4am3 Chain B

Receptor sequence

>4am3B (length=621) Species: 190650 (Caulobacter vibrioides CB15)

GSMFDIKRKTIEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAK
SQKPGQDFFPLTVNYQEKTFAAGKIPGGFFKREGRPSEKETLVSRLIDRP
IRPLFVKGFKNEVQVVVTVLQHDLENDPDILGMVAASAALCLSGAPFMGP
IGAARVGWVDGAYVLNPTLDEMKESKMDLVVAGTADAVMMVESEIQELSE
EIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPEDTDAIKAKMKDL
VGADIAAAYKIQKKQDRYEAVGAAKKKAIAALGLSDENPTGYDPLKLGAI
FKELEADVVRRGILDTGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRG
ETQAIVVATLGTGDDEQFIDALEGTYKESFLLHYNFPPYSVGETGRMGSP
GRREIGHGKLAWRALRPMLPTKEDFPYTIRLVSEITESNGSSSMATVCGS
SLAMMDAGVPLVRPVSGIAMGLILEQDGFAVLSDILGDEDHLGDMDFKVA
GTSEGLTSLQMDIKIAGITPAIMEQALAQAKEGRAHILGEMNKAMDAPRA
DVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDDGVVK
VSASDGAKIKAAIDWIKSITD

3D structure

• PDB: 4am3 Crystal Structure of Caulobacter Crescentus Polynucleotide Phosphorylase Reveals a Mechanism of RNA Substrate Channelling and RNA Degradosome Assembly.
• Chain: B
• Resolution: 3.0 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.8: polyribonucleotide nucleotidyltransferase.

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	rna	B	G574 G575 I578	G576 G577 I580
BS02	rna	B	G82 R83	G84 R85

Gene Ontology

Molecular Function

• GO:0000175 3'-5'-RNA exonuclease activity
• GO:0000287 magnesium ion binding
• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding
• GO:0004654 polyribonucleotide nucleotidyltransferase activity
• GO:0016779 nucleotidyltransferase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006396 RNA processing
• GO:0006401 RNA catabolic process
• GO:0006402 mRNA catabolic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:4am3, PDBe:4am3, PDBj:4am3
• PDBsum: 4am3
• PubMed: 22724061
• UniProt: Q9AC32|PNP_CAUVC Polyribonucleotide nucleotidyltransferase (Gene Name=pnp)