Structure of PDB 7ld5 Chain B

Receptor sequence

>7ld5B (length=587) Species: 1772 (Mycolicibacterium smegmatis)

DGVYESTAVIDNGSFGTRTIRFETGRLAQQAAGSAVAYLDDETMLLSATT
ASKNPKDHFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLI
DRPLRPSFVDGLRNEIQVVVTVMSLDPKDLYDVLAINAASMSTQLAGLPF
SGPVGGARIALIDGTWVAFPTVEQLERAVFDMVVAGRIVGDGDSADVAIM
MVEAEATENVVELVAGGAQAPTEAVVAEGLEAAKPFIKALCAAQQELADR
AAKPAGEYPVFPDYEADVYDAVASVATEALAEALTIAGKTERNDRTDEIK
VEVLERLAEPYAGREKEIGAAFRSLTKKLVRQRILTDHFRIDGRGITDIR
ALSAEVAVIPRAHGSALFERGETQILGVTTLDMIKMAQQIDSLGPENTKR
YMHHYNFPPYSTGETGRVGSPKRREIGHGALAERALVPVLPSIEEFPYAI
RQVSEALGSNGSTSMGSVCASTLALLNAGVPLKAPVAGIAMGLVSDDVDV
DGKVEKRYVALTDILGAEDAFGDMDFKVAGTKDFVTALQLDTKLDGIPSQ
VLAGALSQAKDARLTILDVMAEAIDRPDEMSPYAPRI

3D structure

• PDB: 7ld5 Structure and mechanism of Mycobacterium smegmatis polynucleotide phosphorylase.
• Chain: B
• Resolution: 3.07 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	G87 R424	G80 R417
BS02	rna	B	F66 F68 F89 R431	F59 F61 F82 R424
BS03	MG	B	D526 D532	D519 D525
BS04	MG	B	D532 Q546	D525 Q539

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:7ld5, PDBe:7ld5, PDBj:7ld5
• PDBsum: 7ld5
• PubMed: 34088850
• UniProt: A0QVQ5|PNP_MYCS2 Polyribonucleotide nucleotidyltransferase (Gene Name=pnp)