Structure of PDB 4bjr Chain B

Receptor sequence

>4bjrB (length=494) Species: 196627 (Corynebacterium glutamicum ATCC 13032)

TVESALTRRIMGIETEYGLTFVDGDSKKLRPDEIARRMFRPIVEKYSSSN
IFIPNGSRLYLNVGSHPEYATAECDNLTQLINFEKAGDVIADRMAVDAEE
SLAKEDIAGQVYLFKNNVDSVGNSYGCHENYLVGRSMPLKALGKRLMPFL
ITRQLICGAGRIHHPNPSFPLGYCISQRSDHVWEGVSSASRPIINTRDEP
HADSHSYRRLHVIVGDANMAEPSIALKVGSTLLVLEMIEADFGLPSLELA
NDIASIREISRDATGSTLLSLKDGTTMTALQIQQVVFEHASKWLEQRPEP
EFSGTSNTEMARVLDLWGRMLKAIESGDFSEVDTEIDWVIKKKLIDRFIQ
RGNLGLDDPKLAQVDLTYHDIRPGRGLFSVLQSRGMIKRWTTDEAILAAV
DTAPDTTRAHLRGRILKAADTLGVPVTVDWMRHKVNRPEPQSVELGDPFS
AVNSEVDQLIEYMTVHASLLDEIDGLLENNAEEFVRSYVQKGGE

3D structure

• PDB: 4bjr Crystal Structure of the Complex between Prokaryotic Ubiquitin-Like Protein Pup and its Ligase Pafa.
• Chain: B
• Resolution: 2.8 Å

Enzymatic activity

• Enzyme Commision number: 6.3.1.19: prokaryotic ubiquitin-like protein ligase.
  6.3.2.-

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	ATP	B	I12 G14 I15 E16 R60 Y62 T73 E75 N132 L134 P210 H211 R219 W440	I10 G12 I13 E14 R58 Y60 T71 E73 N130 L132 P200 H201 R209 W430
BS02	MG	B	E16 Y62 E70	E14 Y60 E68
BS03	MG	B	E16 H221	E14 H211

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0005524 ATP binding
• GO:0016874 ligase activity
• GO:0016879 ligase activity, forming carbon-nitrogen bonds
• GO:0019787 ubiquitin-like protein transferase activity
• GO:0031386 protein tag activity
• GO:0046872 metal ion binding
• GO:0070628 proteasome binding

Biological Process

• GO:0010498 proteasomal protein catabolic process
• GO:0019941 modification-dependent protein catabolic process
• GO:0070490 protein pupylation

External links

• PDB: RCSB:4bjr, PDBe:4bjr, PDBj:4bjr
• PDBsum: 4bjr
• PubMed: 23601177
• UniProt: Q8NQE0;
  Q8NQE1|PAFA_CORGL Pup--protein ligase (Gene Name=pafA)