6TMM

BIL2 domain from T.thermophila BUBL1 locus (C1A-N143A)

PDB DOI: https://doi.org/10.2210/pdb6TMM/pdb

Classification: SPLICING
Organism(s): Tetrahymena thermophila SB210
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2019-12-04 Released: 2020-12-16
Deposition Author(s): Chiarini, V., Ilari, A.
Funding Organization(s): Italian Ministry of Education

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.267
R-Value Work: 0.198

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural basis of ubiquitination mediated by protein splicing in early Eukarya.

Chiarini, V., Fiorillo, A., Camerini, S., Crescenzi, M., Nakamura, S., Battista, T., Guidoni, L., Colotti, G., Ilari, A.

(2021) Biochim Biophys Acta Gen Subj 1865: 129844-129844

PubMed: 33444728 Search on PubMed
DOI: https://doi.org/10.1016/j.bbagen.2021.129844
Primary Citation of Related Structures:
6TMM, 6Y75

PubMed Abstract:
Inteins are intervening proteins, which are known to perform protein splicing. The reaction results in the production of an intein domain and an inteinless protein, which shows no trace of the insertion. BIL2 is part of the polyubiquitin locus of Tetrahymena thermophila (BUBL), where two bacterial-intein-like (BIL) domains lacking the C + 1 nucleophile, are flanked by two independent ubiquitin-like domains (ubl4/ubl5).

Organizational Affiliation

Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014 Helsinki, Finland.

Macromolecule Content

Total Structure Weight: 72.6 kDa
Atom Count: 5,204
Modelled Residue Count: 622
Deposited Residue Count: 622
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)(+)--arginine ADP-ribosyltransferase	A [auth AAA], C [auth CCC]	156	Tetrahymena thermophila SB210	Mutation(s): 2 Gene Names: TTHERM_00085190 EC: 2.4.2.31
UniProt
Find proteins for Q236S9 (Tetrahymena thermophila (strain SB210)) Explore Q236S9 Go to UniProtKB: Q236S9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q236S9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)(+)--arginine ADP-ribosyltransferase	B [auth BBB], D [auth DDD]	155	Tetrahymena thermophila SB210	Mutation(s): 2 Gene Names: TTHERM_00085190 EC: 2.4.2.31
UniProt
Find proteins for Q236S9 (Tetrahymena thermophila (strain SB210)) Explore Q236S9 Go to UniProtKB: Q236S9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q236S9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HG Query on HG Download Ideal Coordinates CCD File SDF format, chain J [auth AAA] SDF format, chain O [auth BBB] SDF format, chain R [auth CCC] SDF format, chain U [auth DDD] MOL2 format, chain J [auth AAA] MOL2 format, chain O [auth BBB] MOL2 format, chain R [auth CCC] MOL2 format, chain U [auth DDD]	J [auth AAA], O [auth BBB], R [auth CCC], U [auth DDD]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N		Interactions Focus chain J [auth AAA] Focus chain O [auth BBB] Focus chain R [auth CCC] Focus chain U [auth DDD] Interactions & Density Focus chain J [auth AAA] Focus chain O [auth BBB] Focus chain R [auth CCC] Focus chain U [auth DDD]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain H [auth AAA] MOL2 format, chain H [auth AAA]	H [auth AAA]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth AAA] Interactions & Density Focus chain H [auth AAA]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain E [auth AAA] SDF format, chain F [auth AAA] SDF format, chain G [auth AAA] SDF format, chain I [auth AAA] SDF format, chain L [auth BBB] SDF format, chain M [auth BBB] SDF format, chain N [auth BBB] SDF format, chain P [auth CCC] SDF format, chain Q [auth CCC] SDF format, chain S [auth DDD] SDF format, chain T [auth DDD] MOL2 format, chain E [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain L [auth BBB] MOL2 format, chain M [auth BBB] MOL2 format, chain N [auth BBB] MOL2 format, chain P [auth CCC] MOL2 format, chain Q [auth CCC] MOL2 format, chain S [auth DDD] MOL2 format, chain T [auth DDD]	E [auth AAA] F [auth AAA] G [auth AAA] I [auth AAA] L [auth BBB] E [auth AAA], F [auth AAA], G [auth AAA], I [auth AAA], L [auth BBB], M [auth BBB], N [auth BBB], P [auth CCC], Q [auth CCC], S [auth DDD], T [auth DDD]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain I [auth AAA] Focus chain L [auth BBB] Focus chain M [auth BBB] Focus chain N [auth BBB] Focus chain P [auth CCC] Focus chain Q [auth CCC] Focus chain S [auth DDD] Focus chain T [auth DDD] Interactions & Density Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain I [auth AAA] Focus chain L [auth BBB] Focus chain M [auth BBB] Focus chain N [auth BBB] Focus chain P [auth CCC] Focus chain Q [auth CCC] Focus chain S [auth DDD] Focus chain T [auth DDD]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain K [auth AAA] MOL2 format, chain K [auth AAA]	K [auth AAA]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain K [auth AAA] Interactions & Density Focus chain K [auth AAA]