3OL3

Crystal structure of a putative uncharacterized protein from Mycobacterium smegamtis, an ortholog of Rv0543c, iodide phased

PDB DOI: 10.2210/pdb3OL3/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Mycolicibacterium smegmatis MC2 155
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-08-25 Released: 2010-09-08
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.236
R-Value Work: 0.197
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structural diversity in the Mycobacteria DUF3349 superfamily.

Buchko, G.W., Abendroth, J., Robinson, J.I., Phan, I.Q., Myler, P.J., Edwards, T.E.

(2020) Protein Sci 29: 670-685

PubMed: 31658388 Search on PubMedSearch on PubMed Central
DOI: 10.1002/pro.3758
Primary Citation of Related Structures:
2LKY, 2M0N, 3OL3, 3OL4

PubMed Abstract:

A protein superfamily with a "Domain of Unknown Function,", DUF3349 (PF11829), is present predominately in Mycobacterium and Rhodococcus bacterial species suggesting that these proteins may have a biological function unique to these bacteria. We previously reported the inaugural structure of a DUF3349 superfamily member, Mycobacterium tuberculosis Rv0543c. Here, we report the structures determined for three additional DUF3349 proteins: Mycobacterium smegmatis MSMEG_1063 and MSMEG_1066 and Mycobacterium abscessus MAB_3403c. Like Rv0543c, the NMR solution structure of MSMEG_1063 revealed a monomeric five α-helix bundle with a similar overall topology. Conversely, the crystal structure of MSMEG_1066 revealed a five α-helix protein with a strikingly different topology and a tetrameric quaternary structure that was confirmed by size exclusion chromatography. The NMR solution structure of a fourth member of the DUF3349 superfamily, MAB_3403c, with 18 residues missing at the N-terminus, revealed a monomeric α-helical protein with a folding topology similar to the three C-terminal helices in the protomer of the MSMEG_1066 tetramer. These structures, together with a GREMLIN-based bioinformatics analysis of the DUF3349 primary amino acid sequences, suggest two subfamilies within the DUF3349 family. The division of the DUF3349 into two distinct subfamilies would have been lost if structure solution had stopped with the first structure in the DUF3349 family, highlighting the insights generated by solving multiple structures within a protein superfamily. Future studies will determine if the structural diversity at the tertiary and quaternary levels in the DUF3349 protein superfamily have functional roles in Mycobacteria and Rhodococcus species with potential implications for structure-based drug discovery.

Related Citations:

Increasing the structural coverage of tuberculosis drug targets.
Baugh, L., Phan, I., Begley, D.W., Clifton, M.C., Armour, B., Dranow, D.M., Taylor, B.M., Muruthi, M.M., Abendroth, J., Fairman, J.W., Fox, D., Dieterich, S.H., Staker, B.L., Gardberg, A.S., Choi, R., Hewitt, S.N., Napuli, A.J., Myers, J., Barrett, L.K., Zhang, Y., Ferrell, M., Mundt, E., Thompkins, K., Tran, N., Lyons-Abbott, S., Abramov, A., Sekar, A., Serbzhinskiy, D., Lorimer, D., Buchko, G.W., Stacy, R., Stewart, L.J., Edwards, T.E., Van Voorhis, W.C., Myler, P.J.
(2015) Tuberculosis (Edinb) 95: 142

Organizational Affiliation:

UCB, Bainbridge Island, Washington.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A, B	107	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 Gene Names: MSMEG_1066
UniProt
Find proteins for A0QRC4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QRC4 Go to UniProtKB: A0QRC4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0QRC4
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A]	M [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Ligand Interaction
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A]	N [auth A], O [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Ligand Interaction
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Ligand Interaction