PDBsum entry 3ol3

Unknown function

PDB id: 3ol3

Contents

Protein chains

98 a.a. *

92 a.a. *

Ligands

PG4

PGE ×2

Metals

IOD ×21

Waters ×154

* Residue conservation analysis

PDB id:

3ol3

Name:

Unknown function

Title:

Crystal structure of a putative uncharacterized protein from mycobacterium smegamtis, an ortholog of rv0543c, iodide phased

Structure:

Putative uncharacterized protein. Chain: a, b. Engineered: yes

Source:

Mycobacterium smegmatis. Organism_taxid: 246196. Strain: atcc 700084 / mc(2)155. Gene: msmeg_1066. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.95Å R-factor: 0.199 R-free: 0.236

Authors:

Seattle Structural Genomics Center For Infectious Disease (Ssgcid)

Key ref:

G.W.Buchko et al. (2020). Structural diversity in the Mycobacteria DUF3349 superfamily. Protein Sci, 29, 670-685. PubMed id: 31658388 DOI: 10.1002/pro.3758

Date:

25-Aug-10 Release date: 08-Sep-10

Protein chain

A0QRC4  (A0QRC4_MYCS2) -  EndoIII-related endonuclease from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)

Seq: 103 a.a.

Struc: 98 a.a.

Protein chain

A0QRC4  (A0QRC4_MYCS2) -  EndoIII-related endonuclease from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)

Seq: 103 a.a.

Struc: 92 a.a.

Enzyme reactions

• Enzyme class: Chains A, B: E.C.?

DOI no: 10.1002/pro.3758

Protein Sci 29:670-685 (2020)

PubMed id: 31658388

Structural diversity in the Mycobacteria DUF3349 superfamily.

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

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.