PDBsum entry 2ba2

Structural genomics, unknown function

PDB id: 2ba2

Contents

Protein chains

81 a.a. *

Waters ×190

* Residue conservation analysis

PDB id:

2ba2

Name:

Structural genomics, unknown function

Title:

Crystal structure of the duf16 domain of mpn010 from mycoplasma pneumoniae

Structure:

Hypothetical upf0134 protein mpn010. Chain: a, b, c. Fragment: duf16 domain, residues 46-130. Synonym: d12_orf131. Engineered: yes

Source:

Mycoplasma pneumoniae. Organism_taxid: 2104. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Trimer (from PQS)

Resolution:

1.80Å R-factor: 0.229 R-free: 0.281

Authors:

D.H.Shin,J.-S.Kim,H.Yokota,R.Kim,S.-H.Kim,Berkeley Structural Genomics Center (Bsgc)

Key ref:

D.H.Shin et al. (2006). Crystal structure of the DUF16 domain of MPN010 from Mycoplasma pneumoniae. Protein Sci, 15, 921-928. PubMed id: 16522803 DOI: 10.1110/ps.051993506

Date:

13-Oct-05 Release date: 07-Mar-06

Protein chains

P75103  (Y010_MYCPN) -  UPF0134 protein MPN_010 from Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)

Seq: 131 a.a.

Struc: 81 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1110/ps.051993506

Protein Sci 15:921-928 (2006)

PubMed id: 16522803

Crystal structure of the DUF16 domain of MPN010 from Mycoplasma pneumoniae.

D.H.Shin, J.S.Kim, H.Yokota, R.Kim, S.H.Kim.

ABSTRACT

We have determined the crystal structure of the DUF16 domain of unknown function encoded by the gene MPN010 of Mycoplasma pneumoniae at 1.8 A resolution. The crystal structure revealed that this domain is composed of two separated homotrimeric coiled-coils. The shorter one consists of 11 highly conserved residues. The sequence comprises noncanonical heptad repeats that induce a right-handed coiled-coil structure. The longer one is composed of approximately nine heptad repeats. In this coiled-coil structure, there are three distinguishable regions that confer unique structural properties compared with other known homotrimeric coiled-coils. The first part, containing one stutter, is an unusual phenylalanine-rich region that is not found in any other coiled-coil structures. The second part is a highly conserved glutamine-rich region, frequently found in other trimeric coiled-coil structures. The last part is composed of prototype heptad repeats. The phylogenetic analysis of the DUF16 family together with a secondary structure prediction shows that the DUF16 family can be classified into five subclasses according to N-terminal sequences. Based on the structural comparison with other coiled-coil structures, a probable molecular function of the DUF16 family is discussed.

Selected figure(s)

Figure 1.
Sequence comparisons of the DUF16 family in M. pneumoniae. The yellow region indicates the short helical bundle of the DUF16 domain based on the MPNOIO structure. The front of this region is the approximate N-terminal domain of the DUF 16 family and the back is the long helical bundle region of the DUF 16 domain based on the MPNOIO structure. Except for the secondary structure of MPNOIO, the other secondary structures are predictions obtained with PSIPRED (http://bioinf.cs.ucl.ac.uk/psipred). Blue, [alpha]-helix; red, [beta]-strand; minus symbol ([minus sign]), a gap; period (.), less than mean value plus 1 SD; plus symbol (+), less than mean value plus 2 SD; and asterisk (*), less than mean value plus 3 SD. "TWISTER" represents each position of the heptad repeats of the DUF16 domain of MPN010 obtained using the program TWISTER. In here, "z" indicates a potential location of stutters. The percent sequence identities against MPN010 are also shown. Members of each subclass are as follows: (1) subfamily I: MPN104, MPN675, MPN038, MPN287, MPN484, and MPN151; (2) subfamily II: MPN010, MPN137, and MPN145; (3) subfamily III: MPN283, MPN504, and MPN524; (4) subfamily IV: MPN501, MPN100, MPN204, MPN410, MPN094, MPN130, MPN368, MPN138, and MPN139; and (5) subfamily V: MPN655, MPN344, MPN013, and MPN127. The insertions are abbreviated with the number of amino acids. The proline-rich regions are in these abbreviations.

Figure 2.
Diagrams of the DUF16 domain of MPN010. (A) A stereo view of a refined electron-density map around a phenyalanine-rich region countered at 1.5[sigma]. The 2Fo-Fc map from finally refined phases was calculated using all reflection data between 20 A and 1.8 A. The figure was generated using the program RIBBONS (Carson 1991). The residues around the phenylalanine-rich region are represented by ball-and-stick models (blue, nitrogen atoms; red, oxygen; green, carbon). The front phenylalanines are Phe75 and the ones below are Phe72. (B) A stereo drawing of a C[alpha] atom trace of the DUF16 domain of MPN010. Each model was colored differently. Every 20th residue is numbered and represented by a dot. The phenylalanine (blue) and glutamine (pink) residues that occupy trimer interfaces are represented by a ball-and-stick model. The figure was generated by MOLSCRIPT (Kraulis 1991). (C) The electrostatic surface potential of the DUF16 domain of MPN010. A molecular surface is created by the program GRASP (red, negative; blue, positive; white, uncharged) (Nicholls et al. 1991). (D) Local coiled-coil parameters plotted against the residue numbers. The gray squares represent a coiled-coil radius and the black diamonds indicate coiled-coil pitch. "SH" and "LH" represent the range of the short and the long helical bundles, respectively. The small arrows indicate the positions showing properties of stutters.

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (2006, 15, 921-928) copyright 2006.