PDBsum entry 2e12

Translation

PDB id: 2e12

Contents

Protein chains

93 a.a.

Waters ×122

PDB id:

2e12

Name:

Translation

Title:

The crystal structure of xc5848 from xanthomonas campestris adopting a novel variant of sm-like motif

Structure:

Hypothetical protein xcc3642. Chain: a, b. Synonym: sm-like motif. Engineered: yes

Source:

Xanthomonas campestris pv. Campestris. Organism_taxid: 340. Strain: pv. Campestris. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.70Å R-factor: 0.220 R-free: 0.280

Authors:

K.-H.Chin,S.-K.Ruan,A.H.-J.Wang,S.-H.Chou

Key ref:

K.H.Chin et al. (2007). XC5848, an ORFan protein from Xanthomonas campestris, adopts a novel variant of Sm-like motif. Proteins, 68, 1006-1010. PubMed id: 17546661 DOI: 10.1002/prot.21375

Date:

17-Oct-06 Release date: 30-Oct-07

Protein chains

Q8P4R5  (Q8P4R5_XANCP) -  DUF3247 family protein from Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)

Seq: 101 a.a.

Struc: 93 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1002/prot.21375

Proteins 68:1006-1010 (2007)

PubMed id: 17546661

XC5848, an ORFan protein from Xanthomonas campestris, adopts a novel variant of Sm-like motif.

K.H.Chin, S.K.Ruan, A.H.Wang, S.H.Chou.

ABSTRACT

No abstract given.

Selected figure(s)

Figure 1.
Figure 1. (a) The monomer structure of XC5848 color-coded from blue (N-terminal) to red (C-terminal). Distinct interactions between the N-terminal residues with the extended 3/ 2 hairpin were circled in red and shown expanded in (b). (b) The 10 N-terminal residues were marked in blue, while other residues in red. The conventional H-bonds/salt-bridges were annotated in dotted green lines, while unconventional CH bonds in dotted gray lines. The unique bonding force at the N-terminal region are: (1) K3C O R55H^N; (2) Y4OH R55NH; (3) Y4OH R59O^ ; (4) A5H^N R55C O; (5) H7C O N64N^ ; (6) Y9H^N S63C O; (7) Y9C O S63H^N; (8) Y9OH D84O^ ; (9) T10C O Q12H^N; (10) W82C^ 3H Y54; (11) P6C^ H W82. (c) The dimer structure of XC5858. The interface is mainly comprised of helix-helix interactions, which were shown expanded in (d). (d) The interaction forces at this interface: (1) K23N^ E19O^ ; (2) H20N^ E19O^ ; (3) H20N^ Q12O^ and vice versa.

Figure 2.
Figure 2. (a) Multiple superimposition of Sm-like protein structures produced from the MUSTANG program.[15] While the core -sheet structure of these Sm-like proteins superimposed very well, the -helices and loops 4 vary to a great extent. XC5858 (shown in red) contains an extra N-terminal structure that interacts substantially with the extended 2 / 3 structure. (b) Multiple sequence alignments of XC5848 with the two bacterial Sm-like Hfq proteins (1HK9/1KQ1), the six archaeal Sm-like proteins (1H64, 1I4K, 1I81, 1I8F, 1LJ0, 1M8V), the two human Sm-like proteins (1B34, DD3B), and the yeast Sm-like protein (1N9S) produced from same program. Colors indicate the chemical nature of the amino acid (small hydrophobic including aromatic, red; acidic, blue; basic, magenta; basic amino acids with hydroxyl group and/or amino groups, black). The secondary structure elements for -helix (green tube) and -strand (red arrows) were also shown for the top and bottom sequences, along with their annotations. The -helices and -strands for each individual sequence were boxed in green and red, respectively. The essential residues responsible for subunit interactions and/or protein-RNA interactions were further marked with unique symbols in blue.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2007, 68, 1006-1010) copyright 2007.