1H, 13C and 15N resonance assignment of the PDZ domain of HtrA from Streptococcus pneumoniae

HtrA is a major virulence factor of Streptococcus pneumoniae (pneumococcus). HtrA is involved in the ability of the pneumococcus to grow at high temperature, to resist oxidative stress and control the bacteriocin activity. Here we report the resonance assignment of the PDZ domain of HtrA from Streptococcus pneumoniae TIGR4.     

1H, 13C, and 15N resonance assignment of the SPFH domain of human stomatin

Stomatin, a 288-residue protein, is a component of the membrane skeleton of red blood cells (RBCs), which helps to physically support the membrane and maintains its function. In RBCs, stomatin binds to the glucose transporter GLUT-1 and may regulate its function. Stomatin has a stomatin/prohibitin/flotillin/HflK (SPFH) domain at the center of its polypeptide chain. There are 12 SPFH domain-containing proteins, most of which are localized at the cellular or subcellular membranes. Although the molecular function of the SPFH domain has not yet been established, the domain may be involved in protein oligomerization. The SPFH domain of the archaeal stomatin homolog has been shown to form unique oligomers. Here we report the ¹⁵N, ¹³C, and ¹H chemical shift assignments of the SPFH domain of human stomatin [hSTOM(SPFH)]. These may help in determining the structure of hSTOM(SPFH) in solution as well as in clarifying its involvement in protein oligomerization.     

1H, 13C, and 15N resonance assignment of the TIR domain of human MyD88

Myeloid differentiating factor 88 (MyD88) is one of a critical adaptor molecule in the Toll-like receptor (TLR) signaling pathway. The TIR domain of MyD88 serves as a protein–protein interaction module and interacts with other TIR-containing proteins such as Mal (MyD88 adaptor-like) and Toll-like receptor 4 to form signal initiation complexes. Here we report the ¹⁵N, ¹³C, and ¹H chemical shift assignments of the TIR domain of MyD88. The resonance assignments obtained in this work will contribute to the study of heteromeric TIR–TIR interactions between MyD88 and TIR-containing receptors or adaptors.     

1H, 13C, and 15N resonance assignment of the ubiquitin-like domain from Dsk2p

The ubiquitin-like domain (UBL) of yeast protein Dsk2p is widely believed to recognize and bind to ubiquitin receptors on the proteasome and, as part of Dsk2p, to bridge polyubiquitinated substrates and proteasomal degradation machinery. Here we report NMR resonance assignment for ¹H, ¹⁵N, and ¹³C nuclei in the backbone and side chains of the UBL domain of Dsk2p. This assignment will aid in NMR studies focused on understanding of Dsk2’s interactions with proteasomal receptors and its role as a polyubiquitin shuttle in the ubiquitin-dependent proteasomal degradation as well as other cellular pathways.     

1H, 15N and 13C resonance assignment of darcin, a mouse major urinary protein

Darcin is an important lipocalin of the urinary MUP family. These beta-barrel structures differ subtly in sequence and function and facilitate communication between members of the mouse population via scent marks. Polymorphism within the family has led to the hypothesis that individual MUPs can also contribute to social and physiological information of the scent owner and thus demonstrates the necessity for structural investigation of these variations. Using conventional triple resonance experiments, ¹H ¹⁵N and ¹³C assignment of recombinant N terminal hexa-histidine tagged Darcin has been achieved. The corresponding chemical shifts have been deposited in the BioMagResBank; Accession No. 16840.     

1H, 13C, and 15N resonance assignment of photoactive yellow protein

Photoactive yellow protein (PYP) is involved in the negative phototactic response towards blue light of the bacterium Halorhodospira halophila. Here, we report nearly complete backbone and side chain ¹H, ¹³C and ¹⁵N resonance assignments at pH 5.8 and 20 °C of PYP in its electronic ground state.     

Sequence-specific 1H, 13C, and 15N assignment of the extended PDZ3 domain of the protein tyrosine phosphatase basophil-like PTP-BL

Protein tyrosine phosphatase basophil-like (PTP-BL), also known as PTPN13, represents a large multi domain non-transmembrane scaffolding protein that contains five PDZ domains. Here we report the complete resonance assignments of the extended PDZ3 domain of PTP-BL. These assignments provide a basis for the detailed structural investigation of the interaction between the PDZ domains of PTP-BL as well as of their interaction with ligands. It will also lead to a better understanding of the proposed scaffolding function of these domains in multi-protein complexes assembled by PTB-BL.     

1H, 13C and 15N resonance assignment of Urm1 from Trypanosoma brucei

Urm1 (ubiquitin-related modifier), involved in diverse biological processes in yeast, is proved to be a “molecular fossil” in ubiquitin superfamily. Here we report the resonance assignment of Urm1 from Trypanosoma brucei.     

1H, 13C and 15N resonance assignment of phage T4 endoribonuclease RegB

RegB is involved in the control of the phage T4 life cycle. It inactivates the phage early mRNAs when their translation is no more required. We determined its structure and identified residues involved in substrate binding. For this, all backbone and 90% of side-chain resonance frequencies were assigned.     

1H, 13C and 15N resonance assignment of truncated SUMO from Trypanosoma brucei

SUMO (small ubiquitin-like modifier) plays important roles in diverse processes by posttranslationally modifying many proteins. Here we report the resonance assignment of the truncated SUMO from Trypanosoma brucei.     

Sequence-specific 1H, 13C, and 15N resonance assignments of GRP1 PH domain

The carboxy-terminal pleckstrin homology (PH) domain recruits GRP1 to the plasma membrane through the specific binding to phosphatidylinositol 3,4,5-trisphosphate [PtdIns(3,4,5)P₃]. Here, we describe backbone and side chain assignments of the GRP1 PH domain determined by triple resonance experiments. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.