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Instruments / Technical Area	Publication Details	Published
I04-Macromolecular Crystallography	Structural basis of a novel repressor SghR controlling Agrobacterium infection by cross-talking to plants Fuzhou Ye , Chao Wang , Qinqin Fu , Xin-fu Yan , Sakshibeedu R. Bharath , Arnau Casanas , Meitian Wang , Haiwei Song , Lian-hui Zhang , Yong-gui Gao Journal Of Biological Chemistry DOI: 10.1074/jbc.RA120.012908 Show Abstract ▼ Abstract: Agrobacterium tumefaciens infects various plants and causes crown gall diseases involving temporal expression of virulence factors. SghA is a newly-identified virulence factor enzymatically releasing salicylic acid from its glucoside conjugate and controlling the plant tumor development. Here we report the structural basis of SghR, a LacI-type transcription factor and highly conserved in Rhizobiaceae family, regulating the expression of SghA and involved in tumorigenesis. We identified and characterized the binding site of SghR on the promoter region of sghA, and then determined the crystal structures of apo-SghR, SghR complexed with its operator DNA and ligand sucrose, respectively. These results provide detailed insights into how SghR recognizes its cognate DNA and shed a mechanistic light on how sucrose attenuates the affinity of SghR with DNA to modulate the expression of SghA. Given the important role of SghR in mediating the signaling crosstalk during Agrobacterium infection, our results pave the way for structure-based inducer analogue design, which has potential applications for agricultural industry.	Jul 2020
I02-Macromolecular Crystallography	Structural basis of suppression of host translation termination by Moloney Murine Leukemia Virus Xuhua Tang , Yiping Zhu , Stacey L. Baker , Matthew W. Bowler , Benjamin Jieming Chen , Chen Chen , J. Robert Hogg , Stephen P. Goff , Haiwei Song Nature Communications 7 DOI: 10.1038/ncomms12070 Open Access Show Abstract ▼ Abstract: Retroviral reverse transcriptase (RT) of Moloney murine leukemia virus (MoMLV) is expressed in the form of a large Gag–Pol precursor protein by suppression of translational termination in which the maximal efficiency of stop codon read-through depends on the interaction between MoMLV RT and peptidyl release factor 1 (eRF1). Here, we report the crystal structure of MoMLV RT in complex with eRF1. The MoMLV RT interacts with the C-terminal domain of eRF1 via its RNase H domain to sterically occlude the binding of peptidyl release factor 3 (eRF3) to eRF1. Promotion of read-through by MoMLV RNase H prevents nonsense-mediated mRNA decay (NMD) of mRNAs. Comparison of our structure with that of HIV RT explains why HIV RT cannot interact with eRF1. Our results provide a mechanistic view of how MoMLV manipulates the host translation termination machinery for the synthesis of its own proteins.	Jun 2016
I02-Macromolecular Crystallography	Structural and Functional Insights into the Unwinding Mechanism of Bacteroides sp Pif1 Xianglian Zhou , Wendan Ren , Sakshibeedu r. Bharath , Xuhua Tang , Yang He , Chen Chen , Zhou Liu , Dewang Li , Haiwei Song Cell Reports DOI: 10.1016/j.celrep.2016.02.008 Diamond Proposal Number(s): [11068] Open Access Show Abstract ▼ Abstract: Pif1 is a conserved SF1B DNA helicase involved in maintaining genome stability through unwinding double-stranded DNAs (dsDNAs), DNA/RNA hybrids, and G quadruplex (G4) structures. Here, we report the structures of the helicase domain of human Pif1 and Bacteroides sp Pif1 (BaPif1) in complex with ADP-AlF4â€“ and two different single-stranded DNAs (ssDNAs). The wedge region equivalent to the Î²Â hairpin in other SF1B DNA helicases folds into an extended loop followed by an Î± helix. The Pif1 signature motif of BaPif1 interacts with the wedge region and a short helix in order to stabilize these ssDNA binding elements, therefore indirectly exerting its functional role. Domain 2B of BaPif1 undergoes a large conformational change upon concomitant binding of ATP and ssDNA, which is critical for Pif1â€™s activities. BaPif1 cocrystallized with a tailed dsDNA and ADP-AlF4â€“, resulting in a bound ssDNA bent nearly 90Â° at the ssDNA/dsDNA junction. The conformational snapshots of BaPif1 provide insights into the mechanism governing the helicase activity ofÂ Pif1.	Mar 2016
	Structural basis of YAP recognition by TEAD4 in the hippo pathway Liming Chen , Siew Wee Chan , Xiaoqian Zhang , Martin Walsh , Chun Jye Lim , Wanjin Hong , Haiwei Song Genes And Development 24, 290-300 DOI: 10.1101/gad.1865310 Show Abstract ▼ Abstract: The Hippo signaling pathway controls cell growth, proliferation, and apoptosis by regulating the expression of target genes that execute these processes. Acting downstream from this pathway is the YAP transcriptional coactivator, whose biological function is mediated by the conserved TEAD family transcription factors. The interaction of YAP with TEADs is critical to regulate Hippo pathway-responsive genes. Here, we describe the crystal structure of the YAP-interacting C-terminal domain of TEAD4 in complex with the TEAD-interacting N-terminal domain of YAP. The structure reveals that the N-terminal region of YAP is folded into two short helices with an extended loop containing the PXX?P motif in between, while the C-terminal domain of TEAD4 has an immunoglobulin-like fold. YAP interacts with TEAD4 mainly through the two short helices. Point mutations of TEAD4 indicate that the residues important for YAP interaction are required for its transforming activity. Mutagenesis reveals that the PXX?P motif of YAP, although making few contacts with TEAD4, is important for TEAD4 interaction as well as for the transforming activity.	Feb 2010

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