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Our Science – Ji Website

Xinhua Ji, Ph.D.

Selected Publications

1)  Liang Y, Lavoie M, Comeau M, Abou Elela S, Ji X.
Structure of a Eukaryotic RNase III Postcleavage Complex Reveals a Double-Ruler Mechanism for Substrate Selection.
Mol. Cell. 54: 431-444, 2014.
[Journal]
2)  Stagno JR, Ma B, Li J, Altieri AS, Byrd RA, Ji X.
Crystal structure of a plectonemic RNA supercoil.
Nat Commun. 3: 901, 2012.
[Journal]
3)  Tu C, Zhou X, Tarasov SG, Tropea JE, Austin BP, Waugh DS, Court DL, Ji X.
The Era GTPase recognizes the GAUCACCUCC sequence and binds helix 45 near the 3' end of 16S rRNA.
Proc. Natl. Acad. Sci. USA. 108: 10156-10161, 2011.
[Journal]
4)  Shaw G, Gan J, Zhou YN, Zhi H, Subburaman P, Zhang R, Joachimiak A, Jin DJ, Ji X.
Structure of RapA, a Swi2/Snf2 Protein that Recycles RNA Polymerase During Transcription.
Structure. 16: 1417-1427, 2008.
[Journal]
5)  Gan J, Tropea JE, Austin BP, Court DL, Waugh DS, Ji X.
Structural insight into the mechanism of double-stranded RNA processing by ribonuclease III.
Cell. 124: 355-66, 2006.
[Journal]
6)  Nair S, Sanchez-Martinez S, Ji X, Rein A.
Biochemical and Biological Studies on Mouse APOBEC3.
J. Virol. 88: 3850-3860, 2014.
[Journal]
7)  Antony ML, Lee J, Hahm E, Kim S, Marcus AI, Kumari V, Ji X, Yang Z, Vowell CL, Wipf P, Uechi GT, Yates NA, Romero G, Sarkar SN, Singh SV.
Growth Arrest by the Antitumor Steroidal Lactone Withaferin A in Human Breast Cancer Cells Is Associated with Down-regulation and Covalent Binding at Cysteine 303 of beta-Tubulin.
J. Biol. Chem. 289: 1852-65, 2014.
[Journal]
8)  Maciag AE, Holland RJ, Kim Y, Kumari V, Luthers CE, Sehareen WS, Biswas D, Morris NL, Ji X, Anderson LM, Saavedra JE, Keefer LK.
Nitric Oxide (NO) Releasing Poly ADP-ribose Polymerase 1 (PARP-1) Inhibitors Targeted to Glutathione S-Transferase P1-Overexpressing Cancer Cells.
J. Med. Chem. 57: 2292-302, 2014.
[Journal]
9)  Metzger MB, Liang YH, Das R, Mariano J, Li S, Li J, Kostova Z, Byrd RA, Ji X, Weissman AM.
A Structurally Unique E2-Binding Domain Activates Ubiquitination by the ERAD E2, Ubc7p, through Multiple Mechanisms.
Mol. Cell. 50: 516-27, 2013.
[Journal]
10)  Das R, Liang YH, Mariano J, Li J, Huang T, King A, Tarasov SG, Weissman AM, Ji X, Byrd RA.
Allosteric regulation of E2:E3 interactions promote a processive ubiquitination machine.
EMBO J. 32: 2504-16, 2013.
[Journal]
11)  Court DL, Gan J, Liang Y, Shaw GX, Tropea JE, Costantino N, Waugh DS, Ji X.
RNase III: Genetics and Function; Structure and Mechanism.
Annu Rev Genet. 47: 405-431, 2013.
[Journal]
12)  Shi G, Shaw G, Liang YH, Subburaman P, Li Y, Wu Y, Yan H, Ji X.
Bisubstrate analogue inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: New design with improved properties.
Bioorg. Med. Chem. 20: 47-57, 2012.
[Journal]
13)  Shi G, Shaw G, Li Y, Wu Y, Yan H, Ji X.
Bisubstrate analogue inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: New lead exhibits a distinct binding mode.
Bioorg. Med. Chem. 20: 4303-4309, 2012.
[Journal]
14)  Zhao J, Stagno JR, Varticovski L, Nimako E, Rishi V, McKinnon K, Akee R, Shoemaker RH, Ji X, Vinson C.
P6981, an Arylstibonic Acid, is a Novel Low Nanomolar Inhibitor of CREB binding to DNA.
Mol. Pharmacol. 82: 814-23, 2012.
[Journal]
15)  Madina BR, Kuppan G, Vashisht AA, Liang Y, Downey KM, Wohlschlegel JA, Ji X, Sze S, Sacchettini JC, Read LK, Cruz-Reyes J.
Guide RNA biogenesis involves a novel RNase III family endoribonuclease in Trypanosoma brucei.
RNA. 17: 1821-1830, 2011.
[Journal]
16)  Shi G, Ji X.
New ways to derivatize at position 6 of 7,7-dimethyl-7,8-dihydropterin.
Tetrahedron Lett. 52: 6174-6176, 2011.
[Journal]
17)  Yan H, Ji X.
Role of protein conformational dynamics in the catalysis by 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase.
Protein Pept. Lett. 18: 328-35, 2011.
[Journal]
18)  Stagno JR, Altieri AS, Bubunenko M, Tarasov SG, Li J, Court DL, Byrd RA, Ji X.
Structural basis for RNA recognition by NusB and NusE in the initiation of transcription antitermination.
Nucleic Acids Res. 39: 7803-15, 2011.
[Journal]
19)  Jin DJ, Zhou YN, Shaw G, Ji X.
Structure and function of RapA: A bacterial Swi2/Snf2 protein required for RNA polymerase recycling in transcription.
Biochim Biophys Acta. 1809: 470-475, 2011.
[Journal]
20)  Subburaman P, Austin BP, Shaw GX, Waugh DS, Ji X.
Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of macrophage growth locus A (MglA) protein from Francisella tularensis.
Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 66: 554-7, 2010.
[Journal]
21)  Das R, Mariano J, Tsai YC, Kalathur RC, Kostova Z, Li J, Tarasov SG, McFeeters RL, Altieri AS, Ji X, Byrd RA, Weissman AM.
Allosteric activation of E2-RING finger-mediated ubiquitylation by a structurally defined specific E2-binding region of gp78.
Mol. Cell. 34: 674-85, 2009.
[Journal]
22)  Tu C, Tropea JE, Austin BP, Court DL, Waugh DS, Ji X.
Structural basis for binding of RNA and cofactor by a KsgA methyltransferase.
Structure. 17: 374-85, 2009.
[Journal]
23)  Tu C, Zhou X, Tropea JE, Austin BP, Waugh DS, Court DL, Ji X.
Structure of ERA in complex with the 3' end of 16S rRNA: implications for ribosome biogenesis.
Proc. Natl. Acad. Sci. U.S.A. 106: 14843-8, 2009.
[Journal]
24)  Dabrazhynetskaya A, Brendler T, Ji X, Austin S.
Switching protein-DNA recognition specificity by single-amino-acid substitutions in the P1 par family of plasmid partition elements.
J. Bacteriol. 191: 1126-31, 2009.
[Journal]
25)  Gan J, Shaw G, Tropea JE, Waugh DS, Court DL, Ji X.
A stepwise model for double-stranded RNA processing by ribonuclease III.
Mol Microbiol. 67: 143-154, 2008.
[Journal]
26)  Tu C, Tan YH, Shaw G, Zhou Z, Bai Y, Luo R, Ji X.
Impact of low-frequency hotspot mutation R282Q on the structure of p53 DNA-binding domain as revealed by crystallography at 1.54 angstroms resolution.
Acta Crystallogr. D Biol. Crystallogr. 64: 471-7, 2008.
[Journal]
27)  Prabakaran P, Vu BK, Gan J, Feng Y, Dimitrov DS, Ji X.
Structure of an isolated unglycosylated antibody C(H)2 domain.
Acta Crystallogr. D Biol. Crystallogr. 64: 1062-7, 2008.
[Journal]
28)  Ji X, Pal A, Kalathur R, Hu X, Gu Y, Saavedra J, Buzard G, Srinivasan A, Keefer L, Singh S.
Structure-based design of anticancer prodrug PABA/NO.
Drug Des Devel Ther. 2: 123-130, 2008.
[Journal]
29)  Chakrapani H, Kalathur RC, Maciag AE, Citro ML, Ji X, Keefer LK, Saavedra JE.
Synthesis, mechanistic studies, and anti-proliferative activity of glutathione/glutathione S-transferase-activated nitric oxide prodrugs.
Bioorg. Med. Chem. 16: 9764-71, 2008.
[Journal]
30)  Ji X.
The mechanism of RNase III action: How Dicer dices.
Curr. Top. Microbiol. Immunol. 320: 99-116, 2008.
[Journal]
31)  Gan J, Wu Y, Prabakaran P, Gu Y, Li Y, Andrykovitch M, Liu H, Gong Y, Yan H, Ji X.
Structural and Biochemical Analyses of Shikimate Dehydrogenase AroE from Aquifex aeolicus: Implications for the Catalytic Mechanism(,).
Biochemistry. 46: 9513-22, 2007.
[Journal]
32)  Blaszczyk J, Li Y, Gan J, Yan H, Ji X.
Structural basis for the aldolase and epimerase activities of Staphylococcus aureus dihydroneopterin aldolase.
J. Mol. Biol. 368: 161-9, 2007.
[Journal]
33)  Blaszczyk J, Li Y, Cherry S, Alexandratos J, Wu Y, Shaw G, Tropea JE, Waugh DS, Yan H, Ji X.
Structure and activity of Yersinia pestis 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase as a novel target for the development of antiplague therapeutics.
Acta Crystallogr. D Biol. Crystallogr. 63: 1169-77, 2007.
[Journal]
34)  Townsend DM, Findlay VJ, Fazilev F, Ogle M, Fraser J, Saavedra JE, Ji X, Keefer LK, Tew KD.
A glutathione S-transferase pi-activated prodrug causes kinase activation concurrent with S-glutathionylation of proteins.
Mol Pharmacol. 69: 501-8, 2006.
[Journal]
35)  Shami PJ, Saavedra JE, Bonifant CL, Chu J, Udupi V, Malaviya S, Carr BI, Kar S, Wang M, Jia L, Ji X, Keefer LK.
Antitumor activity of JS-K [O2-(2,4-dinitrophenyl) 1-[(4-ethoxycarbonyl)piperazin-1-yl]diazen-1-ium-1,2-diolate] and related O2-aryl diazeniumdiolates in vitro and in vivo.
J. Med. Chem. 49: 4356-66, 2006.
[Journal]
36)  Gan J, Gu Y, Li Y, Yan H, Ji X.
Crystal structure of Mycobacterium tuberculosis shikimate kinase in complex with shikimic acid and an ATP analogue.
Biochemistry. 45: 8539-45, 2006.
[Journal]
37)  Saavedra JE, Srinivasan A, Buzard GS, Davies KM, Waterhouse DJ, Inami K, Wilde TC, Citro ML, Cuellar M, Deschamps JR, Parrish D, Shami PJ, Findlay VJ, Townsend DM, Tew KD, Singh S, Jia L, Ji X, Keefer LK.
PABA/NO as an anticancer lead: analogue synthesis, structure revision, solution chemistry, reactivity toward glutathione, and in vitro activity.
J Med Chem. 49: 1157-64, 2006.
[Journal]
38)  Ji X.
Structural basis for non-catalytic and catalytic activities of ribonuclease III.
Acta Crystallogr. D Biol. Crystallogr. 62: 933-40, 2006.
[Journal]
39)  Prabakaran P, Gan J, Wu Y, Zhang M, Dimitrov DS, Ji X.
Structural Mimicry of CD4 by a Cross-reactive HIV-1 Neutralizing Antibody with CDR-H2 and H3 Containing Unique Motifs.
J Mol Biol. 357: 82-99, 2006.
[Journal]
40)  Prabakaran P, Gan J, Feng Y, Zhu Z, Choudhry V, Xiao X, Ji X, Dimitrov DS.
Structure of severe acute respiratory syndrome coronavirus receptor-binding domain complexed with neutralizing antibody.
J. Biol. Chem. 281: 15829-36, 2006.
[Journal]
41)  Gan J, Tropea JE, Austin BP, Court DL, Waugh DS, Ji X.
Intermediate states of ribonuclease III in complex with double-stranded RNA.
Structure. 13: 1435-42, 2005.
[Journal]
42)  Li Y, Blaszczyk J, Wu Y, Shi G, Ji X, Yan H.
Is the critical role of loop 3 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase in catalysis due to loop-3 residues arginine-84 and tryptophan-89? Site-directed mutagenesis, biochemical, and crystallographic studies.
Biochemistry. 44: 8590-9, 2005.
[Journal]
43)  Hansen AM, Gu Y, Li M, Andrykovitch M, Waugh DS, Jin DJ, Ji X.
Structural basis for the function of stringent starvation protein a as a transcription factor.
J. Biol. Chem. 280: 17380-91, 2005.
[Journal]
44)  Gu Y, Guo J, Pal A, Pan SS, Zimniak P, Singh SV, Ji X.
Crystal structure of human glutathione S-transferase A3-3 and mechanistic implications for its high steroid isomerase activity.
Biochemistry. 43: 15673-9, 2004.
[Journal]
45)  Darbha R, Phogat S, Labrijn AF, Shu Y, Gu Y, Andrykovitch M, Zhang MY, Pantophlet R, Martin L, Vita C, Burton DR, Dimitrov DS, Ji X.
Crystal structure of the broadly cross-reactive HIV-1-neutralizing Fab X5 and fine mapping of its epitope.
Biochemistry. 43: 1410-7, 2004.
[Journal]
46)  Blaszczyk J, Li Y, Wu Y, Shi G, Ji X, Yan H.
Essential roles of a dynamic loop in the catalysis of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase.
Biochemistry. 43: 1469-77, 2004.
[Journal]
47)  Krauss J, Arndt MA, Zhu Z, Newton DL, Vu BK, Choudhry V, Darbha R, Ji X, Courtenay-Luck NS, Deonarain MP, Richards J, Rybak SM.
Impact of antibody framework residue VH-71 on the stability of a humanised anti-MUC1 scFv and derived immunoenzyme.
Br. J. Cancer. 90: 1863-70, 2004.
[Journal]
48)  Blaszczyk J, Gan J, Tropea JE, Court DL, Waugh DS, Ji X.
Noncatalytic assembly of ribonuclease III with double-stranded RNA.
Structure. 12: 457-66, 2004.
[Journal]
49)  Blaszczyk J, Shi G, Li Y, Yan H, Ji X.
Reaction trajectory of pyrophosphoryl transfer catalyzed by 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase.
Structure. 12: 467-75, 2004.
[Journal]
50)  Singh SV, Varma V, Zimniak P, Srivastava SK, Marynowski SW, Desai D, Amin S, Ji X.
Structural basis for catalytic differences between alpha class human glutathione transferases hGSTA1-1 and hGSTA2-2 for glutathione conjugation of environmental carcinogen benzo[a]pyrene-7,8-diol-9,10-epoxide.
Biochemistry. 43: 9708-15, 2004.
[Journal]
51)  Findlay VJ, Townsend DM, Saavedra JE, Buzard GS, Citro ML, Keefer LK, Ji X, Tew KD.
Tumor cell responses to a novel glutathione S-transferase-activated nitric oxide-releasing prodrug.
Mol. Pharmacol. 65: 1070-9, 2004.
[Journal]
52)  Knowlton JR, Bubunenko M, Andrykovitch M, Guo W, Routzahn KM, Waugh DS, Court DL, Ji X.
A spring-loaded state of NusG in its functional cycle is suggested by X-ray crystallography and supported by site-directed mutants.
Biochemistry. 42: 2275-81, 2003.
[Journal]
53)  Li Y, Wu Y, Blaszczyk J, Ji X, Yan H.
Catalytic roles of arginine residues 82 and 92 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: site-directed mutagenesis and biochemical studies.
Biochemistry. 42: 1581-8, 2003.
[Journal]
54)  Andrykovitch M, Routzahn KM, Li M, Gu Y, Waugh DS, Ji X.
Characterization of four orthologs of stringent starvation protein A.
Acta Crystallogr. D Biol. Crystallogr. 59: 881-6, 2003.
[Journal]
55)  Blaszczyk J, Li Y, Shi G, Yan H, Ji X.
Dynamic roles of arginine residues 82 and 92 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: crystallographic studies.
Biochemistry. 42: 1573-80, 2003.
[Journal]
56)  Shami PJ, Saavedra JE, Wang LY, Bonifant CL, Diwan BA, Singh SV, Gu Y, Fox SD, Buzard GS, Citro ML, Waterhouse DJ, Davies KM, Ji X, Keefer LK.
JS-K, a glutathione/glutathione S-transferase-activated nitric oxide donor of the diazeniumdiolate class with potent antineoplastic activity.
Mol. Cancer Ther. 2: 409-17, 2003.
[Journal]
57)  Gu Y, Xiao B, Wargo HL, Bucher MH, Singh SV, Ji X.
Residues 207, 216, and 221 and the catalytic activity of mGSTA1-1 and mGSTA2-2 toward benzo[a]pyrene-(7R,8S)-diol-(9S,10R)-epoxide.
Biochemistry. 42: 917-21, 2003.
[Journal]
58)  Li Y, Gong Y, Shi G, Blaszczyk J, Ji X, Yan H.
Chemical transformation is not rate-limiting in the reaction catalyzed by Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase.
Biochemistry. 41: 8777-83, 2002.
[Journal]
59)  Gu Y, Reshetnikova L, Li Y, Wu Y, Yan H, Singh S, Ji X.
Crystal structure of shikimate kinase from Mycobacterium tuberculosis reveals the dynamic role of the LID domain in catalysis.
J. Mol. Biol. 319: 779-89, 2002.
[Journal]
60)  Andrykovitch M, Guo W, Routzahn KM, Gu Y, Anderson DE, Reshetnikova LS, Knowlton JR, Waugh DS, Ji X.
Crystallization and preliminary X-ray diffraction studies of NusG, a protein shared by the transcription and translation machines.
Acta Crystallogr. D Biol. Crystallogr. 58: 2157-8, 2002.
[Journal]
61)  Keskin O, Ji X, Blaszcyk J, Covell DG.
Molecular motions and conformational changes of HPPK.
Proteins. 49: 191-205, 2002.
[Journal]
62)  Chu R, Takei J, Knowlton JR, Andrykovitch M, Pei W, Kajava AV, Steinbach PJ, Ji X, Bai Y.
Redesign of a four-helix bundle protein by phage display coupled with proteolysis and structural characterization by NMR and X-ray crystallography.
J. Mol. Biol. 323: 253-62, 2002.
[Journal]
63)  Singh S, Nanduri B, Xiao B, Ji X, Awasthi S, Awasthi Y, Zimniak P.
Gupta S, eds.
Catalytic mechanism of mGSTA4-4: an enzyme involved in the response to oxidative stress. In: Pharmacology and Therapeutics in the New Millennium.
New Delhi: Narosa Publishing House; 2001. p. 688-701 [Book Chapter]
64)  Yan H, Blaszczyk J, Xiao B, Shi G, Ji X.
Kuhn L, Thorpe M, eds.
Structure and dynamics of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase. In: Protein Flexibility and Folding.
Amsterdam: Elsevier; 2001. p. 70-77 [Book Chapter]
65)  Shi G, Blaszczyk J, Ji X, Yan H.
Bisubstrate analogue inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: synthesis and biochemical and crystallographic studies.
J. Med. Chem. 44: 1364-71, 2001.
[Journal]
66)  Pal A, Gu Y, Pan SS, Ji X, Singh SV.
C-terminal region amino acid substitutions contribute to catalytic differences between murine class alpha glutathione transferases mGSTA1-1 and mGSTA2-2 toward anti-diol epoxide isomers of benzo[c]phenanthrene.
Biochemistry. 40: 7047-53, 2001.
[Journal]
67)  Blaszczyk J, Li Y, Yan H, Ji X.
Crystal structure of unligated guanylate kinase from yeast reveals GMP-induced conformational changes.
J. Mol. Biol. 307: 247-57, 2001.
[Journal]
68)  Gu Y, Reshetnikova L, Li Y, Yan H, Singh SV, Ji X.
Crystallization and preliminary X-ray diffraction analysis of shikimate kinase from Mycobacterium tuberculosis in complex with MgADP.
Acta Crystallogr. D Biol. Crystallogr. 57: 1870-1, 2001.
[Journal]
69)  Blaszczyk J, Tropea JE, Bubunenko M, Routzahn KM, Waugh DS, Court DL, Ji X.
Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavage.
Structure. 9: 1225-36, 2001.
[Journal]
70)  Engle M, Singh S, Nanduri B, Ji X, Zimniak P.
Invertebrate glutathione transferases conjugating 4-hydroxynonenal: CeGST 5.4 from Caenorhabditis elegans.
Chemico-Biological Interactions. 133: 244-248, 2001.
[Journal]
71)  Pal A, Gu Y, Herzog C, Srivastava SK, Zimniak P, Ji X, Singh SV.
Role of arginine 216 in catalytic activity of murine Alpha class glutathione transferases mGSTAl-1 and mGSTA2-2 toward carcinogenic diol epoxides of polycyclic aromatic hydrocarbons.
Carcinogenesis. 22: 1301-5, 2001.
[Journal]
72)  Yan H, Blaszczyk J, Xiao B, Shi G, Ji X.
Structure and dynamics of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase.
J. Mol. Graph. Model. 19: 70-7, 2001.
[Journal]
73)  Ji X, Blaszczyk J, Chen X.
The absorption edge of protein-bound mercury and a double-edge strategy for HgMAD data acquisition.
Acta Crystallogr. D Biol. Crystallogr. 57: 1003-7, 2001.
[Journal]
74)  Xiao B, Shi G, Gao J, Blaszczyk J, Liu Q, Ji X, Yan H.
Unusual conformational changes in 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase as revealed by X-ray crystallography and NMR.
J. Biol. Chem. 276: 40274-81, 2001.
[Journal]
75)  Blaszczyk J, Shi G, Yan H, Ji X.
Catalytic center assembly of HPPK as revealed by the crystal structure of a ternary complex at 1.25 A resolution.
Structure. 8: 1049-58, 2000.
[Journal]
76)  Blaszczyk J, Coillie EV, Proost P, Damme JV, Opdenakker G, Bujacz GD, Wang JM, Ji X.
Complete crystal structure of monocyte chemotactic protein-2, a CC chemokine that interacts with multiple receptors.
Biochemistry. 39: 14075-81, 2000.
[Journal]
77)  Shi G, Gong Y, Savchenko A, Zeikus JG, Xiao B, Ji X, Yan H.
Dissecting the nucleotide binding properties of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase with fluorescent 3'(2)'-o-anthraniloyladenosine 5'-triphosphate.
Biochim. Biophys. Acta. 1478: 289-99, 2000.
[Journal]
78)  Gu Y, Singh SV, Ji X.
Residue R216 and catalytic efficiency of a murine class alpha glutathione S-transferase toward benzo[a]pyrene 7(R),8(S)-diol 9(S), 10(R)-epoxide.
Biochemistry. 39: 12552-7, 2000.
[Journal]
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This page was last updated on 6/19/2014.