Publications

2014

Citation Associated Structures
Amanda M Schalk and Arnon Lavie(2014) "Structural and kinetic characterization of guinea pig L-asparaginase type III." Biochemistry, 53, 2318-28

4O47
4O48

 

Kiira Ratia, Samuel H Light, Aleksander Antansijevic, Wayne F Anderson ad Arnon Lavie(2014) "Discovery of selective inhibitors of the Clostridium difficile dehydroquinate dehydratase" PLoS One, e89356
Nomme J, Murphy JM, Su Y, Sansone ND, Armijo AL, Olson ST, Radu C, Lavie A (2014) "Structural characterization of new deoxycytidine kinase inhibitors rationalizes the affinity-determining moieties of the molecules." Acta Crystallographica Section D, 70, 68-78
Light SH, Antanasijevic A, Krishna SN, Caffrey M, Anderson WF, Lavie A. WF (2014) "Crystal structures of type I dehydroquinate dehydratase in complex with quinate and shikimate suggest a novel mechanism of Schiff base formation."Biochemistry, 53, 872-80

4IUO
4GUJ
4GUI

Nathanson DA, Armijo AL, Tom M, Li Z, Dimitrova E, Austin WR, Nomme J, Campbell DO, Ta L, Le TM, Lee JT, Darvish R, Gordin A, Wei L, Liao HI, Wilks M, Martin C, Sadeghi S, Murphy JM, Boulos N, Phelps ME, Faull KF, Herschman HR, Jung ME, Czernin J, Lavie A, Radu CG. (2014) "Co-targeting of convergent nucleotide biosynthetic pathways for leukemia eradication." Journal of Experimental Medicine, 11, 473-86
Nomme J, Su Y, Lavie A. (2014) "Elucidation of the Specific Function of the Conserved Threonine Triad Responsible for Human l-Asparaginase Autocleavage and Substrate Hydrolysis." Journal of Molecular Biology,

 

2013

Citation Associated Structures
Light SH, Krishna SN, Bergan RC, Lavie A, Anderson WF (2013) "Crystal structure of a type II dehydroquinate dehydratase-like protein from Bifidobacterium longum" Journal of Structural Functional Genomics, 14, 25-30
Su Y, Karamitros CS, Nomme J, McSorley T, Konrad M, Lavie A (2013) "Free glycine accelerates the autoproteolytic activation of human asparaginase" Chemistry & Biology, 20 , 533-40

4HLP
4HLO

Samuel H Light, Wayne F Anderson, and Arnon Lavie (2013) “Reassessing the type I dehydroquinate dehydratase catalytic triad: Kinetic and structural studies of Glu86 mutants” Protein Science, 22, 418-24

4GUF
4GUG
4GUH

Murphy JM, Armijo AL, Nomme J, Lee CH, Smith QA, Li Z, Campbell DO, Liao HI, Nathanson DA, Austin WR, Lee JT, Darvish R, Wei L, Wang J, Su Y, Damoiseaux R, Sadeghi S, Phelps ME, Herschman HR, Czernin J, Alexandrova AN, Jung ME, Lavie A, Radu CG. (2013) “ Development of new deoxycytidine kinase inhibitors and noninvasive in vivo evaluation using positron emission tomography." Medicinal Chemistry, 56, 6696-708

4L5B
4JLK

Takeya Sato, Anton Neschadim, Arnon Lavie, Teruyuki Yanagisawa, and Jeffrey A. Medin (2013) “ The Engineered Thymidylate Kinase (TMPK)/AZT Enzyme-Prodrug Axis Offers Efficient Bystander Cell Killing for Suicide Gene Therapy of Cancer" PLoS One, e78711




 

2012

Citation Associated Structures
Katy A. Wong, Angela Russo, Xuerong Wang, Yun-Ju Chen, Arnon Lavie, and John P. O'Bryan (2012) “A New Dimension to Ras Function: A Novel Role for Nucleotide-Free Ras in Class II Phosphatidylinositol 3-Kinase Beta (PI3KC2β) Regulation” PLOS ONE 7, e45360.


Julian Nomme, Ying Su, Manfred Konrad, and Arnon Lavie (2012) “Structures of Apo and Product-Bound Human l-Asparaginase: Insights into the Mechanism of Autoproteolysis and Substrate Hydrolysis” Biochemistry 51, 6816-26.

4GDU
4GDT
4GDV
4GDW

Jens Gruber, Wei Cun See Too, Mun T Wong, Arnon Lavie, Theresa McSorley and Manfred Konrad (2012) “Balance of human choline kinase isoforms is critical for cell cycle regulation: implications for the development of choline kinase-targeted cancer therapy” FEBS Journal 279, 1915-28.  
Anton Neschadim, James CM Wang, Arnon Lavie and Jeffrey A Medin (2012) “Bystander killing of malignant cells via the delivery of engineered thymidine-active deoxycytidine kinase for suicide gene therapy of cancer” Cancer Gene Therapy 19, 320-327.  
Anton Neschadim, James CM Wang, Takeya Sato, Daniel H Fowler, Arnon Lavie and Jeffrey A Medin (2012) “Cell fate control gene therapy based on engineered variants of human deoxycytidine kinase” Molecular Therapy 20, 1002-13.  
Dean O Campbell, Shahriar S Yaghoubi, Ying Su, Jason T. Lee, Martin S Auerbach, Harvey Herschman, Nagichettiar Satyamurthy, Johannes Czernin, Arnon Lavie, and Caius Radu (2012) “Structure-guided engineering of human thymidine kinase 2 as a positron emission tomography reporter gene for enhanced phosphorylation of non-natural thymidine analog reporter probe” Journal of Biological Chemistry 287, 446-54.


 

2011

 


Citation Associated Structures
Saugata Hazra, A Szewczak, Stephan Ort, Manfred Konrad, and Arnon Lavie (2011) “Post-translational phosphorylation of serine 74 of human deoxycytidine kinase favors the enzyme adopting the open conformation making it competent for nucleoside binding and releaseBiochemistry 50, 2870-2880.

3QEJ
3QEN
3QEO

Samuel H Light, George Minasov, Ludmilla Shuvalova, SN Peterson, Michael Caffrey, Wayne F Anderson, and Arnon Lavie (2011) “A conserved surface loop in type I dehydroquinate dehydratases positions an active site arginine and functions in substrate bindingBiochemistry 50, 2357-2363.

3L2I
3QEX
3O1N

Samuel H Light, George Minasov, Ludmilla Shuvalova, Michael Caffrey, Wayne F Anderson, and Arnon Lavie (2011) “Insights into the mechanism of type I dehydroquinate dehydratases from structures of reaction intermediatesJournal of Biological Chemistry 286, 3531-3539.
Julian Nomme, Alan S Fanning, Michael M Caffrey, Ming F. Lye, James M Anderson, and Arnon Lavie (2011) “The Src homology 3 domain is required for junctional adhesion molecule binding to the third PDZ domain of the scaffolding protein ZO-1” ” Journal of Biological Chemistry 286, 43352-60.

 

2010

Citation Associated Structures
Saugata Hazra, Manfred Konrad, and Arnon Lavie (2010) “The sugar ring of the nucleoside is required for productive substrate positioning in the active site of human deoxycytidine kinase (dCK): implications for the development of dCK-activated acyclic guanine analoguesJournal of Medicinal Chemistry 53, 5792-5800.

3MJR

Saugata Hazra, Stephan Ort, Manfred Konrad, and Arnon Lavie (2010) “Structural and kinetic characterization of human deoxycytidine kinase variants able to phosphorylate 5-substituted deoxycytidine and thymidine analoguesBiochemistry 49, 6784-6790.

3KFX

Deirdre A Foley, Kristin G Swartzentruber, Arnon Lavie, and Karen J Colley (2010) “Structure and mutagenesis of neural cell adhesion molecule domains: evidence for flexibility in the placement of polysialic acid attachment sitesJournal of Biological Chemistry 285, 27360-27371.

3MTR

Ming Fong Lye, Alan S. Fanning, Ying Su, James M. Anderson, and Arnon Lavie (2010) “Insights into regulated ligand binding sites from the structure of ZO-1 Src homology 3 – guanylate kinase module Journal of Biological Chemistry 285, 13907-13917.

3LH5

James J Kohler, Seyed H Hosseini, Ioan Cucoranu, Olga Zhelyabovska, Elgin Green, Kristopher Ivey, Allison Abuin, Earl Fields, Amy Hoying, Rodney Russ, Robert Santoianni, C Michael Raper, Qinglin Yang, Arnon Lavie and William Lewis (2010) “Transgenic cardiac-targeted overexpression of human thymidylate kinaseLaboratory Investigation 90, 383-90.  

 

2009

Citation Associated Structures
Saugata Hazra, Elisabetta Sabini, Stephan Ort, Manfred Konrad, and Arnon Lavie (2009) “Extending thymidine kinase activity to the catalytic repertoire of human deoxycytidine kinaseBiochemistry 48, 1256–1263.

3EXK

2008

Citation Associated Structures
Elisabetta Sabini, Saugata Hazra, Stephan Ort, Manfred Konrad, and Arnon Lavie (2008) "Structural basis for substrate promiscuity of dCK" Journal of Molecular Biology 378(3):607-621.

2ZI3
2ZI4
2ZI5
2ZI6

Theresa McSorley, Stephan Ort, Saugata Hazra, Arnon Lavie, and Manfred Konrad (2008) "Mimicking phosphorylation of Ser-74 on human deoxycytidine kinase selectively increases catalytic activity for dC and dC analogues" FEBS Letters 582, 720-724.  
Cristina Gabellieri, Steven Reynolds, Arnon Lavie, Geoffrey S. Payne, Martin O. Leach and Thomas R.Eykyn (2008) “Therapeutic target metabolism observed using hyperpolarized 15N cholineJournal of the American Chemical Society 130, 4598-4599.  
Arnon Lavie, Ying Su, Mahmood Ghassemi, Richard M. Novak, Michael Caffrey, Nikolina Sekulic, Christian Monnerjahn, Manfred Konrad and James L. Cook (2008) “Restoration of the antiviral activity of 3'-azido-3'- deoxythymidine (AZT) against AZT-resistant human immunodeficiency virus by delivery of engineered thymidylate kinase to T cellsJournal of General Virology 89, 1672-9.  
Elisabetta Sabini, Saugata Hazra, Manfred Konrad, and Arnon Lavie (2008) “Elucidation of different binding modes of purine nucleosides to human deoxycytidine kinaseJournal of Medicinal Chemistry 51, 4219-4225.

2ZI7
2ZI9
2ZIA

Michael Sacher, Yeon-Gil Kim, Arnon Lavie, Byung-Ha Oh, and Nava Segev (2008) “The TRAPP complex: insights into its architecture and functionTraffic 9, 2032-2042.  
Ingo Paarmann, Ming F. Lye, Arnon Lavie and Manfred Konrad (2008) “Structural requirements for calmodulin binding to membrane-associated guanylate kinase homologsProtein Science 17, 1946-54.  

2007

Citation Associated Structures
Dario Segura-Pena, Joseph Lichter, Manuela Trani, Manfred Konrad, Arnon Lavie, and Stefan Lutz (2007) "Quaternary structure change as a mechanism for the regulation of thymidine kinase 1-like enzymes" Structure 15, 1555-66.

2QQE
2QPO
2QQ0

Alan S. Fanning, Ming F. Lye, James M. Anderson, and Arnon Lavie (2007) "Domain swapping within PDZ2 is responsible for dimerization of ZO proteins" Journal of Biological Chemistry 282, 37710-16

2RCZ

Nikolina Sekulic, Manfred Konrad, and Arnon Lavie (2007) "Structural mechanism for substrate inhibition of the adenosine 5'-phosphosulfate kinase domain of human 3'-phosphoadenosine 5'-phosphosulfate synthetase 1 and its ramifications for enzyme regulation" Journal of Biological Chemistry 282, 22112-21.

2PEY
2PEZ

Elisabetta Sabini, Saugata Hazra, Manfred Konrad, and Arnon Lavie (2007) "Nonenantioselectivity Property of Human Deoxycytidine Kinase Explained by Structures of the Enzyme in Complex with l- and d-Nucleosides" Journal of Medicinal Chemistry 50, 3004-14.

2NO0
2NO1
2NO6
2NO7

Dario Segura-Pena, Stefan Lutz, Christian Monnerjahn, Manfred Konrad, and Arnon Lavie (2007) "Binding of ATP to TK1-like Enzymes Is Associated with a Conformational Change in the Quaternary Structure" Journal of Molecular Biology 369, 129-141.

2ORW
2ORV

Takeya Sato, Anton Neschadim, Manfred Konrad, Daniel H Fowler, Arnon Lavie and Jeffrey A Medin (2007) "Engineered Human tmpk/AZT As a Novel Enzyme/Prodrug Axis for Suicide Gene Therapy" Molecular Therapy 15, 962-70.  
Nikolina Sekulic, Kristen Dietrich, Ingo Paarmann, Stephan Ort, Manfred Konrad and Arnon Lavie (2007) "Elucidation of the Active Conformation of the APS-Kinase Domain of Human PAPS Synthetase 1" Journal of Molecular Biology 367, 488-500. 

2OFX
2OFW

Elisabetta Sabini, Saugata Hazra, Manfred Konrad, Stephen K. Burley, and Arnon Lavie (2007) "Structural basis for activation of the therapeutic l-nucleoside analogs 3TC and troxacitabine by human deoxycytidine kinase" Nucleic Acids Research  35, 186–192.

2NO9
2NOA

2006

Citation Associated Structures
Enrico Malito, Nikolina Sekulic, Wei Cun See Too, Manfred Konrad and Arnon Lavie (2006) "Elucidation of Human Choline Kinase Crystal Structures in Complex with the Products ADP or Phosphocholine" Journal of Molecular Biology 364, 136-151. 

2CKO
2CKP
2CKQ

Shalu Shiv Mendiratta, Nikolina Sekulic, Francisco G. Hernandez-Guzman, Brett E. Close, Arnon Lavie, and Karen J. Colley (2006) "A Novel {alpha}-Helix in the First Fibronectin Type III Repeat of the Neural Cell Adhesion Molecule Is Critical for N-Glycan Polysialylation" Journal of Biological Chemistry  281,  36052-36059.

2HAZ

Michael H. Godsey, Stephan Ort, Elisabetta Sabini, Manfred Konrad, and Arnon Lavie (2006) "Structural Basis for the Preference of UTP over ATP in Human Deoxycytidine Kinase: Illuminating the Role of Main-Chain Reorganization" Biochemistry 45, 452 - 461.

2A2Z
2A30

2005

Citation Associated Structures
Yuanhe Li, Alan S. Fanning, James M. Anderson, and Arnon Lavie (2005) "Structure of the conserved cytoplasmic C-terminal domain of occludin: identification of the ZO-1 binding surface" Journal of Molecular Biology 352, 151-64. 

1WPA
1XAW

Shalu Shiv Mendiratta, Nikolina Sekulic, Arnon Lavie, and Karen J. Colley (2005) "Specific amino acids in the first fibronectin type III repeat of the neural cell adhesion molecule play a role in its recognition and polysialylation by the polysialyltransferase ST8Sia IV/PST" Journal of Biological Chemistry 280, 32340-8.  

2004

Citation Associated Structures
Yuanhe Li, David Karnak, Borries Demeler, Ben Margolis, and Arnon Lavie (2004) "Structural basis for L27 domain-mediated assembly of signaling and cell polarity complexes" EMBO Journal 23, 2723-33. 

1VF6

Dario Segura-Pena, Nikolina Sekulic, Stephan Ort, Manfred Konrad, and Arnon Lavie (2004) "Substrate-induced conformational changes in human UMP/CMP kinase" Journal of Biological Chemistry 279, 33882-9. 

1TEV

Arnon Lavie and Manfred Konrad (2004) "Structural requirements for efficient phosphorylation of nucleotide analogs by human thymidylate kinase" Mini Reviews in Medicinal Chemistry 4, 351-9.

 

2003

Citation Associated Structures
Anna Gardberg, Ludmilla Shuvalova, Christian Monnerjahn, Manfred Konrad, and Arnon Lavie (2003) "Structural basis for the dual thymidine and thymidylate kinase activity of herpes thymidine kinases" Structure 11, 1265-77.

1P6X
1P72
1P73
1P75
1P7C

Elisabetta Sabini, Stephan Ort, Christian Monnerjahn, Manfred Konrad, and Arnon Lavie (2003) "Structure of human dCK suggests strategies to improve anticancer and antiviral therapy" Nature Structural Biology 10, 513-9.

1P5Z
1P60
1P61
1P62

Nils Ostermann, Dario Segura-Pena, Chris Meier, Thomas Veit, Christian Monnerjahn, Manfred Konrad, and Arnon Lavie (2003) "Structures of human thymidylate kinase in complex with prodrugs: implications for the structure-based design of novel compounds" Biochemistry 42, 2568-77.

1NMX
1NMY
1NMZ
1NN0
1NN1
1NN3
1NN5

2002

Citation Associated Structures
Ingo Paarmann, Oliver Spangenberg, Arnon Lavie, and Manfred Konrad (2002) "Formation of complexes between Ca2+.calmodulin and the synapse-associated protein SAP97 requires the SH3 domain-guanylate kinase domain-connecting HOOK region"  Journal of Biological Chemistry 277, 40832-8.  
Nikolina Sekulic, Ludmilla Shuvalova, Oliver Spangenberg, Manfred Konrad, and Arnon Lavie "Structural characterization of the closed conformation of mouse guanylate kinase" (2002) Journal of Biological Chemistry 277, 30236-43.

1LVG

Yunahe Li, Oliver Spangenberg, Ingo Paarmann, Manfred Konrad, and Arnon Lavie "Structural basis for nucleotide-dependent regulation of membrane-associated guanylate kinase-like domains" (2002) Journal of Biological Chemistry 277, 4159-65.

1KGD

2000

Citation Associated Structures
Nils Ostermann, Arnon Lavie, Sreekanta Padiyar, Ralf Brundiers, Thomas Veit, Jochen Reinstein, Roger S. Goody, Manfred Konrad, and Ilme Schlichting "Potentiating AZT activation: Structures of wild-type and mutant human thymidylate kinase suggest reasons for the mutants' improved kinetics with the HIV prodrug metabolite AZTMP" (2000) Journal of Molecular Biology 304, 43-53.

1E98
1E99
1E9A
1E9B
1E9C
1E9D
1E9E
1E9F

Nils Ostermann, Ilme Schlichting, Ralf Brundiers, Manfred Konrad, Jochen Reinstein, Thomas Veit, Roger S. Goody, and Arnon Lavie "Insights into the phosphoryltransfer mechanism of human thymidylate kinase gained from crystal structures of enzyme complexes along the reaction coordinate" (2000) Structure with Folding Design 8, 629-42.

1E2D
1E2E
1E2F
1E2G
1E2Q

1999

Citation Associated Structures
Ralf Brundiers R, Arnon Lavie, Thomas Veit, Jochen Reinstein, Ilme Schlichting, Niles Ostermann, Roger S. Goody, and Manfred Konrad "Modifying human thymidylate kinase to potentiate azidothymidine activation" (1999) Journal of Biological Chemistry 274, 35289-92.  
Heino Prinz , Arnon Lavie , Axel J. Scheidig, Oliver Spangenberg, and Manfred Konrad"Binding of nucleotides to guanylate kinase, p21(ras), and nucleoside-diphosphate kinase studied by nano-electrospray mass spectrometry" (1999) Journal of Biological Chemistry 274, 35337-42.  

1998

Citation Associated Structures
Arnon Lavie, Nils Ostermann, Ralf Brundiers, Roger S. Goody, Jochen Reinstein, Manfred Konrad, and Ilme Schlichting"Structural basis for efficient phosphorylation of 3'-azidothymidine monophosphate by Escherichia coli thymidylate kinase" (1998) Proceedings of the National Academy of Sciences 95, 14045-14050.

4TMK
5TMP

Arnon Lavie, Manfred Konrad, Ralf Brundiers, Roger S. Goody, Ilme Schlichting, and Jochen Reinstein "Crystal structure of yeast thymidylate kinase complexed with the bisubstrate inhibitor P1-(5'-adenosyl)P5-thymidyl) pentaphosphate (TP5A) at 2.0 Å: Implications for catalysis and AZT activation" (1998) Biochemistry 37, 3677-3686.

3TMK

Arnon Lavie, Jochen Reinstein, Roger S. Goody, Ilme Schlichting, and Manfred Konrad "Improving AZT efficacy" (1998) Nature Medicine 4, 132.  

1997

Citation Associated Structures
Arnon Lavie, Ilme Schlichting, Ingrid R. Vetter, Manfred Konrad, Jochen Reinstein, and Roger S. Goody "The bottleneck in AZT activation" (1997) Nature Medicine 3, 922-924.  
Arnon Lavie, Ingrid R. Vetter, Manfred Konrad, Roger S. Goody, Jochen Reinstein, and Ilme Schlichting "Structure of thymidylate kinase reveals the cause behind the limiting step in AZT activation" (1997) Nature Structural Biology 4, 601-604.

1TMK
2TMK

1995

Citaiton Associated Structures
Karen N. Allen, Arnon Lavie, Gregory A. Petsko, and Dagmar Ringe "Design, synthesis, and characterization of a potent xylose isomerase inhibitor, d-threonohydroxamic acid, and high resolution X-ray crystallographic structure of the enzyme-inhibitor complex" (1995) Biochemistry 34, 3742-3749.

2GYI

 

 

 

 

1994

Citation Associated Structures
Arnon Lavie, Karen N. Allen, Gregory A. Petsko, and Dagmar Ringe "X-ray crystallographic structures of d-xylose isomerase-substrate complexes position the substrate and provide evidence for metal movement during catalysis" (1994) Biochemistry 33, 5469-5480.

1XYA
1XYB
1XYC

Karen N. Allen, Arnon Lavie, Arthur Glasfeld, Timothy N. Tanada, Daniel P. Gerrity, Steven C. Carlson, Gregory K. Farber, Gregory A. Petsko, and Dagmar Ringe "Role of the divalent metal ion in sugar binding, ring opening, and isomerization by d-xylose isomerase: Replacement of a catalytic metal by an amino-acid" (1994) Biochemistry 33, 1488-1494.

1XYL
1XYM

Karen N. Allen, Arnon Lavie, Gregory K. Farber, Arthur Glasfeld, Gregory A. Petsko, and Dagmar Ringe "Isotopic exchange plus substrate and inhibition kinetics of d-xylose isomerase do not support a proton-transfer mechanism" (1994) Biochemistry 33, 1481-1487.