Structures and Coordinates
Atomic Coordinates Page
LINKS TO COORDINATES OF STRUCTURES DETERMINED IN THE STODDARD LAB MAY BE ACCESSED AT THE PDB DATABASE FROM HERE.
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| Homing endonucleases & Maturases | Pyruvate Kinase | Time-resolved structures |
| Nucleotide synthesis and salvage | Blood Coagulation Factors | Nucleotide Kinases and Hydrolases |
| Engineering |
Other Structures |
I. Intron-encoded endonuclease coordinates
1. I- CreI homing endonuclease, apo-enzyme
Heath, P. J., Stephens, K., Monnat, R. and Stoddard, B. L. (1997) "Structure of the I-CreI intron-encoded endonuclease: a novel fold that binds and cleaves a long DNA target sequence" Nature Structural Biology 4 (6) 468-476.
RCSB ID Code = 1af5 2. Crystal Structure of I-CreI endonuclease/homing site complex (3 angstrom resolution from 1998)
Jurica, M. S., Monnat, R. J. Jr. and Stoddard, B. L. (1998) "DNA recognition and cleavage by the LAGLIDADG homing endonuclease I-CreI" Molecular Cell 2:469 - 476.Notes: Coordinates contain two copies of I-CreI dimer, each bound to a 24 bp DNA duplex representing the wild type homing site. In this structure, density for a third metal ion on the enzyme dyad axis was present, but was not modeled as a metal due to low resolution. In the subsequent high-resolution analysis including anomalous Fourier mapping (4, 20 and 21 below from Chevalier et al. and 20/21 below ), this site was unambiguously identified as corresponding to a bound divalent cation in the product complex with manganese, and a mixture of sodium and water in the substrate complex in the presence of calcium.
RCSB ID Code = 1BP7.
3. Crystal Structure of I-CreI endonuclease /homing site complex (uncleaved with calcium; 1.8 angstrom resolution from 2001)
Chevalier, B. S., Monnat, R. J. Jr. and Stoddard, B. L. "The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites" Nature Structural Biology 8 4: 312 - 316.Notes: Coordinates contain one copy of I-CreI dimer, bound to a 24 bp DNA duplex representing the wild type homing site determined at 1.8 angstrom resolution with calcium. This structure and a related cleaved magnesium complex (next entry) provide the best current view of the structural mechanism of catalysis for this enzyme.
RCSB ID code 1g9y.
Chevalier, B. S., Monnat, R. J. Jr. and Stoddard, B. L. "The homing endon uclease I-CreI uses three metals, one of which is shared between the two active sites" Nature Structural Biology 8 4: 312 - 316.
Notes: Coordinates contain one copy of I-CreI dimer, bound to a 24 bp DNA duplex representing the wild type homing site.
RCSB ID code = 1g9z
5. I- PpoI homing endonuclease (palindromic DNA homing site substrate complex)
Flick, K.E., Jurica, M. S., Monnat, R. J. Jr., and Stoddard, B. L. (1998) "DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI"Nature 394: 96 - 101.Notes: Coordinates available here are for a single I-PpoI dimer, bound to a palindromic, 21 bp variant of the wild type DNA homing site. The substrate complex was trapped by thiol substitution of the 3' leaving group hydroxyl oxygen.
Protein Databank ID Code = 1a74
6. I-PpoI homing endonuclease (palindromic DNA homing site product complex)
Flick, K.E., Jurica, M. S., Monnat, R. J. Jr., and Stoddard, B. L. (1998) "DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI"Nature 394: 96 - 101.Note: Coordinates available here are for an I-PpoI dimer, bound to a palindromic, 21 bp variant of the wild type DNA homing site. This structure is of the cleaved complex, crystallized in the presence of magnesium.
RCSB ID Code = 1a73
7. I-PpoI homing endonuclease (palindromic DNA homing site product complex)
Flick, K.E., Jurica, M. S., Monnat, R. J. Jr., and Stoddard, B. L. (1998) "DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI"Nature 394: 96 - 101.Notes: Coordinates available here are for an I-PpoI dimer, bound to a palindromic, 21 bp variant of the wild type DNA homing site. This structure is also of the cleaved complex, determined in the presence of magnesium. The protein contains bound two bound cadmium ions per protein subunit ions in place of Zn2+, as described in Protein Science 6: 2677 - 2680 (1997).
RCSB ID Code = 1ipp
8. I-PpoI homing endonuclease H98A mutant (palindromic DNA homing site substrate complex)
Galburt, E.A., Chevalier, B., Tang, W., Jurica, M.S., Flick, K.E., Monnat, R. J. Jr., and Stoddard, B. L. (1999) "A novel endonuclease mechanism directly visualized for I- Ppo I" Nature Structural Biology 6(12):1096 - 1099.Notes: This structure is of the uncleaved complex of a catalytically inactivated point mutant, determined in the presence of magnesium.
RCSB ID Code = 1cqy
9. I-PpoI homing endonuclease sodium substituted (palindromic DNA homing site substrate complex)
Galburt, E.A., Chevalier, B., Tang, W., Jurica, M.S., Flick, K.E., Monnat, R. J. Jr., and Stoddard, B. L. (1999) "A novel endonuclease mechanism directly visualized for I- Ppo I" Nature Structural Biology 6(12):1096 - 1099.Notes: This structure is of the wild-type uncleaved complex, determined in the absence of magnesium (sodium substituted).
10. I-PpoI homing endonuclease L116A mutant DNA complex
Galburt, E.A., Chadsey, M.S., Jurica, M.S., Chevalier, B., Erho, D., Tang, W., Monnat, R.J. Jr., and Stoddard, B. L. (2000) "Conformational Changes and Cleavage by the Homing Endonuclease I-Pp oI: A Critical Role for a Leucine Residue in the Active Site." Journal of Molecular Biology 300(4):877 - 887.RCSB ID Code = 1EVW
11. I-PpoI homing endonuclease (APO structure)
Galburt, E.A., Chadsey, M.S., Jurica, M.S., Chevalier, B., Erho, D., Tang, W., Monnat, R.J. Jr., and Stoddard, B. L. (2000) "Conformational Changes and Cleavage by the Homing Endonuclease I-PpoI: A Critical Role for a Leucine Residue in the Active Site." Journal of Molecular Biology 300(4):877 - 887.RCSB ID Code = 1EVX
12. Hybrid, engineered 'H-DreI' structure bound to DNA
Chevalier, B., Kortemme, T., Chadsey, M., Baker, D., Monnat, R. J. Jr. and Stoddard, B. L. (2002) " Design, activity and structure of a highly specific artificial endonuclease " Molecular Cell 10 : 895 - 905.
Notes: The contents of the asymmetric unit for this structure were four complexes, two of which were well ordered and two of which were very poorly ordered and were modeled as polyalanine backbones.
RCSB ID Code = 1MOW13. I-MsoI (an isoschizomer of I-CreI) bound to DNA
Chevalier, B., Turmel, M., Lemieux, C., Monnat, R. J. Jr. and Stoddard, B. L. (2003) "Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI" J. Mol. Biol. 329: 253 - 269.
RCSB ID Code = 1M5X
14. I-CreI bound to a palindrome consisting of left half-site of wild type DNA target
Chevalier, B., Turmel, M., Lemieux, C., Monnat, R. J. Jr. and Stoddard, B. L. (2003) "Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI" J. Mol. Biol. 329: 253 - 269.
RCSB ID Code = 1N3E
15. I-CreI bound to a palindrome consisting of right half-site of wild type DNA target
Chevalier, B., Turmel, M., Lemieux, C., Monnat, R. J. Jr. and Stoddard, B. L. (2003) "Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI" J. Mol. Biol. 329: 253 - 269.
RCSB ID Code = 1N3F
16. Bifunctional homing endonuclease/maturase I-AniI bound to its asymmetric DNA target
Bolduc, J. M., Spiegel, P. C., Chatterjee, P., Brady, K. L., Downing, M. EW., Caprara, M. G., Waring, R. B. and Stoddard, B. L. (2003) "Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor" Genes and Development 17: 2875-2888.
17. HNH homing endonuclease I-HmuI bound to its DNA target
Shen, B. W., Landthaler, M., Shub, D. A. and Stoddard, B. L. (2004) "DNA binding and cleavage by the HNH homing endonuclease I-HmuI" J. Mol. Biol. 342 (1): 34 - 56.
RCSB ID Code = 1U3E
18. Selected I-CreI variant Y33C bound to its alternate DNA target
Sussman, D., Chadsey, M., Fauce, S., Engel, A., Bruett, A., Monnat, R. J. Jr., Stoddard, B. L. and Seligman, L. (2004) "Isolation and characterization of new homing endonuclease specificities at individual target site positions" J. Mol. Biol. 342 (1): 31 - 41.
RCSB ID Code = 1UOC
19. Selected I-CreI variant Y33H bound to its alternate DNA target
Sussman, D., Chadsey, M., Fauce, S., Engel, A., Bruett, A., Monnat, R. J. Jr., Stoddard, B. L. and Seligman, L. (2004) "Isolation and characterization of new homing endonuclease specificities at individual target site positions" J. Mol. Biol. 342 (1): 31 - 41.
RCSB ID Code = 1UOD
20. I-CreI Q47E point mutant bound to wild-type DNA target
Chevalier, B., Sussman, D., Otis, C., Noel, A. -J., Turmel, M., Lemieux, C., Stephens, K., Monnat, R. J. Jr. and Stoddard, B. L. (2004) "Analysis of the symmetric metal-dependent I-CreI homing endonuclease mechanism" Biochemistry 43: 14015 - 14026.
RCSB ID Code = 1T9J
21. I-CreI D20N point mutant bound to wild-type DNA target
Chevalier, B., Sussman, D., Otis, C., Noel, A. -J., Turmel, M., Lemieux, C., Stephens, K., Monnat, R. J. Jr. and Stoddard, B. L. (2004) "Analysis of the symmetric metal-dependent I-CreI homing endonuclease mechanism" Biochemistry 43: 14015 - 14026.
RCSB ID Code = 1T9I
II. Structures of kinase and hydrolase enzymes
1. T4 PNK tetramer with bound ADP in kinase phosphoryl donor site.Galburt, E., Pelletier, J., Wilson G., and Stoddard, B. L. (2002) "Structure of a tRNA repair enzyme and molecular biology workhorse, T4 polynucleotide kinase" Structure 10 (9): 1249 - 1260.
RCSB ID Code = 1LTQ
2. Human NUDT9 ADPR hydrolase apo enzyme
Shen, B. W., Perraud, A. -L., Scharenberg, A. M and Stoddard, B. L. (2003) "The crystal structure and mutational analysis of human NUDT9" J. Mol. Biol. 332(2):385-98.
RCSB ID Code = 1Q33
3. Human NUDT9 ADPR hydrolase with bound ribose-5-phosphate product
Shen, B. W., Perraud, A. -L., Scharenberg, A. M and Stoddard, B. L. (2003) "The crystal structure and mutational analysis of human NUDT9" J. Mol. Biol. 332(2):385-98.
RCSB ID Code = 1QVJ
4. T4 PNK with bound single stranded DNA substrates:
1: 5' GT (CAC) 3' RCSB ID Code = 1RC8
2. 5' GTC 3' RCSB ID Code = 1RRC
3. 5' TG (CAC) 3' RCSB ID Code = 1RPZ
Eastberg, J., Pelletier, J., and Stoddard, B. L. (2004) "Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase" Nucleic Acids Research 32 (2): 653 - 660.
III. Allosteric regulation of pyruvate kinase
1. Yeast Pyruvate Kinase inhibitor complex, no FBP
Jurica, M. S., Heath, P. J., Shi, W., Mesecar, A., and Stoddard, B. L. (1998) "The allosteric regulation of pyruvate kinase by fructose-1,6-bis-phosphate" Structure 6 (2) 195 - 210.RCSB ID Code = 1A3X
2. Yeast Pyruvate Kinase inhibitor complex, with bound FBP
Jurica, M. S., Heath, P. J., Shi, W., Mesecar, A., and Stoddard, B. L. (1998) "The allosteric regulation of pyruvate kinase by fructose-1,6-bis-phosphate" Structure 6 (2) 195 - 210.RCSB ID Code = 1A3W
IV. Time-resolved crystallographic studies of enzyme intermediates
1. IDH Y160F mutant: ES complex (steady-state trapping; Laue Data)
Bolduc, J., Dyer, D., Lee, M., Scott, W. G., Singer, P., Sweet, R. M., Koshland, D. E. Jr. and Stoddard, B. L. (1995) "Mutagenesis and laue structures of enzyme intermediates: isocitrate dehydrogenase" Science 268: 1312 - 1318.2. IDH K230M mutant: oxalosuccinate complex (steady-state trapping; Laue Data)
Bolduc, J., Dyer, D., Lee, M., Scott, W. G., Singer, P., Sweet, R. M., Koshland, D. E. Jr. and Stoddard, B. L. (1995) "Mutagenesis and laue structures of enzyme intermediates: isocitrate dehydrogenase" Science 268: 1312 - 1318.RCSB ID Code = 1IDC
3. WT IDH: NHDP/isocitrate/Mg2+ steady state complex (cryotrapping)
Mesecar, A., Stoddard, B. L. and Koshland, D. E. Jr. (1997) "Orbital steering in the catalytic power of enzymes: small structural changes with large catalytic consequences" Science 277: 202 - 206.RCSB ID Code = 1AI3
4. WT IDH: NADP/isocitrate/Ca2+ steady state complex (cryotrapping)
Mesecar, A., Stoddard, B. L. and Koshland, D. E. Jr. (1997) "Orbital steering in the catalytic power of enzymes: small structural changes with large catalytic consequences" Science 277: 202 - 206.RCSB ID Code = 1AI2
5. WT IDH: NADPH/2-ketoglutarate/Mg2+ (flash-photolysis; single-turnover; Laue data)
Stoddard, B. L., Cohen, B., Brubaker, M., Mesecar, A. D. and Koshland, D. E. Jr. (1998) "Millisecond Laue structures of an enzyme product complex using photocaged substrate analogues" Nature Structural Biology 5 (10) 891 - 897.RCSB ID code = 1BL5
V. Structures of enzymes involved in nucleotide synthesis and salvage pathways
1. Crystal Structure of bacterial 5,10-methylene THF dehdyrogenase/cyclohydrolase
Shen, B. W., Dyer, D. H., Huang, J. -Y., D'Ari, L., Rabinowitz, J., and Stoddard, B. L. "The crystal structure of a bacterial bifunctional 5,10-methylene tetrahydrofolate cyclohydrolase/dehydrogenase" Protein Science 8(6): 1342 - 1349.RCSB ID code = 1B0A
Shen, B. W., Dyer, D. H., Huang, J. -Y., D'Ari, L., Rabinowitz, J., and Stoddard, B. L. "The crystal structure of a bacterial bifunctional 5,10-methylene tetrahydrofolate cyclohydrolase/dehydrogenase" Protein Science 8(6): 1342 - 1349.
Note: This model is not experimentally verified, and therefore is not submitted to the PDB and is strictly intended to induce further experimentation. Please contact the manuscript authors with any questions.
3. Crystal structure of E. coli cytosine deaminase apo enzyme
Ireton, G., McDermitt, G., Black, M. and Stoddard, B. L. (2002) "The crystal structure of E. coli cytosine deaminase at 1.5 angstrom resolution" J. Mol. Biol. 315(4): 687 - 697.RCSB ID Code = 1K6W
4. Crystal structure of E. coli cytosine deaminase complexed with the inhibitor 2-hydroxypyrimidine
Ireton, G., McDermitt, G., Black, M. and Stoddard, B. L. (2002) "The crystal structure of E. coli cytosine deaminase at 1.5 angstrom resolution" J. Mol. Biol. 315 (4): 687 - 697.RCSB ID Code = 1K70
5. Crystal structure of yeast cytosine deaminase apo enzyme
Ireton, G., McDermitt, G., Black, M. and Stoddard, B. L. (2003) "The 1.14 angstrom crystal structure of yeast cytosine deaminase: evolution of nucleotide salvage enzymes and implications for genetic chemotherapy" Structure 11: 961 - 972.RCSB ID Code = 1OX7
6. Crystal structure of yeast cytosine deaminase complexed with the inhibitor 2-hydroxypyrimidine
Ireton, G., McDermitt, G., Black, M. and Stoddard, B. L. (2003) "The 1.14 angstrom crystal structure of yeast cytosine deaminase: evolution of nucleotide salvage enzymes and implications for genetic chemotherapy" Structure 11: 961 - 972.RCSB ID Code = 1P6O
7. Crystal structure of yeast cytosine deaminase in alternate, sodium-dependent space group
RCSB ID Code = 1RB7
8. Bacterial cytosine deaminase mutants with altered preference for 5-fluorocytosine vs. cytosine
Mahan, S. D., Ireton, G. C., Stoddard, B. L. and Black, M. E. (2004) "Alanine-Scanning Mutagenesis Reveals a Cytosine Deaminase Mutant with Altered Substrate Preference" Biochemistry 43: 8957 - 8964.
Mahan, S. D., Ireton, G. C., Stoddard, B. L. and Black, M. E. (2004) “Directed evolution and selection of bacterial cytosine deaminase with altered substrate specificity towards 5-fluorocytosine” submitted.
1: D314A apo enzyme RCSB ID Code = 1R9Y
2. D34A complex with 5F-HDP RCSB ID Code = 1RA5
3. D314S apo enzyme RCSB ID Code = 1R9Z
4: D314S complex with 5F-HDP RCSB ID Code = 1RAK
5. D314G apo enzyme RCSB ID Code = 1R9X
6. D314G complex with 5F-HDP RCSB ID Code = 1RA0
VI. Blood coagulation protein factors
1. Crystal structure of human factor VIII C2 domain at 1.5 angstrom resolution
Pratt, K. P., Shen, B. W.,Takeshima, K., Kavie, E. W., Fujikawa, K. and Stoddard, B. L. (1999) "Structure of the C2 domain of human factor VIII at 1.5 angstrom resolution" Nature 402: 439 - 442.RCSB ID Code = 1D7P
2. Homology model of human factor VIII C1 domain.
Liu, M., Shen, B. W., Nakaya, S., Pratt, K. P., Fujikawa, K., Davie, E. W. and Stoddard, B . L. (1999) "Hemophilic factor VIII C1- and C2-domain missense mutations and their modeling to the 1.5 angstrom human C2-domain crystal structure" Blood 96(3): 979 - 987.Note: This model is not experimentally verified, and therefore is not submitted to the PDB and is strictly intended to induce further experimentation. Please contact the manuscript authors with any questions.
3. Human factor VIII C2 domain complexed with BO2C11 Antibody Inhibitor Fab fragment from hemophilia A patient
Spiegel, P. C., Jacquemin, M., Saint-Remy, J. -M. R.,Stoddard, B. L., and Pratt, K. P. (2001) "Structure of a factor VIII C2 domain-immunoglobulin G4K Fab complex: identification of an inhibitory antibody epitope on the surface of factor VIII" Blood 98(1): 13 - 19.RCSB ID code = 1IQD
VII. Protein Engineering
1. Hybrid, engineered 'E-DreI' structure bound to DNA
Chevalier, B., Kortemme, T., Chadsey, M., Baker, D., Monnat, R. J. Jr. and Stoddard, B. L. (2002) " Design, activity and structure of a highly specific artificial endonuclease " Molecular Cell 10 : 895 - 905.
Notes: The contents of the asymmetric unit for this structure were four complexes, two of which were well ordered and two of which were very poorly ordered and were modeled as polyalanine backbones.
RCSB ID Code = 1MOW2. Structure of a novel designed protein (TOP7) with a globular alpha/beta fold
Kuhlman, B., Dantas, G., Ireton, G. C., Varani, G., Stoddard, B. L. and Baker, D. (2003) "Design of a novel globular protein fold with atomic accuracy" Science 302:1364 - 1368.
3. Crystal Structure Of The E7_C/Im7_C Complex; A Computationally Designed Interface Between The Colicin E7 Dnase and The Im7 Immunity Protein
Kortemme, T., Joachimiak, L. A., Bullock, A. N., Stoddard, B. L. and Baker, D. (2004) "Computational redesign of protein-protein interaction specificity" Nature Structural and Molecular Biology 11: 371 - 379.
VIII. Other structures
1. Structure of secreted phospholipase A2 (sPLA2) complexed with 1,3-dioxane-1,4-dione-5-carboxamide based inhibitorBryant, M. D., Flick, K. E., Koduri, R. S., Wilton, D. C., Stoddard, B. L., and Gelb, M. H. (1999) "1,3-dioxane-4,6-dione-5-carboxamide-based inhibitors of human group IIA phospholipase A2: X-ray structure of the complex and interfacial selection of inhibitors from a structural library" Bioorg. & Med. Chem. Letters 9 1097 - 1102.
2. Structure of Ps. ovalis (Ps. putida) iron superoxide dismutase (Fe-SOD) apo enzyme
Bond, C. J., Huang, J. -Y., Hajduk, R., Heath, P. J., Flick, K. E., and Stoddard, B. L. (2000) "Cloning, sequence and crystallographic structure of recombinant iron superoxide dismutase from Pseudomonas ovalis" Acta Cryst D56 1359 - 1366.
RCSB ID Code = 1DT0
Note: This completely re-determined structure of iron SOD from Ps. ovalis supercedes PDB entry 3SDP (deposited in 1991), which suffered from a variety of significant pathologies, including an incorrect amino acid sequence, twinned data, a lack of experience in proper refinement methodologies, all compounded by the lack of easily available validation checks (such as the free R-factor, WHATIF, PROCHECK, etc.) in the late 1980s that are now routinely used during model building and refinement. For details on the corrections to the original structure determination provided through this analysis, please see the corresponding manuscript.
