Xinhua  Ji, Ph.D.
Xinhua Ji, Ph.D.
Senior Investigator
Head, Biomolecular Structure Section

Center for Cancer Research
National Cancer Institute

Building 538, Room 103
Frederick, MD 21702-1201
301-846-5035

Dr. Ji pioneered the structural analysis of double-stranded RNA (dsRNA) in complex with RNase III enzymes. Over the past decade, he has provided the structural view of dsRNA processing by bacterial RNase III. Recently, his structure of a eukaryotic RNase III has revealed a picking motif in structured RNA and a double-ruler mechanism for substrate selection.

As Head, Dr. Ji directs the Section’s basic and translational research program that is focused on the structural biology of RNA biogenesis, especially post-transcriptional RNA processing, and structure-based development of anticancer and antimicrobial agents.

Areas of Expertise
1) X-ray crystallography, 2) structural biology, 3) chemical biology, 4) structure-based drug design, 5) RNA biogenesis, 6) RNase III enzymes

Biomolecular Structure and Mechanism, Structure-Based Drug Design

Our research is focused on the structural biology of RNA biogenesis, with an emphasis on RNA-processing proteins and RNA polymerase-associated transcription factors, and structure-based development of therapeutic agents. The goal for structural analysis is to map the reaction trajectory or functional cycle of selected biological macromolecules, and that for drug development is to design, synthesize, and characterize novel anticancer and antimicrobial agents. See Research Gallery and Drug Discovery Patents for the scope and depth of our science. Examples of  biomolecular systems under investigation are described below.

RNase III (ribonuclease III) enzymes, exemplified by bacterial RNase III and eukaryotic Rnt1p, Drosha, and Dicer, play important  roles in RNA processing and maturation, post-transcriptional gene silencing, and defense against viral infection. For mechanistic  studies, the bacterial enzyme is a valuable model system for the  entire family. We have shown how the dimerization of the  endonuclease domain of RNase III creates a catalytic valley where  two cleavage sites are located, how the catalytic valley accommodates a dsRNA in a manner such that each of the two RNA strands is aligned with one of the two cleavage sites, how the  hydrolysis of each strand involves both subunits, and how RNase  III uses the two cleavage sites to create the 2-nucleotide 3' overhangs in its products (View). We have also shown how magnesium is essential for the formation of a catalytically  competent protein-RNA complex, how the use of two magnesium ions can drive the hydrolysis of each phosphodiester bond, and how  conformational changes in both the substrate and the protein are critical elements for assembling the catalytic complex. Moreover,  we have provided a stepwise mechanism for the enzyme to execute  the phosphoryl transfer reaction (View). As informative as the bacterial enzyme for the mechanism of RNase III action, yeast  Rnt1p is a valuable model system for eukaryotic RNase III enzymes. Unlike bacterial enzyme that uses four catalytic side  chains, eukaryotic RNase III uses six. Also distinguished from the bacterial enzyme, every eukaryotic RNase III has an N-terminal extension. What is more, Rnt1p exhibits a strict guanine nucleotide specificity, which is unique among RNase III enzymes. We have shown how the substrate-binding mode of Rnt1p is  distinct from that of bacterial RNase III (View), how all of the six  catalytic side chains are engaged in the cleavage site (View), how a new RNA-binding  motif of Rnt1p functions as a guanine-specific clamp (View), and how the double-stranded RNA-binding domain and N-terminal domain of Rnt1p  function as two rulers measuring the distance between the guanine  nucleotide to the cleavage sites (View). This unusual mechanism of substrate selectivity represents an example of the evolution  of substrate selectivity and provides a framework for understanding the mechanism of action of other eukaryotic RNase  III enzymes, including Drosha, and Dicer.

HPPK (6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase) catalyzes magnesium-dependent pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP). The reaction follows a bi-bi mechanism with ATP as the first substrate and AMP and HP pyrophosphate (HPPP) as the two product molecules. HPPK is a key enzyme in the folate biosynthetic pathway. It is essential for microorganisms but absent from mammals. Unlike dihydropteroate  synthase (another key enzyme in the folate pathway), which is the target of sulfonamides (the first widely used synthetic antibiotics), HPPK is not the target for any existing antibiotics. Therefore, HPPK is an attractive target for developing novel antimicrobial agents. We have constructed a reaction coordinate on the basis of thermodynamic and transient kinetic data and mapped out the reaction trajectory by determining five crystal structures of the enzyme at various liganded states (View). On the basis of structural and mechanistic information, we have been attempting the development of HPPK inhibitors as novel antimicrobial agents (View).

Scientific Focus Areas:
Cancer Biology, Chemical Biology, Microbiology and Infectious Diseases, Molecular Biology and Biochemistry, Structural Biology
  1. Liang Y, Lavoie M, Comeau M, Abou Elela S, Ji X.
    Mol. Cell. 54: 431-444, 2014. [ Journal Article ]
  2. Stagno JR, Ma B, Li J, Altieri AS, Byrd RA, Ji X.
    Nat Commun. 3: 901, 2012. [ Journal Article ]
  3. Tu C, Zhou X, Tarasov SG, Tropea JE, Austin BP, Waugh DS, Court DL, Ji X.
    Proc. Natl. Acad. Sci. USA. 108: 10156-10161, 2011. [ Journal Article ]
  4. Shaw G, Gan J, Zhou YN, Zhi H, Subburaman P, Zhang R, Joachimiak A, Jin DJ, Ji X.
    Structure. 16: 1417-1427, 2008. [ Journal Article ]
  5. Gan J, Tropea JE, Austin BP, Court DL, Waugh DS, Ji X.
    Cell. 124: 355-66, 2006. [ Journal Article ]

Dr. Ji earned his Ph.D. degree at the University of Oklahoma (1985-1990) and performed his postdoctoral research at the University of Maryland (1991-1994), where he became a Research Assistant Professor (1994-1995) before joining the National Cancer Institute (NCI), National Institutes of Health (NIH). At the NCI at Frederick, Dr. Ji established his laboratory in the ABL-Basic Research Program in 1995, moved to the Center for Cancer Research in 1999, gained tenure in 2001 as an NIH Senior Investigator, and in 2008 became a member of the Senior Biomedical Research Service (SBRS). The SBRS, established under the Public Health Service Act, was created for scientists who are considered by their peers to be outstanding in their work.

Name Position
Lan Jin Ph.D. Research Fellow
Xing Jing Ph.D. Postdoctoral Fellow (Visiting)
Smita Kakar Ph.D. Postdoctoral Fellow (Visiting)
Vandana Kumari Ph.D. Postdoctoral Fellow (Visiting)
Gary Shaw Ph.D. Research Biologist
Genbin Shi, Ph.D. Staff Scientist
He Song Ph.D. Postdoctoral Fellow (Visiting)
Chao Wang M.Eng. Special Volunteer

Click the thumbnail to see the full size image.

Dr. ji Image

Figure 1. Superposition of apo- and holo-CRABPII structures. The crystal structure of CRABPII (cellular retinoic acid-binding protein II, in green) in complex with RA (retinoic acid, in red) (PDB: 1CBS) is superimposed with the apo-CRABPII structure (in orange, PDB: 1XCA). The view is along the long axis of RA into the ligand-binding cavity of CRABPII (Chen X, et al. J. Mol. Biol. 278:641-653, 1998). 

 

 

Dr Ji figure 2Figure 2. Models of three GST isozymes with bound Meisenheimer complex of compound 1, 2, or 4 (PABA/NO). The active sites of GST (glutathione S-transferase) are illustrated as non-transparent surfaces, except that the transparent surfaces in panels c and g show the unfavorable interaction between the ligand and the protein (indicated with red arrows), and the ligands as stick models in atomic color scheme: C in green, N in blue, O in red, and S in orange (Ji X, et al. Drug. Des. Devel. Ther. 2:123-130, 2008).

 

Dr. Ji image

Figure 3. Critical interactions between the SARS coronavirus (SCV) envelope (spike, S) glycoprotein and a neutralizing antibody m396. The crystal structure of the receptor-binding domain (RBD) of the SCV S glycoprotein in complex with m396 was determined at 2.3-Å resolution (PDB: 2DD8). The SCV is illustrated as a red loop, and the heavy and light chains of m396 are shown as molecular surfaces in orange and cyan, respectively. Side chains are displayed as stick models in atomic color scheme: C in... read more

 

Dr. Ji imageFigure 4. Allosteric regulation of E2-E3 interactions promote a processive ubiquitination machine. Comparative analysis of the crystal structures of the E2 enzyme Ube2g2 (PDB: 2CYX), Ube2g2 in complex with the G2BR domain of E3 molecule gp78 (PDB: 3H8K), and Ube2g2 in complex with both the G2BR and RING domains of gp78 (PDB: 4LAD) reveal the allosteric regulation between Ube2g2-gp78 interactions (Das R, et al. EMBO J. 32:2504-2516, 2013).

 

 

Dr. Ji imageFigure 5. Van der Waals surface representation of apo-HPPK. The crystal structure of HPPK (6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase) was determined at 1.5-Å resolution (PDB: 1HKA). Blue and red colors indicate positive and negative electrostatic potentials, respectively (Xiao B, et al. Structure 7:486-496, 1999).

 

 

 

Dr. Ji imageFigure 6. Van der Waals surface representation of the HPPKoHPoMgADP complex. The crystal structure of HPPK (6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase) in complex with HP (6-hydroxymethyl-7,8-dihydropterin) and MgADP was determined at 1.5-Å resolution (PDB: 1EQM). Blue and red colors indicate positive and negative electrostatic potentials, respectively. The ADP molecule is illustrated as a stick model with the atomic color scheme (C, white; N, blue; O, red; and P, yellow) employed... read more.

 

Dr. Ji imageFigure 7. Van der Waals surface representation of the HPPKoHPoMgAMPCPP complex. The crystal structure of HPPK (6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase) in complex with HP (6-hydroxymethyl-7,8-dihydropterin) and MgAMPCPP (an non-hydrolysable analogue of MgATP) was determined at 1.25-Å resolution (PDB: 1Q0N). Blue and red colors indicate positive and negative electrostatic potentials, respectively. The AMPCPP molecule is illustrated as a stick model with the atomic... read more.

 

Dr. Ji imageFigure 8. Reaction trajectory of HPPK-catalyzed pyrophosphoryl transfer. Five distinct states are proposed along the reaction coordinate, including apo-HPPK, HPPK:MgATP, HPPKoMgATPoHP, HPPKoMgAMPoHPPP, and HPPKoHPPP. For each catalytic state, a snapshot is provided with a crystal structure, including apo-HPPK (1.50 Å, PDB: 1HKA), HPPKoMgADP (1.50 Å, PDB: 1EQM), HPPKoMgAMPCPPoHP (1.25 Å, PDB: 1Q0N), HPPKoAMPoHPPP (1.56 Å, PDB: 1RAO), and HPPKoHPPP... read more.

 

Dr. Ji figure 9Figure 9. Schematic illustration of apo-ERA. The crystal structure of apo-ERA (Escherichia coli Ras-like protein) was determined at 2.4-Å resolution (PDB: 1EGA). Helices are illustrated as green spirals, strands as red arrows and loops as orange pipes. The C-terminal domain is shown above the N-terminal domain. (Xin Chen et al. Proc. Natl. Acad. Sci. USA 96:8396-8410, 1999).

 

 

Figure 10. Schematic illustration of ERA complexes. On the left, the crystal structure of ERA (Escherichia coli Ras-like protein) in complex with MgGNP (a non-hydrolysable analogue of MgGTP) and RNA was determined at 1.9-Å resolution (PDB: 3IEV); on the right, the crystal structure of ERA in complex with GDP was determined at 2.8-Å resolution (PDB: 3IEU). Helices are illustrated as cylinders, strands as arrows, loops as pipes, and the Mg ion as a sphere. The C-terminal domain, in orange and red, is shown above... read more.

 

Dr. Ji figure 11

Figure 11. Functional cycle of ERA. As an essential GTPase, ERA couples cell growth with cell division in bacteria. The functional cycle of ERA is established by four crystal structures: apo-ERA (PDB: 1EGA), the ERA-GNP complex (PDB: 1WF3), the ERA-GNP-RNA complex (PDB: 3IEV), and the ERA-GDP complex (PDB: 3IEU) (Chao Tu, Xiaomei Zhou et al. Proc. Natl. Acad. Sci. USA 106:14843-14848, 2009).

 

 

Dr. Ji figure 12

Schematic illustration of the functional cycle of ERA and its role in ribosome biogenesis. The GTPase domain is represented by a grey rectangle, the KH domain by an orange oval, GTP and GDP by purple cartoons, and the conformations of ERA by numbers in red. The pre-30S particle and 30S r-subunit are represented by larger grey ovals. The pre-16S rRNA and 16S rNRA are represented by a grey line with embedded AUCACCUCC sequence. The unoccupied ERA-binding pocket in the pre-30S particle and... read more.

 

Summary

Dr. Ji pioneered the structural analysis of double-stranded RNA (dsRNA) in complex with RNase III enzymes. Over the past decade, he has provided the structural view of dsRNA processing by bacterial RNase III. Recently, his structure of a eukaryotic RNase III has revealed a picking motif in structured RNA and a double-ruler mechanism for substrate selection.

As Head, Dr. Ji directs the Section’s basic and translational research program that is focused on the structural biology of RNA biogenesis, especially post-transcriptional RNA processing, and structure-based development of anticancer and antimicrobial agents.

Areas of Expertise
1) X-ray crystallography, 2) structural biology, 3) chemical biology, 4) structure-based drug design, 5) RNA biogenesis, 6) RNase III enzymes

Research

Biomolecular Structure and Mechanism, Structure-Based Drug Design

Our research is focused on the structural biology of RNA biogenesis, with an emphasis on RNA-processing proteins and RNA polymerase-associated transcription factors, and structure-based development of therapeutic agents. The goal for structural analysis is to map the reaction trajectory or functional cycle of selected biological macromolecules, and that for drug development is to design, synthesize, and characterize novel anticancer and antimicrobial agents. See Research Gallery and Drug Discovery Patents for the scope and depth of our science. Examples of  biomolecular systems under investigation are described below.

RNase III (ribonuclease III) enzymes, exemplified by bacterial RNase III and eukaryotic Rnt1p, Drosha, and Dicer, play important  roles in RNA processing and maturation, post-transcriptional gene silencing, and defense against viral infection. For mechanistic  studies, the bacterial enzyme is a valuable model system for the  entire family. We have shown how the dimerization of the  endonuclease domain of RNase III creates a catalytic valley where  two cleavage sites are located, how the catalytic valley accommodates a dsRNA in a manner such that each of the two RNA strands is aligned with one of the two cleavage sites, how the  hydrolysis of each strand involves both subunits, and how RNase  III uses the two cleavage sites to create the 2-nucleotide 3' overhangs in its products (View). We have also shown how magnesium is essential for the formation of a catalytically  competent protein-RNA complex, how the use of two magnesium ions can drive the hydrolysis of each phosphodiester bond, and how  conformational changes in both the substrate and the protein are critical elements for assembling the catalytic complex. Moreover,  we have provided a stepwise mechanism for the enzyme to execute  the phosphoryl transfer reaction (View). As informative as the bacterial enzyme for the mechanism of RNase III action, yeast  Rnt1p is a valuable model system for eukaryotic RNase III enzymes. Unlike bacterial enzyme that uses four catalytic side  chains, eukaryotic RNase III uses six. Also distinguished from the bacterial enzyme, every eukaryotic RNase III has an N-terminal extension. What is more, Rnt1p exhibits a strict guanine nucleotide specificity, which is unique among RNase III enzymes. We have shown how the substrate-binding mode of Rnt1p is  distinct from that of bacterial RNase III (View), how all of the six  catalytic side chains are engaged in the cleavage site (View), how a new RNA-binding  motif of Rnt1p functions as a guanine-specific clamp (View), and how the double-stranded RNA-binding domain and N-terminal domain of Rnt1p  function as two rulers measuring the distance between the guanine  nucleotide to the cleavage sites (View). This unusual mechanism of substrate selectivity represents an example of the evolution  of substrate selectivity and provides a framework for understanding the mechanism of action of other eukaryotic RNase  III enzymes, including Drosha, and Dicer.

HPPK (6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase) catalyzes magnesium-dependent pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP). The reaction follows a bi-bi mechanism with ATP as the first substrate and AMP and HP pyrophosphate (HPPP) as the two product molecules. HPPK is a key enzyme in the folate biosynthetic pathway. It is essential for microorganisms but absent from mammals. Unlike dihydropteroate  synthase (another key enzyme in the folate pathway), which is the target of sulfonamides (the first widely used synthetic antibiotics), HPPK is not the target for any existing antibiotics. Therefore, HPPK is an attractive target for developing novel antimicrobial agents. We have constructed a reaction coordinate on the basis of thermodynamic and transient kinetic data and mapped out the reaction trajectory by determining five crystal structures of the enzyme at various liganded states (View). On the basis of structural and mechanistic information, we have been attempting the development of HPPK inhibitors as novel antimicrobial agents (View).

Scientific Focus Areas:
Cancer Biology, Chemical Biology, Microbiology and Infectious Diseases, Molecular Biology and Biochemistry, Structural Biology

Publications

  1. Liang Y, Lavoie M, Comeau M, Abou Elela S, Ji X.
    Mol. Cell. 54: 431-444, 2014. [ Journal Article ]
  2. Stagno JR, Ma B, Li J, Altieri AS, Byrd RA, Ji X.
    Nat Commun. 3: 901, 2012. [ Journal Article ]
  3. Tu C, Zhou X, Tarasov SG, Tropea JE, Austin BP, Waugh DS, Court DL, Ji X.
    Proc. Natl. Acad. Sci. USA. 108: 10156-10161, 2011. [ Journal Article ]
  4. Shaw G, Gan J, Zhou YN, Zhi H, Subburaman P, Zhang R, Joachimiak A, Jin DJ, Ji X.
    Structure. 16: 1417-1427, 2008. [ Journal Article ]
  5. Gan J, Tropea JE, Austin BP, Court DL, Waugh DS, Ji X.
    Cell. 124: 355-66, 2006. [ Journal Article ]

Biography

Dr. Ji earned his Ph.D. degree at the University of Oklahoma (1985-1990) and performed his postdoctoral research at the University of Maryland (1991-1994), where he became a Research Assistant Professor (1994-1995) before joining the National Cancer Institute (NCI), National Institutes of Health (NIH). At the NCI at Frederick, Dr. Ji established his laboratory in the ABL-Basic Research Program in 1995, moved to the Center for Cancer Research in 1999, gained tenure in 2001 as an NIH Senior Investigator, and in 2008 became a member of the Senior Biomedical Research Service (SBRS). The SBRS, established under the Public Health Service Act, was created for scientists who are considered by their peers to be outstanding in their work.

Team

Name Position
Lan Jin Ph.D. Research Fellow
Xing Jing Ph.D. Postdoctoral Fellow (Visiting)
Smita Kakar Ph.D. Postdoctoral Fellow (Visiting)
Vandana Kumari Ph.D. Postdoctoral Fellow (Visiting)
Gary Shaw Ph.D. Research Biologist
Genbin Shi, Ph.D. Staff Scientist
He Song Ph.D. Postdoctoral Fellow (Visiting)
Chao Wang M.Eng. Special Volunteer

Science Gallery

Click the thumbnail to see the full size image.

Dr. ji Image

Figure 1. Superposition of apo- and holo-CRABPII structures. The crystal structure of CRABPII (cellular retinoic acid-binding protein II, in green) in complex with RA (retinoic acid, in red) (PDB: 1CBS) is superimposed with the apo-CRABPII structure (in orange, PDB: 1XCA). The view is along the long axis of RA into the ligand-binding cavity of CRABPII (Chen X, et al. J. Mol. Biol. 278:641-653, 1998). 

 

 

Dr Ji figure 2Figure 2. Models of three GST isozymes with bound Meisenheimer complex of compound 1, 2, or 4 (PABA/NO). The active sites of GST (glutathione S-transferase) are illustrated as non-transparent surfaces, except that the transparent surfaces in panels c and g show the unfavorable interaction between the ligand and the protein (indicated with red arrows), and the ligands as stick models in atomic color scheme: C in green, N in blue, O in red, and S in orange (Ji X, et al. Drug. Des. Devel. Ther. 2:123-130, 2008).

 

Dr. Ji image

Figure 3. Critical interactions between the SARS coronavirus (SCV) envelope (spike, S) glycoprotein and a neutralizing antibody m396. The crystal structure of the receptor-binding domain (RBD) of the SCV S glycoprotein in complex with m396 was determined at 2.3-Å resolution (PDB: 2DD8). The SCV is illustrated as a red loop, and the heavy and light chains of m396 are shown as molecular surfaces in orange and cyan, respectively. Side chains are displayed as stick models in atomic color scheme: C in... read more

 

Dr. Ji imageFigure 4. Allosteric regulation of E2-E3 interactions promote a processive ubiquitination machine. Comparative analysis of the crystal structures of the E2 enzyme Ube2g2 (PDB: 2CYX), Ube2g2 in complex with the G2BR domain of E3 molecule gp78 (PDB: 3H8K), and Ube2g2 in complex with both the G2BR and RING domains of gp78 (PDB: 4LAD) reveal the allosteric regulation between Ube2g2-gp78 interactions (Das R, et al. EMBO J. 32:2504-2516, 2013).

 

 

Dr. Ji imageFigure 5. Van der Waals surface representation of apo-HPPK. The crystal structure of HPPK (6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase) was determined at 1.5-Å resolution (PDB: 1HKA). Blue and red colors indicate positive and negative electrostatic potentials, respectively (Xiao B, et al. Structure 7:486-496, 1999).

 

 

 

Dr. Ji imageFigure 6. Van der Waals surface representation of the HPPKoHPoMgADP complex. The crystal structure of HPPK (6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase) in complex with HP (6-hydroxymethyl-7,8-dihydropterin) and MgADP was determined at 1.5-Å resolution (PDB: 1EQM). Blue and red colors indicate positive and negative electrostatic potentials, respectively. The ADP molecule is illustrated as a stick model with the atomic color scheme (C, white; N, blue; O, red; and P, yellow) employed... read more.

 

Dr. Ji imageFigure 7. Van der Waals surface representation of the HPPKoHPoMgAMPCPP complex. The crystal structure of HPPK (6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase) in complex with HP (6-hydroxymethyl-7,8-dihydropterin) and MgAMPCPP (an non-hydrolysable analogue of MgATP) was determined at 1.25-Å resolution (PDB: 1Q0N). Blue and red colors indicate positive and negative electrostatic potentials, respectively. The AMPCPP molecule is illustrated as a stick model with the atomic... read more.

 

Dr. Ji imageFigure 8. Reaction trajectory of HPPK-catalyzed pyrophosphoryl transfer. Five distinct states are proposed along the reaction coordinate, including apo-HPPK, HPPK:MgATP, HPPKoMgATPoHP, HPPKoMgAMPoHPPP, and HPPKoHPPP. For each catalytic state, a snapshot is provided with a crystal structure, including apo-HPPK (1.50 Å, PDB: 1HKA), HPPKoMgADP (1.50 Å, PDB: 1EQM), HPPKoMgAMPCPPoHP (1.25 Å, PDB: 1Q0N), HPPKoAMPoHPPP (1.56 Å, PDB: 1RAO), and HPPKoHPPP... read more.

 

Dr. Ji figure 9Figure 9. Schematic illustration of apo-ERA. The crystal structure of apo-ERA (Escherichia coli Ras-like protein) was determined at 2.4-Å resolution (PDB: 1EGA). Helices are illustrated as green spirals, strands as red arrows and loops as orange pipes. The C-terminal domain is shown above the N-terminal domain. (Xin Chen et al. Proc. Natl. Acad. Sci. USA 96:8396-8410, 1999).

 

 

Figure 10. Schematic illustration of ERA complexes. On the left, the crystal structure of ERA (Escherichia coli Ras-like protein) in complex with MgGNP (a non-hydrolysable analogue of MgGTP) and RNA was determined at 1.9-Å resolution (PDB: 3IEV); on the right, the crystal structure of ERA in complex with GDP was determined at 2.8-Å resolution (PDB: 3IEU). Helices are illustrated as cylinders, strands as arrows, loops as pipes, and the Mg ion as a sphere. The C-terminal domain, in orange and red, is shown above... read more.

 

Dr. Ji figure 11

Figure 11. Functional cycle of ERA. As an essential GTPase, ERA couples cell growth with cell division in bacteria. The functional cycle of ERA is established by four crystal structures: apo-ERA (PDB: 1EGA), the ERA-GNP complex (PDB: 1WF3), the ERA-GNP-RNA complex (PDB: 3IEV), and the ERA-GDP complex (PDB: 3IEU) (Chao Tu, Xiaomei Zhou et al. Proc. Natl. Acad. Sci. USA 106:14843-14848, 2009).

 

 

Dr. Ji figure 12

Schematic illustration of the functional cycle of ERA and its role in ribosome biogenesis. The GTPase domain is represented by a grey rectangle, the KH domain by an orange oval, GTP and GDP by purple cartoons, and the conformations of ERA by numbers in red. The pre-30S particle and 30S r-subunit are represented by larger grey ovals. The pre-16S rRNA and 16S rNRA are represented by a grey line with embedded AUCACCUCC sequence. The unoccupied ERA-binding pocket in the pre-30S particle and... read more.