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PDBsum entry 1g3r

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protein ligands metals links
Cell cycle, hydrolase PDB id
1g3r
Jmol
Contents
Protein chain
237 a.a. *
Ligands
ACP
Metals
_MG
Waters ×70
* Residue conservation analysis
PDB id:
1g3r
Name: Cell cycle, hydrolase
Title: Crystal structure analysis of pyrococcus furiosus cell division atpase mind
Structure: Cell division inhibitor. Chain: a. Synonym: mind atpase. Engineered: yes. Other_details: amppcp-bound form
Source: Pyrococcus furiosus. Organism_taxid: 2261. Gene: mind. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Trimer (from PQS)
Resolution:
2.70Å     R-factor:   0.209     R-free:   0.251
Authors: I.Hayashi,T.Oyama,K.Morikawa
Key ref:
I.Hayashi et al. (2001). Structural and functional studies of MinD ATPase: implications for the molecular recognition of the bacterial cell division apparatus. EMBO J, 20, 1819-1828. PubMed id: 11296216 DOI: 10.1093/emboj/20.8.1819
Date:
25-Oct-00     Release date:   21-Apr-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q8U3I1  (Q8U3I1_PYRFU) -  Site-determining protein
Seq:
Struc:
245 a.a.
237 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cell division   1 term 
  Biochemical function     nucleotide binding     2 terms  

 

 
DOI no: 10.1093/emboj/20.8.1819 EMBO J 20:1819-1828 (2001)
PubMed id: 11296216  
 
 
Structural and functional studies of MinD ATPase: implications for the molecular recognition of the bacterial cell division apparatus.
I.Hayashi, T.Oyama, K.Morikawa.
 
  ABSTRACT  
 
Proper placement of the bacterial cell division site requires the site-specific inactivation of other potential division sites. In Escherichia coli, selection of the correct mid-cell site is mediated by the MinC, MinD and MinE proteins. To clarify the functional role of the bacterial cell division inhibitor MinD, which is a membrane-associated ATPase that works as an activator of MinC, we determined the crystal structure of a Pyrococcus furiosus MinD homologue complexed with a substrate analogue, AMPPCP, and with the product ADP at resolutions of 2.7 and 2.0 A, respectively. The structure reveals general similarities to the nitrogenase iron protein, the H-Ras p21 and the RecA-like ATPase domain. Alanine scanning mutational analyses of E.coli MinD were also performed in vivo. The results suggest that the residues around the ATP-binding site are required for the direct interaction with MinC, and that ATP binding and hydrolysis play a role as a molecular switch to control the mechanisms of MinCDE-dependent bacterial cell division.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Nucleotide binding of P.furiosus MinD. (A and B) Scheme showing the interactions between P.furiosus MinD and the nucleotide [AMPPCP (A) and ADP (B)]. Dashed lines indicate hydrogen bonds (<3.5 Ć). Water molecules are indicated by 'w'; van der Waals contacts are indicated by arcs. The differences between AMPPCP- and ADP-bound MinD are highlighted in red. The attacking water molecule is shown in white inside the closed circle. (C) Walker motif sequence conservation in MinD family proteins. Bacterial MinD homologues (Eco, E.coli; Bsu, Bacillus subtilis; Nme, Neisseria meningitidis; Xfa, Xylella fastidiosa; Aae, Aquifex aeolicus), archaeal MinD homologues (Mja, Methanococcus jannaschii; Pfu, P.furiosus) and MinD-related proteins (Avi, Azotobacter vinelandii) were aligned with CLUSTAL_W (Thompson et al., 1994) and edited manually. Key motifs are highlighted in yellow. The Lys11 residue is boxed. Triangles indicate residues involved in the specific binding of phosphate (red), magnesium (yellow) and attacking water (blue).
Figure 4.
Figure 4 Effects of the local conformation around the K11 residue. (A) Stereo diagram of the interface between the Walker A motif region (green) and 7 (red). K11, ADP and the coordinating side chains are shown as ball-and-stick, with ADP and oxygens in red, and nitrogens in blue. (B) Phenotypes of mutations at residues around E.coli K11 (ecK11). Fixed cells were stained with DAPI to observe the nucleoids and photographed. From left to right: BL21(DE3) [minCDE^+] with control pET21a, pEMDwt [P[T7]::minD^+], pEMD11 [P[T7]::minD^ecK11A], pEMD16 [P[T7]::minD^ecK16A], pEMD146 [P[T7]::minD^ecE146A] and pEMD152 [P[T7]::minD^ecD152A]. The amino acids in P.furiosus (pfu) are also indicated in parentheses.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2001, 20, 1819-1828) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21545286 M.Loose, K.Kruse, and P.Schwille (2011).
Protein self-organization: lessons from the min system.
  Annu Rev Biophys, 40, 315-336.  
21231967 W.Wu, K.T.Park, T.Holyoak, and J.Lutkenhaus (2011).
Determination of the structure of the MinD-ATP complex reveals the orientation of MinD on the membrane and the relative location of the binding sites for MinE and MinC.
  Mol Microbiol, 79, 1515-1528.
PDB code: 3q9l
20398219 G.B.Kang, H.E.Song, M.K.Kim, H.S.Youn, J.G.Lee, J.Y.An, J.S.Chun, H.Jeon, and S.H.Eom (2010).
Crystal structure of Helicobacter pylori MinE, a cell division topological specificity factor.
  Mol Microbiol, 76, 1222-1231.
PDB codes: 3ku7 3mcd
20930386 T.Okuno, T.Ohgita, T.Sasa, A.Nonaka, N.Funasaki, and K.Kogure (2010).
Fluorescence polarization analysis for revealing molecular mechanism of nucleotide-dependent phospholipid membrane binding of MinD adenosine 5'-triphosphate, adenosine triphosphatase.
  Biol Pharm Bull, 33, 1746-1750.  
19675567 A.Mateja, A.Szlachcic, M.E.Downing, M.Dobosz, M.Mariappan, R.S.Hegde, and R.J.Keenan (2009).
The structural basis of tail-anchored membrane protein recognition by Get3.
  Nature, 461, 361-366.
PDB codes: 2woj 2woo
19789705 B.P.Downing, A.D.Rutenberg, A.Touhami, and M.Jericho (2009).
Subcellular Min oscillations as a single-cell reporter of the action of polycations, protamine, and gentamicin on Escherichia coli.
  PLoS One, 4, e7285.  
19525115 D.C.Lee, and Z.Jia (2009).
Emerging structural insights into bacterial tyrosine kinases.
  Trends Biochem Sci, 34, 351-357.  
19948960 G.Bozkurt, G.Stjepanovic, F.Vilardi, S.Amlacher, K.Wild, G.Bange, V.Favaloro, K.Rippe, E.Hurt, B.Dobberstein, and I.Sinning (2009).
Structural insights into tail-anchored protein binding and membrane insertion by Get3.
  Proc Natl Acad Sci U S A, 106, 21131-21136.
PDB codes: 3iqw 3iqx
19114487 J.M.Boyd, R.M.Drevland, D.M.Downs, and D.E.Graham (2009).
Archaeal ApbC/Nbp35 homologs function as iron-sulfur cluster carrier proteins.
  J Bacteriol, 191, 1490-1497.  
18497741 D.C.Lee, J.Zheng, Y.M.She, and Z.Jia (2008).
Structure of Escherichia coli tyrosine kinase Etk reveals a novel activation mechanism.
  EMBO J, 27, 1758-1766.
PDB code: 3cio
18430139 I.Barák, K.Muchová, A.J.Wilkinson, P.J.O'Toole, and N.Pavlendová (2008).
Lipid spirals in Bacillus subtilis and their role in cell division.
  Mol Microbiol, 68, 1315-1327.  
18760994 S.Mazor, T.Regev, E.Mileykovskaya, W.Margolin, W.Dowhan, and I.Fishov (2008).
Mutual effects of MinD-membrane interaction: I. Changes in the membrane properties induced by MinD binding.
  Biochim Biophys Acta, 1778, 2496-2504.  
18547145 V.Olivares-Illana, P.Meyer, E.Bechet, V.Gueguen-Chaignon, D.Soulat, S.Lazereg-Riquier, I.Mijakovic, J.Deutscher, A.J.Cozzone, O.Laprévote, S.Morera, C.Grangeasse, and S.Nessler (2008).
Structural basis for the regulation mechanism of the tyrosine kinase CapB from Staphylococcus aureus.
  PLoS Biol, 6, e143.
PDB codes: 2ved 3bfv
17635186 D.Jakimowicz, P.Zydek, A.Kois, J.Zakrzewska-CzerwiƄska, and K.F.Chater (2007).
Alignment of multiple chromosomes along helical ParA scaffolding in sporulating Streptomyces hyphae.
  Mol Microbiol, 65, 625-641.  
17627778 D.Soulat, J.M.Jault, C.Geourjon, P.Gouet, A.J.Cozzone, and C.Grangeasse (2007).
Tyrosine-kinase Wzc from Escherichia coli possesses an ATPase activity regulated by autophosphorylation.
  FEMS Microbiol Lett, 274, 252-259.  
17483175 E.N.Cytrynbaum, and B.D.Marshall (2007).
A multistranded polymer model explains MinDE dynamics in E. coli cell division.
  Biophys J, 93, 1134-1150.  
17326815 I.Barák, and A.J.Wilkinson (2007).
Division site recognition in Escherichia coli and Bacillus subtilis.
  FEMS Microbiol Rev, 31, 311-326.  
17328675 J.Lutkenhaus (2007).
Assembly dynamics of the bacterial MinCDE system and spatial regulation of the Z ring.
  Annu Rev Biochem, 76, 539-562.  
17166176 J.Y.Bouet, Y.Ah-Seng, N.Benmeradi, and D.Lane (2007).
Polymerization of SopA partition ATPase: regulation by DNA binding and SopB.
  Mol Microbiol, 63, 468-481.  
17161598 M.A.Schumacher (2007).
Structural biology of plasmid segregation proteins.
  Curr Opin Struct Biol, 17, 103-109.  
16565080 D.Soulat, J.M.Jault, B.Duclos, C.Geourjon, A.J.Cozzone, and C.Grangeasse (2006).
Staphylococcus aureus operates protein-tyrosine phosphorylation through a specific mechanism.
  J Biol Chem, 281, 14048-14056.  
16415929 F.Hayes, and D.Barillà (2006).
The bacterial segrosome: a dynamic nucleoprotein machine for DNA trafficking and segregation.
  Nat Rev Microbiol, 4, 133-143.  
16959967 Y.L.Shih, and L.Rothfield (2006).
The bacterial cytoskeleton.
  Microbiol Mol Biol Rev, 70, 729-754.  
16014621 C.Aldridge, and S.G.Møller (2005).
The plastid division protein AtMinD1 is a Ca2+-ATPase stimulated by AtMinE1.
  J Biol Chem, 280, 31673-31678.  
15775965 D.Barillà, M.F.Rosenberg, U.Nobbmann, and F.Hayes (2005).
Bacterial DNA segregation dynamics mediated by the polymerizing protein ParF.
  EMBO J, 24, 1453-1464.  
15629934 H.Zhou, R.Schulze, S.Cox, C.Saez, Z.Hu, and J.Lutkenhaus (2005).
Analysis of MinD mutations reveals residues required for MinE stimulation of the MinD ATPase and residues required for MinC interaction.
  J Bacteriol, 187, 629-638.  
15897178 T.A.Leonard, J.Møller-Jensen, and J.Löwe (2005).
Towards understanding the molecular basis of bacterial DNA segregation.
  Philos Trans R Soc Lond B Biol Sci, 360, 523-535.  
15635448 T.A.Leonard, P.J.Butler, and J.Löwe (2005).
Bacterial chromosome segregation: structure and DNA binding of the Soj dimer--a conserved biological switch.
  EMBO J, 24, 270-282.
PDB codes: 1wcv 2bej 2bek
14973039 H.Zhou, and J.Lutkenhaus (2004).
The switch I and II regions of MinD are required for binding and activating MinC.
  J Bacteriol, 186, 1546-1555.  
15060045 J.E.Johnson, L.L.Lackner, C.A.Hale, and P.A.de Boer (2004).
ZipA is required for targeting of DMinC/DicB, but not DMinC/MinD, complexes to septal ring assemblies in Escherichia coli.
  J Bacteriol, 186, 2418-2429.  
15139810 J.Löwe, F.van den Ent, and L.A.Amos (2004).
Molecules of the bacterial cytoskeleton.
  Annu Rev Biophys Biomol Struct, 33, 177-198.  
15489428 J.Szeto, S.Acharya, N.F.Eng, and J.A.Dillon (2004).
The N terminus of MinD contains determinants which affect its dynamic localization and enzymatic activity.
  J Bacteriol, 186, 7175-7185.  
15130131 K.Mazouni, F.Domain, C.Cassier-Chauvat, and F.Chauvat (2004).
Molecular analysis of the key cytokinetic components of cyanobacteria: FtsZ, ZipN and MinCDE.
  Mol Microbiol, 52, 1145-1158.  
15037301 L.A.Amos, F.van den Ent, and J.Löwe (2004).
Structural/functional homology between the bacterial and eukaryotic cytoskeletons.
  Curr Opin Cell Biol, 16, 24-31.  
15458408 L.Ma, G.F.King, and L.Rothfield (2004).
Positioning of the MinE binding site on the MinD surface suggests a plausible mechanism for activation of the Escherichia coli MinD ATPase during division site selection.
  Mol Microbiol, 54, 99.  
15554957 P.J.Lewis (2004).
Bacterial subcellular architecture: recent advances and future prospects.
  Mol Microbiol, 54, 1135-1150.  
15090526 S.Ramirez-Arcos, V.Greco, H.Douglas, D.Tessier, D.Fan, J.Szeto, J.Wang, and J.R.Dillon (2004).
Conserved glycines in the C terminus of MinC proteins are implicated in their functionality as cell division inhibitors.
  J Bacteriol, 186, 2841-2855.  
12970194 A.Roy, N.Solodovnikova, T.Nicholson, W.Antholine, and W.E.Walden (2003).
A novel eukaryotic factor for cytosolic Fe-S cluster assembly.
  EMBO J, 22, 4826-4835.  
12486045 E.Skovran, and D.M.Downs (2003).
Lack of the ApbC or ApbE protein results in a defect in Fe-S cluster metabolism in Salmonella enterica serovar Typhimurium.
  J Bacteriol, 185, 98.  
12970183 I.Mijakovic, S.Poncet, G.Boël, A.Mazé, S.Gillet, E.Jamet, P.Decottignies, C.Grangeasse, P.Doublet, P.Le Maréchal, and J.Deutscher (2003).
Transmembrane modulator-dependent bacterial tyrosine kinase activates UDP-glucose dehydrogenases.
  EMBO J, 22, 4709-4718.  
12626683 J.Errington, R.A.Daniel, and D.J.Scheffers (2003).
Cytokinesis in bacteria.
  Microbiol Mol Biol Rev, 67, 52.  
12675792 J.Lutkenhaus, and M.Sundaramoorthy (2003).
MinD and role of the deviant Walker A motif, dimerization and membrane binding in oscillation.
  Mol Microbiol, 48, 295-303.  
12682065 K.McLuskey, J.A.Harrison, A.W.Schuttelkopf, D.H.Boxer, and W.N.Hunter (2003).
Insight into the role of Escherichia coli MobB in molybdenum cofactor biosynthesis based on the high resolution crystal structure.
  J Biol Chem, 278, 23706-23713.
PDB code: 1np6
12533449 L.L.Lackner, D.M.Raskin, and P.A.de Boer (2003).
ATP-dependent interactions between Escherichia coli Min proteins and the phospholipid membrane in vitro.
  J Bacteriol, 185, 735-749.  
14527275 L.Romberg, and P.A.Levin (2003).
Assembly dynamics of the bacterial cell division protein FTSZ: poised at the edge of stability.
  Annu Rev Microbiol, 57, 125-154.  
12694607 R.Bernander (2003).
The archaeal cell cycle: current issues.
  Mol Microbiol, 48, 599-604.  
12492861 S.Autret, and J.Errington (2003).
A role for division-site-selection protein MinD in regulation of internucleoid jumping of Soj (ParA) protein in Bacillus subtilis.
  Mol Microbiol, 47, 159-169.  
12486056 Z.Hu, C.Saez, and J.Lutkenhaus (2003).
Recruitment of MinC, an inhibitor of Z-ring formation, to the membrane in Escherichia coli: role of MinD and MinE.
  J Bacteriol, 185, 196-203.  
12519187 Z.Hu, and J.Lutkenhaus (2003).
A conserved sequence at the C-terminus of MinD is required for binding to the membrane and targeting MinC to the septum.
  Mol Microbiol, 47, 345-355.  
12003935 J.E.Johnson, L.L.Lackner, and P.A.de Boer (2002).
Targeting of (D)MinC/MinD and (D)MinC/DicB complexes to septal rings in Escherichia coli suggests a multistep mechanism for MinC-mediated destruction of nascent FtsZ rings.
  J Bacteriol, 184, 2951-2962.  
12191487 J.Easter, and J.W.Gober (2002).
ParB-stimulated nucleotide exchange regulates a switch in functionally distinct ParA activities.
  Mol Cell, 10, 427-434.  
12457696 J.Lutkenhaus (2002).
Dynamic proteins in bacteria.
  Curr Opin Microbiol, 5, 548-552.  
12482939 K.Suefuji, R.Valluzzi, and D.RayChaudhuri (2002).
Dynamic assembly of MinD into filament bundles modulated by ATP, phospholipids, and MinE.
  Proc Natl Acad Sci U S A, 99, 16776-16781.  
12209147 P.Chène (2002).
ATPases as drug targets: learning from their structure.
  Nat Rev Drug Discov, 1, 665-673.  
12424340 T.H.Szeto, S.L.Rowland, L.I.Rothfield, and G.F.King (2002).
Membrane localization of MinD is mediated by a C-terminal motif that is conserved across eubacteria, archaea, and chloroplasts.
  Proc Natl Acad Sci U S A, 99, 15693-15698.  
11983867 Z.Hu, E.P.Gogol, and J.Lutkenhaus (2002).
Dynamic assembly of MinD on phospholipid vesicles regulated by ATP and MinE.
  Proc Natl Acad Sci U S A, 99, 6761-6766.  
11532954 E.Fung, J.Y.Bouet, and B.E.Funnell (2001).
Probing the ATP-binding site of P1 ParA: partition and repression have different requirements for ATP binding and hydrolysis.
  EMBO J, 20, 4901-4911.  
11752455 G.Ebersbach, and K.Gerdes (2001).
The double par locus of virulence factor pB171: DNA segregation is correlated with oscillation of ParA.
  Proc Natl Acad Sci U S A, 98, 15078-15083.  
11461697 L.I.Rothfield, Y.L.Shih, and G.King (2001).
Polar explorers: membrane proteins that determine division site placement.
  Cell, 106, 13-16.  
11886553 M.E.Karoui, and J.Errington (2001).
Isolation and characterization of topological specificity mutants of minD in Bacillus subtilis.
  Mol Microbiol, 42, 1211-1221.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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