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PDBsum entry 2lcd
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Transcription PDB id
2lcd

 

 

 

 

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Contents
Protein chain
118 a.a.
Superseded by: 2mam
PDB id:
2lcd
Name: Transcription
Title: Solution structure of rbbp1 tudor domain
Structure: At-rich interactive domain-containing protein 4a. Chain: a. Fragment: unp residues 4-121. Synonym: arid domain-containing protein 4a, retinoblastoma-binding protein 1, rbbp-1. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: arid4a, rbbp1, rbp1. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 20 models
Authors: W.Gong,Y.Feng
Key ref:
M.W.Bowler et al. (2006). How azide inhibits ATP hydrolysis by the F-ATPases. Proc Natl Acad Sci U S A, 103, 8646-8649. PubMed id: 16728506 DOI: 10.1073/pnas.0602915103
Date:
28-Apr-11     Release date:   16-May-12    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P29374  (ARI4A_HUMAN) -  AT-rich interactive domain-containing protein 4A from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1257 a.a.
118 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1073/pnas.0602915103 Proc Natl Acad Sci U S A 103:8646-8649 (2006)
PubMed id: 16728506  
 
 
How azide inhibits ATP hydrolysis by the F-ATPases.
M.W.Bowler, M.G.Montgomery, A.G.Leslie, J.E.Walker.
 
  ABSTRACT  
 
In the structure of bovine F1-ATPase determined at 1.95-A resolution with crystals grown in the presence of ADP, 5'-adenylyl-imidodiphosphate, and azide, the azide anion interacts with the beta-phosphate of ADP and with residues in the ADP-binding catalytic subunit, betaDP. It occupies a position between the catalytically essential amino acids, beta-Lys-162 in the P loop and the "arginine finger" residue, alpha-Arg-373, similar to the site occupied by the gamma-phosphate in the ATP-binding subunit, betaTP. Its presence in the betaDP-subunit tightens the binding of the side chains to the nucleotide, enhancing its affinity and thereby stabilizing the state with bound ADP. This mechanism of inhibition appears to be common to many other ATPases, including ABC transporters, SecA, and DNA topoisomerase IIalpha. It also explains the stimulatory effect of azide on ATP-sensitive potassium channels by enhancing the binding of ADP.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. The [DP] catalytic site in the structure of bovine F[1]-ATPase inhibited with azide. The view is in stereo. Catalytically important residues are shown with the difference electron density (F[o] – F[c]) for azide (green mesh, contoured at 3 ) before its inclusion in the model. 		Figure 2.
Fig. 2. The interactions of azide with catalytic side chains in bovine F[1]-ATPase. The two negatively charged outer nitrogen atoms of azide are hydrogen-bonded to -Lys-162 and -Arg-373, and the inner positively charged nitrogen atom forms an ionic interaction with the oxygen atom of the -phosphate of ADP. The tight interaction between azide and the side chains prevents the conversion of the subunit to the open conformation and the release of ADP.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21602818 G.Cingolani, and T.M.Duncan (2011).
Structure of the ATP synthase catalytic complex (F(1)) from Escherichia coli in an autoinhibited conformation.
  Nat Struct Mol Biol, 18, 701-707.  
21481781 K.Okazaki, and S.Takada (2011).
Structural Comparison of F(1)-ATPase: Interplay among Enzyme Structures, Catalysis, and Rotations.
  Structure, 19, 588-598.  
21118484 A.Fagerlund, T.Lindbäck, and P.E.Granum (2010).
Bacillus cereus cytotoxins Hbl, Nhe and CytK are secreted via the Sec translocation pathway.
  BMC Microbiol, 10, 304.  
20693684 M.W.Bowler, M.Guijarro, S.Petitdemange, I.Baker, O.Svensson, M.Burghammer, C.Mueller-Dieckmann, E.J.Gordon, D.Flot, S.M.McSweeney, and G.A.Leonard (2010).
Diffraction cartography: applying microbeams to macromolecular crystallography sample evaluation and data collection.
  Acta Crystallogr D Biol Crystallogr, 66, 855-864.  
20304971 R.Blum, K.C.Meyer, J.Wünschmann, K.J.Lendzian, and E.Grill (2010).
Cytosolic action of phytochelatin synthase.
  Plant Physiol, 153, 159-169.  
20871600 R.Watanabe, R.Iino, and H.Noji (2010).
Phosphate release in F1-ATPase catalytic cycle follows ADP release.
  Nat Chem Biol, 6, 814-820.  
20096592 W.Chen, Y.J.Huang, S.R.Gundala, H.Yang, M.Li, P.C.Tai, and B.Wang (2010).
The first low microM SecA inhibitors.
  Bioorg Med Chem, 18, 1617-1625.  
19363114 B.A.Bensing, and P.M.Sullam (2009).
Characterization of Streptococcus gordonii SecA2 as a paralogue of SecA.
  J Bacteriol, 191, 3482-3491.  
19489730 C.von Ballmoos, A.Wiedenmann, and P.Dimroth (2009).
Essentials for ATP synthesis by F1F0 ATP synthases.
  Annu Rev Biochem, 78, 649-672.  
19966409 J.Sanchez-Weatherby, M.W.Bowler, J.Huet, A.Gobbo, F.Felisaz, B.Lavault, R.Moya, J.Kadlec, R.B.Ravelli, and F.Cipriani (2009).
Improving diffraction by humidity control: a novel device compatible with X-ray beamlines.
  Acta Crystallogr D Biol Crystallogr, 65, 1237-1246.
PDB codes: 2w6e 2w6f 2w6g 2w6h 2w6i 2w6j
19477165 L.S.Chen, B.J.Nowak, M.L.Ayres, N.L.Krett, S.T.Rosen, S.Zhang, and V.Gandhi (2009).
Inhibition of ATP synthase by chlorinated adenosine analogue.
  Biochem Pharmacol, 78, 583-591.  
19423706 M.Vollmar, D.Schlieper, M.Winn, C.Büchner, and G.Groth (2009).
Structure of the c14 rotor ring of the proton translocating chloroplast ATP synthase.
  J Biol Chem, 284, 18228-18235.
PDB code: 2w5j
19240022 W.Li, L.E.Brudecki, A.E.Senior, and Z.Ahmad (2009).
Role of {alpha}-subunit VISIT-DG sequence residues Ser-347 and Gly-351 in the catalytic sites of Escherichia coli ATP synthase.
  J Biol Chem, 284, 10747-10754.  
19280602 W.Zheng (2009).
Normal-mode-based modeling of allosteric couplings that underlie cyclic conformational transition in F(1) ATPase.
  Proteins, 76, 747-762.  
19075235 D.Okuno, R.Fujisawa, R.Iino, Y.Hirono-Hara, H.Imamura, and H.Noji (2008).
Correlation between the conformational states of F1-ATPase as determined from its crystal structure and single-molecule rotation.
  Proc Natl Acad Sci U S A, 105, 20722-20727.  
18723591 H.Sielaff, H.Rennekamp, S.Engelbrecht, and W.Junge (2008).
Functional halt positions of rotary FOF1-ATPase correlated with crystal structures.
  Biophys J, 95, 4979-4987.  
18579516 H.Z.Mao, C.G.Abraham, A.M.Krishnakumar, and J.Weber (2008).
A functionally important hydrogen-bonding network at the betaDP/alphaDP interface of ATP synthase.
  J Biol Chem, 283, 24781-24788.  
18216260 J.Pu, and M.Karplus (2008).
How subunit coupling produces the gamma-subunit rotary motion in F1-ATPase.
  Proc Natl Acad Sci U S A, 105, 1192-1197.  
18631376 K.Yura, and M.Go (2008).
Correlation between amino acid residues converted by RNA editing and functional residues in protein three-dimensional structures in plant organelles.
  BMC Plant Biol, 8, 79.  
19052322 S.Hong, and P.L.Pedersen (2008).
ATP synthase and the actions of inhibitors utilized to study its roles in human health, disease, and other scientific areas.
  Microbiol Mol Biol Rev, 72, 590.  
18326647 T.Hornung, O.A.Volkov, T.M.Zaida, S.Delannoy, J.G.Wise, and P.D.Vogel (2008).
Structure of the cytosolic part of the subunit b-dimer of Escherichia coli F0F1-ATP synthase.
  Biophys J, 94, 5053-5064.  
19011636 T.Masaike, F.Koyama-Horibe, K.Oiwa, M.Yoshida, and T.Nishizaka (2008).
Cooperative three-step motions in catalytic subunits of F(1)-ATPase correlate with 80 degrees and 40 degrees substep rotations.
  Nat Struct Mol Biol, 15, 1326-1333.  
17904517 B.A.Feniouk, A.Rebecchi, D.Giovannini, S.Anefors, A.Y.Mulkidjanian, W.Junge, P.Turina, and B.A.Melandri (2007).
Met23Lys mutation in subunit gamma of F(O)F(1)-ATP synthase from Rhodobacter capsulatus impairs the activation of ATP hydrolysis by protonmotive force.
  Biochim Biophys Acta, 1767, 1319-1330.  
18003896 H.Z.Mao, and J.Weber (2007).
Identification of the betaTP site in the x-ray structure of F1-ATPase as the high-affinity catalytic site.
  Proc Natl Acad Sci U S A, 104, 18478-18483.  
17698806 J.R.Gledhill, M.G.Montgomery, A.G.Leslie, and J.E.Walker (2007).
Mechanism of inhibition of bovine F1-ATPase by resveratrol and related polyphenols.
  Proc Natl Acad Sci U S A, 104, 13632-13637.
PDB codes: 2jiz 2jj1 2jj2
17895376 J.R.Gledhill, M.G.Montgomery, A.G.Leslie, and J.E.Walker (2007).
How the regulatory protein, IF(1), inhibits F(1)-ATPase from bovine mitochondria.
  Proc Natl Acad Sci U S A, 104, 15671-15676.
PDB code: 2v7q
18058004 J.York, D.Spetzler, T.Hornung, R.Ishmukhametov, J.Martin, and W.D.Frasch (2007).
Abundance of Escherichia coli F(1)-ATPase molecules observed to rotate via single-molecule microscopy with gold nanorod probes.
  J Bioenerg Biomembr, 39, 435-439.  
17721548 T.Ariga, E.Muneyuki, and M.Yoshida (2007).
F1-ATPase rotates by an asymmetric, sequential mechanism using all three catalytic subunits.
  Nat Struct Mol Biol, 14, 841-846.  
16929099 M.W.Bowler, M.G.Montgomery, A.G.Leslie, and J.E.Walker (2006).
Reproducible improvements in order and diffraction limit of crystals of bovine mitochondrial F(1)-ATPase by controlled dehydration.
  Acta Crystallogr D Biol Crystallogr, 62, 991-995.  
17082766 V.Kabaleeswaran, N.Puri, J.E.Walker, A.G.Leslie, and D.M.Mueller (2006).
Novel features of the rotary catalytic mechanism revealed in the structure of yeast F1 ATPase.
  EMBO J, 25, 5433-5442.
PDB code: 2hld
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 codes are shown on the right.

 

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