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PDBsum entry 1ctf
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Ribosomal protein PDB id
1ctf

 

 

 

 

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Contents
Protein chain
68 a.a. *
Ligands
SO4
Waters ×62
* Residue conservation analysis
PDB id:
1ctf
Name: Ribosomal protein
Title: Structure of thE C-terminal domain of the ribosomal protein l7/l12 from escherichia coli at 1.7 angstroms
Structure: Ribosomal protein l7/l12. Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
1.70Å     R-factor:   0.174    
Authors: M.Leijonmarck,A.Liljas
Key ref: M.Leijonmarck and A.Liljas (1987). Structure of the C-terminal domain of the ribosomal protein L7/L12 from Escherichia coli at 1.7 A. J Mol Biol, 195, 555-579. PubMed id: 3309338
Date:
02-Sep-86     Release date:   15-Jan-87    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A7K2  (RL7_ECOLI) -  Large ribosomal subunit protein bL12 from Escherichia coli (strain K12)
Seq:
Struc: 		121 a.a.
68 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
J Mol Biol 195:555-579 (1987)
PubMed id: 3309338  
 
 
Structure of the C-terminal domain of the ribosomal protein L7/L12 from Escherichia coli at 1.7 A.
M.Leijonmarck, A.Liljas.
 
  ABSTRACT  
 
The structure of a C-terminal fragment of the ribosomal protein L7/L12 from Escherichia coli has been refined using crystallographic data to 1.7 A resolution. The R-value is 17.4%. Six residues at the N terminus are too disordered in the structure to be localized. These residues are probably part of a hinge in the complete L7/L12 molecule. The possibility that a 2-fold crystallographic axis is a molecular 2-fold axis is discussed. A patch of invariant residues on the surface of the dimer is probably involved in functional interactions with elongation factors.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20151727 P.Koehl, and M.Delarue (2010).
AQUASOL: An efficient solver for the dipolar Poisson-Boltzmann-Langevin equation.
  J Chem Phys, 132, 064101.  
19727514 E.G.Marklund, D.S.Larsson, D.van der Spoel, A.Patriksson, and C.Caleman (2009).
Structural stability of electrosprayed proteins: temperature and hydration effects.
  Phys Chem Chem Phys, 11, 8069-8078.  
19074194 J.Ederth, C.S.Mandava, S.Dasgupta, and S.Sanyal (2009).
A single-step method for purification of active His-tagged ribosomes from a genetically engineered Escherichia coli.
  Nucleic Acids Res, 37, e15.  
18936095 T.Miyoshi, T.Nomura, and T.Uchiumi (2009).
Engineering and Characterization of the Ribosomal L10{middle dot}L12 Stalk Complex: A STRUCTURAL ELEMENT RESPONSIBLE FOR HIGH TURNOVER OF THE ELONGATION FACTOR G-DEPENDENT GTPase.
  J Biol Chem, 284, 85-92.  
18780355 Z.Cao, Z.Lin, J.Wang, and H.Liu (2009).
Refining the description of peptide backbone conformations improves protein simulations using the GROMOS 53A6 force field.
  J Comput Chem, 30, 645-660.  
18688361 A.Patriksson, and D.van der Spoel (2008).
A temperature predictor for parallel tempering simulations.
  Phys Chem Chem Phys, 10, 2073-2077.  
17296314 E.Shacham, B.Sheehan, and N.Volkmann (2007).
Density-based score for selecting near-native atomic models of unknown structures.
  J Struct Biol, 158, 188-195.  
17600832 J.Maupetit, P.Tuffery, and P.Derreumaux (2007).
A coarse-grained protein force field for folding and structure prediction.
  Proteins, 69, 394-408.  
17148487 R.Fedorov, G.Witte, C.Urbanke, D.J.Manstein, and U.Curth (2006).
3D structure of Thermus aquaticus single-stranded DNA-binding protein gives insight into the functioning of SSB proteins.
  Nucleic Acids Res, 34, 6708-6717.
PDB codes: 2ihe 2ihf
16292341 A.Savelsbergh, D.Mohr, U.Kothe, W.Wintermeyer, and M.V.Rodnina (2005).
Control of phosphate release from elongation factor G by ribosomal protein L7/12.
  EMBO J, 24, 4316-4323.  
16337596 P.P.Datta, M.R.Sharma, L.Qi, J.Frank, and R.K.Agrawal (2005).
Interaction of the G' domain of elongation factor G and the C-terminal domain of ribosomal protein L7/L12 during translocation as revealed by cryo-EM.
  Mol Cell, 20, 723-731.
PDB code: 2bcw
15263071 J.Christodoulou, G.Larsson, P.Fucini, S.R.Connell, T.A.Pertinhez, C.L.Hanson, C.Redfield, K.H.Nierhaus, C.V.Robinson, J.Schleucher, and C.M.Dobson (2004).
Heteronuclear NMR investigations of dynamic regions of intact Escherichia coli ribosomes.
  Proc Natl Acad Sci U S A, 101, 10949-10954.  
15598351 S.Cheek, Y.Qi, S.S.Krishna, L.N.Kinch, and N.V.Grishin (2004).
4SCOPmap: automated assignment of protein structures to evolutionary superfamilies.
  BMC Bioinformatics, 5, 197.  
12945054 H.Fan, and A.E.Mark (2003).
Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: a molecular dynamics simulation study.
  Proteins, 53, 111-120.  
12235156 F.Guo, L.Esser, S.K.Singh, M.R.Maurizi, and D.Xia (2002).
Crystal structure of the heterodimeric complex of the adaptor, ClpS, with the N-domain of the AAA+ chaperone, ClpA.
  J Biol Chem, 277, 46753-46762.
PDB codes: 1mbu 1mbv 1mbx
11792838 M.Glick, A.Rayan, and A.Goldblum (2002).
A stochastic algorithm for global optimization and for best populations: a test case of side chains in proteins.
  Proc Natl Acad Sci U S A, 99, 703-708.  
11997946 G.A.Arteca, C.T.Reimann, and O.Tapia (2001).
Proteins in vacuo: denaturing and folding mechanisms studied with computer-simulated molecular dynamics.
  Mass Spectrom Rev, 20, 402-422.  
10799526 D.I.Svergun, and K.H.Nierhaus (2000).
A map of protein-rRNA distribution in the 70 S Escherichia coli ribosome.
  J Biol Chem, 275, 14432-14439.  
10637222 M.C.Wahl, G.P.Bourenkov, H.D.Bartunik, and R.Huber (2000).
Flexibility, conformational diversity and two dimerization modes in complexes of ribosomal protein L12.
  EMBO J, 19, 174-186.
PDB codes: 1dd3 1dd4
10782993 M.C.Wahl, R.Huber, S.Marinkoviç, E.Weyher-Stingl, and S.Ehlert (2000).
Structural investigations of the highly flexible recombinant ribosomal protein L12 from Thermotoga maritima.
  Biol Chem, 381, 221-229.  
10450094 D.J.Diller, M.R.Redinbo, E.Pohl, and W.G.Hol (1999).
A database method for automated map interpretation in protein crystallography.
  Proteins, 36, 526-541.  
10368288 J.M.Pérez, G.Siegal, J.Kriek, K.Hård, J.Dijk, G.W.Canters, and W.Möller (1999).
The solution structure of the guanine nucleotide exchange domain of human elongation factor 1beta reveals a striking resemblance to that of EF-Ts from Escherichia coli.
  Structure, 7, 217-226.
PDB code: 1b64
10535955 P.Koehl, and M.Levitt (1999).
Structure-based conformational preferences of amino acids.
  Proc Natl Acad Sci U S A, 96, 12524-12529.  
10531479 R.Fedorov, N.Nevskaya, A.Khairullina, S.Tishchenko, A.Mikhailov, M.Garber, and S.Nikonov (1999).
Structure of ribosomal protein L30 from Thermus thermophilus at 1.9 A resolution: conformational flexibility of the molecule.
  Acta Crystallogr D Biol Crystallogr, 55, 1827-1833.
PDB code: 1bxy
9539716 A.V.Oleinikov, G.G.Jokhadze, and R.R.Traut (1998).
A single-headed dimer of Escherichia coli ribosomal protein L7/L12 supports protein synthesis.
  Proc Natl Acad Sci U S A, 95, 4215-4218.  
9430711 D.Dey, D.E.Bochkariov, G.G.Jokhadze, and R.R.Traut (1998).
Cross-linking of selected residues in the N- and C-terminal domains of Escherichia coli protein L7/L12 to other ribosomal proteins and the effect of elongation factor Tu.
  J Biol Chem, 273, 1670-1676.  
9862810 J.Unge, A.berg, S.Al-Kharadaghi, A.Nikulin, S.Nikonov, N.Davydova, N.Nevskaya, M.Garber, and A.Liljas (1998).
The crystal structure of ribosomal protein L22 from Thermus thermophilus: insights into the mechanism of erythromycin resistance.
  Structure, 6, 1577-1586.
PDB code: 1bxe
  9705143 S.V.Nikonov, N.A.Nevskaya, R.V.Fedorov, A.R.Khairullina, S.V.Tishchenko, A.D.Nikulin, and M.B.Garber (1998).
Structural studies of ribosomal proteins.
  Biol Chem, 379, 795-805.  
9644974 V.Ramakrishnan, and S.W.White (1998).
Ribosomal protein structures: insights into the architecture, machinery and evolution of the ribosome.
  Trends Biochem Sci, 23, 208-212.  
9331423 H.Hosaka, A.Nakagawa, I.Tanaka, N.Harada, K.Sano, M.Kimura, M.Yao, and S.Wakatsuki (1997).
Ribosomal protein S7: a new RNA-binding motif with structural similarities to a DNA architectural factor.
  Structure, 5, 1199-1208.
PDB code: 1hus
9094327 J.Frank (1997).
The ribosome at higher resolution--the donut takes shape.
  Curr Opin Struct Biol, 7, 266-272.  
9309225 J.L.Hansen, A.M.Long, and S.C.Schultz (1997).
Structure of the RNA-dependent RNA polymerase of poliovirus.
  Structure, 5, 1109-1122.
PDB code: 1rdr
9236009 J.Zurdo, J.M.Sanz, C.González, M.Rico, and J.P.Ballesta (1997).
The exchangeable yeast ribosomal acidic protein YP2beta shows characteristics of a partly folded state under physiological conditions.
  Biochemistry, 36, 9625-9635.  
8989327 M.A.Markus, A.P.Hinck, S.Huang, D.E.Draper, and D.A.Torchia (1997).
High resolution solution structure of ribosomal protein L11-C76, a helical protein with a flexible loop that becomes structured upon binding to RNA.
  Nat Struct Biol, 4, 70-77.
PDB codes: 1fow 1fox
9016712 M.M.Thunnissen, N.Taddei, G.Liguri, G.Ramponi, and P.Nordlund (1997).
Crystal structure of common type acylphosphatase from bovine testis.
  Structure, 5, 69-79.
PDB code: 2acy
9370344 W.Weglöhner, R.Jünemann, K.von Knoblauch, and A.R.Subramanian (1997).
Different consequences of incorporating chloroplast ribosomal proteins L12 and S18 into the bacterial ribosomes of Escherichia coli.
  Eur J Biochem, 249, 383-392.  
8988003 B.D.Hamman, A.V.Oleinikov, G.G.Jokhadze, R.R.Traut, and D.M.Jameson (1996).
Rotational and conformational dynamics of Escherichia coli ribosomal protein L7/L12.
  Biochemistry, 35, 16672-16679.  
8988004 B.D.Hamman, A.V.Oleinikov, G.G.Jokhadze, R.R.Traut, and D.M.Jameson (1996).
Dimer/monomer equilibrium and domain separations of Escherichia coli ribosomal protein L7/L12.
  Biochemistry, 35, 16680-16686.  
8805594 C.Davies, V.Ramakrishnan, and S.W.White (1996).
Structural evidence for specific S8-RNA and S8-protein interactions within the 30S ribosomal subunit: ribosomal protein S8 from Bacillus stearothermophilus at 1.9 A resolution.
  Structure, 4, 1093-1104.
PDB code: 1sei
8626705 L.Marty, and P.Fort (1996).
A delayed-early response nuclear gene encoding MRPL12, the mitochondrial homologue to the bacterial translational regulator L7/L12 protein.
  J Biol Chem, 271, 11468-11476.  
8962470 R.T.Todorova, V.V.Rogov, K.S.Vasilenko, and E.A.Permyakov (1996).
Study of tyrosine-containing mutants of ribosomal protein L7/L12 from Escherichia coli.
  Biophys Chem, 62, 39-45.  
  8635468 S.Nikonov, N.Nevskaya, I.Eliseikina, N.Fomenkova, A.Nikulin, N.Ossina, M.Garber, B.H.Jonsson, C.Briand, S.Al-Karadaghi, A.Svensson, A.Aevarsson, and A.Liljas (1996).
Crystal structure of the RNA binding ribosomal protein L1 from Thermus thermophilus.
  EMBO J, 15, 1350-1359.  
  8722010 R.R.Traut, D.Dey, D.E.Bochkariov, A.V.Oleinikov, G.G.Jokhadze, B.Hamman, and D.Jameson (1995).
Location and domain structure of Escherichia coli ribosomal protein L7/L12: site specific cysteine crosslinking and attachment of fluorescent probes.
  Biochem Cell Biol, 73, 949-958.  
7704530 D.I.Liao, and O.Herzberg (1994).
Refined structures of the active Ser83-->Cys and impaired Ser46-->Asp histidine-containing phosphocarrier proteins.
  Structure, 2, 1203-1216.
PDB codes: 1sph 2hpr
  7703840 D.V.Laurents, S.Subbiah, and M.Levitt (1994).
Different protein sequences can give rise to highly similar folds through different stabilizing interactions.
  Protein Sci, 3, 1938-1944.  
7518079 E.V.Koonin, P.Bork, and C.Sander (1994).
A novel RNA-binding motif in omnipotent suppressors of translation termination, ribosomal proteins and a ribosome modification enzyme?
  Nucleic Acids Res, 22, 2166-2167.  
  7849580 M.Perutz (1994).
Polar zippers: their role in human disease.
  Protein Sci, 3, 1629-1637.  
  7920265 S.Bromberg, and K.A.Dill (1994).
Side-chain entropy and packing in proteins.
  Protein Sci, 3, 997.  
8234320 A.V.Oleinikov, G.G.Jokhadze, and R.R.Traut (1993).
Escherichia coli ribosomal protein L7/L12 dimers remain fully active after interchain crosslinking of the C-terminal domains in two orientations.
  Proc Natl Acad Sci U S A, 90, 9828-9831.  
8069624 C.A.Orengo, and J.M.Thornton (1993).
Alpha plus beta folds revisited: some favoured motifs.
  Structure, 1, 105-120.  
15335780 C.A.Orengo, T.P.Flores, D.T.Jones, W.R.Taylor, and J.M.Thornton (1993).
Recurring structural motifs in proteins with different functions.
  Curr Biol, 3, 131-139.  
15335744 M.F.Perutz, R.Staden, L.Moens, and I.De Baere (1993).
Polar zippers.
  Curr Biol, 3, 249-253.  
8346036 N.Ohara, M.Kimura, N.Wada, and T.Yamada (1993).
Cloning and sequencing of the gene encoding the ribosomal L7/L12-like protein of Mycobacterium bovis BCG.
  Nucleic Acids Res, 21, 3579.  
1542565 G.A.Elhag, F.J.Thomas, T.P.McCreery, and D.P.Bourque (1992).
Nuclear-encoded chloroplast ribosomal protein L12 of Nicotiana tabacum: characterization of mature protein and isolation and sequence analysis of cDNA clones encoding its cytoplasmic precursor.
  Nucleic Acids Res, 20, 689-697.  
1446741 M.G.Bubunenko, S.V.Chuikov, and A.T.Gudkov (1992).
The length of the interdomain region of the L7/L12 protein is important for its function.
  FEBS Lett, 313, 232-234.  
1826055 D.W.Hoffman, C.C.Query, B.L.Golden, S.W.White, and J.D.Keene (1991).
RNA-binding domain of the A protein component of the U1 small nuclear ribonucleoprotein analyzed by NMR spectroscopy is structurally similar to ribosomal proteins.
  Proc Natl Acad Sci U S A, 88, 2495-2499.  
  1989878 M.Coll, A.Guasch, F.X.Avilés, and R.Huber (1991).
Three-dimensional structure of porcine procarboxypeptidase B: a structural basis of its inactivity.
  EMBO J, 10, 1-9.
PDB code: 1nsa
2163490 A.Ghetti, M.Bolognesi, F.Cobianchi, and C.Morandi (1990).
Modelling by homology of RNA binding domain.
  Mol Biol Rep, 14, 87-88.  
2166604 M.Nilges, G.M.Clore, and A.M.Gronenborn (1990).
1H-NMR stereospecific assignments by conformational data-base searches.
  Biopolymers, 29, 813-822.  
2515294 L.C.Shimmin, C.Ramirez, A.T.Matheson, and P.P.Dennis (1989).
Sequence alignment and evolutionary comparison of the L10 equivalent and L12 equivalent ribosomal proteins from archaebacteria, eubacteria, and eucaryotes.
  J Mol Evol, 29, 448-462.  
2660100 P.A.Rice, and T.A.Steitz (1989).
Ribosomal protein L7/L12 has a helix-turn-helix motif similar to that found in DNA-binding regulatory proteins.
  Nucleic Acids Res, 17, 3757-3762.  
3197716 J.A.Ferro, and F.C.Reinach (1988).
The complete sequence of a chicken-muscle cDNA encoding the acidic ribosomal protein P1.
  Eur J Biochem, 177, 513-516.  
3047743 M.Leijonmarck, K.Appelt, J.Badger, A.Liljas, K.S.Wilson, and S.W.White (1988).
Structural comparison of the prokaryotic ribosomal proteins L7/L12 and L30.
  Proteins, 3, 243-251.  
  3323886 B.E.Rich, and J.A.Steitz (1987).
Human acidic ribosomal phosphoproteins P0, P1, and P2: analysis of cDNA clones, in vitro synthesis, and assembly.
  Mol Cell Biol, 7, 4065-4074.  
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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