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PDBsum entry 1hq1
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protein dna_rna metals links
Signaling protein/RNA PDB id
1hq1

 

 

 

 

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Contents
Protein chain
76 a.a. *
DNA/RNA
Metals
__K ×3
_MG ×4
Waters ×287
* Residue conservation analysis
PDB id:
1hq1
Name: Signaling protein/RNA
Title: Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle
Structure: 4.5s RNA domain iv. Chain: b. Fragment: residues 32-74. Engineered: yes. Signal recognition particle protein. Chain: a. Fragment: c terminal domain (residues 328-432). Synonym: fifty-four homolog, ffh-m domain, p48. Engineered: yes
Source: Synthetic: yes. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.52Å     R-factor:   0.156     R-free:   0.199
Authors: R.T.Batey,M.B.Sagar,J.A.Doudna
Key ref:
R.T.Batey et al. (2001). Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle. J Mol Biol, 307, 229-246. PubMed id: 11243816 DOI: 10.1006/jmbi.2000.4454
Date:
13-Dec-00     Release date:   03-Jan-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
P0AGD7  (SRP54_ECOLI) -  Signal recognition particle protein from Escherichia coli (strain K12)
Seq:
Struc: 		453 a.a.
76 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chain
  G-G-C-U-C-U-G-U-U-U-A-C-C-A-G-G-U-C-A-G-G-U-C-C-G-A-A-A-G-G-A-A-G-C-A-G-C-C-A- 49 bases

 Enzyme reactions 
   Enzyme class: E.C.3.6.5.4  - signal-recognition-particle GTPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: GTP + H2O = GDP + phosphate + H+
GTP
 + H2O
 = GDP
 + phosphate
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.2000.4454 J Mol Biol 307:229-246 (2001)
PubMed id: 11243816  
 
 
Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle.
R.T.Batey, M.B.Sagar, J.A.Doudna.
 
  ABSTRACT  
 
The signal recognition particle (SRP) is a ribonucleoprotein complex responsible for targeting proteins to the endoplasmic reticulum in eukarya or to the inner membrane in prokarya. The crystal structure of the universally conserved RNA-protein core of the Escherichia coli SRP, refined here to 1.5 A resolution, revealed minor groove recognition of the 4.5 S RNA component by the M domain of the Ffh protein. Within the RNA, nucleotides comprising two phylogenetically conserved internal loops create a unique surface for protein recognition. To determine the energetic importance of conserved nucleotides for SRP assembly, we measured the affinity of the M domain for a series of RNA mutants. This analysis reveals how conserved nucleotides within the two internal loop motifs establish the architecture of the macromolecular interface and position essential functional groups for direct recognition by the protein.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Summary of the M domain-RNA interactions and crystal contacts observed. The intermolecular contacts made by protein and RNA that are boxed in red. Crystal contacts made by neighboring complexes in the crystal are boxed in light blue, purple, orange, and green, with each color representing a physically distinct molecule. The thick broken lines between Arg398 and A39, C40 and C41 represent stacking interactions and blue spheres denote water-mediated interactions. 		Figure 7.
Figure 7. Tetraloop-minor groove interaction. (a) Stereo representation of the GAAA tetraloop of one molecule interacting with the minor groove of an adjacent RNA. (b) Base triples formed by this contact, with the final 2F[o] - F[c] electron density map contoured at 1.6s superimposed. The hydrogen bond between A54 and U34 is mediated by a solvent molecule.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 307, 229-246) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20179341 K.Wild, G.Bange, G.Bozkurt, B.Segnitz, A.Hendricks, and I.Sinning (2010).
Structural insights into the assembly of the human and archaeal signal recognition particles.
  Acta Crystallogr D Biol Crystallogr, 66, 295-303.
PDB codes: 3ktv 3ktw
19427322 D.Lambert, D.Leipply, R.Shiman, and D.E.Draper (2009).
The influence of monovalent cation size on the stability of RNA tertiary structures.
  J Mol Biol, 390, 791-804.  
19029307 I.A.Buskiewicz, J.Jöckel, M.V.Rodnina, and W.Wintermeyer (2009).
Conformation of the signal recognition particle in ribosomal targeting complexes.
  RNA, 15, 44-54.  
19159486 T.Oyama, H.Oka, K.Mayanagi, T.Shirai, K.Matoba, R.Fujikane, Y.Ishino, and K.Morikawa (2009).
Atomic structures and functional implications of the archaeal RecQ-like helicase Hjm.
  BMC Struct Biol, 9, 2.
PDB codes: 2zj2 2zj5 2zj8 2zja
18178619 I.J.MacRae, E.Ma, M.Zhou, C.V.Robinson, and J.A.Doudna (2008).
In vitro reconstitution of the human RISC-loading complex.
  Proc Natl Acad Sci U S A, 105, 512-517.  
18805981 J.M.Peterson, and G.J.Phillips (2008).
Characterization of conserved bases in 4.5S RNA of Escherichia coli by construction of new F' factors.
  J Bacteriol, 190, 7709-7718.  
18617187 X.Zhang, S.Kung, and S.O.Shan (2008).
Demonstration of a multistep mechanism for assembly of the SRP x SRP receptor complex: implications for the catalytic role of SRP RNA.
  J Mol Biol, 381, 581-593.  
17637337 A.Y.Keel, R.P.Rambo, R.T.Batey, and J.S.Kieft (2007).
A general strategy to solve the phase problem in RNA crystallography.
  Structure, 15, 761-772.
PDB codes: 2pxb 2pxd 2pxe 2pxf 2pxk 2pxl 2pxp 2pxq 2pxt 2pxu 2pxv
17164479 F.Y.Siu, R.J.Spanggord, and J.A.Doudna (2007).
SRP RNA provides the physiologically essential GTPase activation function in cotranslational protein targeting.
  RNA, 13, 240-250.  
17186523 J.Gawronski-Salerno, J.S.Coon, P.J.Focia, and D.M.Freymann (2007).
X-ray structure of the T. aquaticus FtsY:GDP complex suggests functional roles for the C-terminal helix of the SRP GTPases.
  Proteins, 66, 984-995.
PDB code: 2iyl
17299128 Q.Vicens, A.R.Gooding, A.Laederach, and T.R.Cech (2007).
Local RNA structural changes induced by crystallization are revealed by SHAPE.
  RNA, 13, 536-548.  
17660743 X.Zhong, X.Tao, J.Stombaugh, N.Leontis, and B.Ding (2007).
Tertiary structure and function of an RNA motif required for plant vascular entry to initiate systemic trafficking.
  EMBO J, 26, 3836-3846.  
17041599 G.Fuchs, A.J.Stein, C.Fu, K.M.Reinisch, and S.L.Wolin (2006).
Structural and biochemical basis for misfolded RNA recognition by the Ro autoantigen.
  Nat Struct Mol Biol, 13, 1002-1009.
PDB code: 2i91
16425174 L.Grajcar, C.El Amri, M.Ghomi, S.Fermandjian, V.Huteau, R.Mandel, S.Lecomte, and M.H.Baron (2006).
Assessment of adenyl residue reactivity within model nucleic acids by surface enhanced Raman spectroscopy.
  Biopolymers, 82, 6.  
17381305 S.D.Gilbert, R.K.Montange, C.D.Stoddard, and R.T.Batey (2006).
Structural studies of the purine and SAM binding riboswitches.
  Cold Spring Harb Symp Quant Biol, 71, 259-268.  
16894217 W.J.Melchers, J.Zoll, M.Tessari, D.V.Bakhmutov, A.P.Gmyl, V.I.Agol, and H.A.Heus (2006).
A GCUA tetranucleotide loop found in the poliovirus oriL by in vivo SELEX (un)expectedly forms a YNMG-like structure: Extending the YNMG family with GYYA.
  RNA, 12, 1671-1682.
PDB code: 2evy
15907467 A.J.Stein, G.Fuchs, C.Fu, S.L.Wolin, and K.M.Reinisch (2005).
Structural insights into RNA quality control: the Ro autoantigen binds misfolded RNAs via its central cavity.
  Cell, 121, 529-539.
PDB codes: 1yvp 1yvr
15923378 I.Buskiewicz, A.Kubarenko, F.Peske, M.V.Rodnina, and W.Wintermeyer (2005).
Domain rearrangement of SRP protein Ffh upon binding 4.5S RNA and the SRP receptor FtsY.
  RNA, 11, 947-957.  
16120832 L.B.Szewczak, J.S.Gabrielsen, S.J.Degregorio, S.A.Strobel, and J.A.Steitz (2005).
Molecular basis for RNA kink-turn recognition by the h15.5K small RNP protein.
  RNA, 11, 1407-1419.  
16299512 R.J.Spanggord, F.Siu, A.Ke, and J.A.Doudna (2005).
RNA-mediated interaction between the peptide-binding and GTPase domains of the signal recognition particle.
  Nat Struct Mol Biol, 12, 1116-1122.  
16043501 S.Q.Gu, J.Jöckel, P.Beinker, J.Warnecke, Y.P.Semenkov, M.V.Rodnina, and W.Wintermeyer (2005).
Conformation of 4.5S RNA in the signal recognition particle and on the 30S ribosomal subunit.
  RNA, 11, 1374-1384.  
  15215462 I.W.Davis, L.W.Murray, J.S.Richardson, and D.C.Richardson (2004).
MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes.
  Nucleic Acids Res, 32, W615-W619.  
15189152 J.A.Doudna, and R.T.Batey (2004).
Structural insights into the signal recognition particle.
  Annu Rev Biochem, 73, 539-557.  
15574498 M.Marino (2004).
Biography of Jennifer A. Doudna.
  Proc Natl Acad Sci U S A, 101, 16987-16989.  
12581661 A.E.Sauer-Eriksson, and T.Hainzl (2003).
S-domain assembly of the signal recognition particle.
  Curr Opin Struct Biol, 13, 64-70.  
12592009 C.C.Correll, and K.Swinger (2003).
Common and distinctive features of GNRA tetraloops based on a GUAA tetraloop structure at 1.4 A resolution.
  RNA, 9, 355-363.
PDB code: 1msy
12824344 H.Yang, F.Jossinet, N.Leontis, L.Chen, J.Westbrook, H.Berman, and E.Westhof (2003).
Tools for the automatic identification and classification of RNA base pairs.
  Nucleic Acids Res, 31, 3450-3460.  
13130142 J.C.Cochrane, R.T.Batey, and S.A.Strobel (2003).
Quantitation of free energy profiles in RNA-ligand interactions by nucleotide analog interference mapping.
  RNA, 9, 1282-1289.  
12777762 J.Deng, Y.Xiong, B.Pan, and M.Sundaralingam (2003).
Structure of an RNA dodecamer containing a fragment from SRP domain IV of Escherichia coli.
  Acta Crystallogr D Biol Crystallogr, 59, 1004-1011.
PDB code: 1lnt
12853463 K.Nagai, C.Oubridge, A.Kuglstatter, E.Menichelli, C.Isel, and L.Jovine (2003).
Structure, function and evolution of the signal recognition particle.
  EMBO J, 22, 3479-3485.  
14657338 K.R.Rosendal, K.Wild, G.Montoya, and I.Sinning (2003).
Crystal structure of the complete core of archaeal signal recognition particle and implications for interdomain communication.
  Proc Natl Acad Sci U S A, 100, 14701-14706.
PDB codes: 1qzw 1qzx
12717724 S.B.Howerton, A.Nagpal, and L.D.Williams (2003).
Surprising roles of electrostatic interactions in DNA-ligand complexes.
  Biopolymers, 69, 87-99.
PDB code: 1p20
12736311 T.Leeper, N.Leulliot, and G.Varani (2003).
The solution structure of an essential stem-loop of human telomerase RNA.
  Nucleic Acids Res, 31, 2614-2621.
PDB code: 1oq0
11839493 K.Wild, O.Weichenrieder, K.Strub, I.Sinning, and S.Cusack (2002).
Towards the structure of the mammalian signal recognition particle.
  Curr Opin Struct Biol, 12, 72-81.  
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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