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PDBsum entry 1eif
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Initiation factor PDB id
1eif

 

 

 

 

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Contents
Protein chain
128 a.a. *
Waters ×95
* Residue conservation analysis
PDB id:
1eif
Name: Initiation factor
Title: Eukaryotic translation initiation factor 5a from methanococcus jannaschii
Structure: Eukaryotic translation initiation factor 5a. Chain: a. Engineered: yes
Source: Methanocaldococcus jannaschii. Organism_taxid: 2190. Cell_line: bl21. Atcc: dsm 2661. Collection: dsm 2661. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.90Å     R-factor:   0.205     R-free:   0.289
Authors: K.K.Kim,L.W.Hung,H.Yokota,R.Kim,S.H.Kim
Key ref:
K.K.Kim et al. (1998). Crystal structures of eukaryotic translation initiation factor 5A from Methanococcus jannaschii at 1.8 A resolution. Proc Natl Acad Sci U S A, 95, 10419-10424. PubMed id: 9724718 DOI: 10.1073/pnas.95.18.10419
Date:
29-Jul-98     Release date:   14-Oct-98    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q58625  (IF5A_METJA) -  Translation initiation factor 5A from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Seq:
Struc: 		132 a.a.
128 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

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

 

 
DOI no: 10.1073/pnas.95.18.10419 Proc Natl Acad Sci U S A 95:10419-10424 (1998)
PubMed id: 9724718  
 
 
Crystal structures of eukaryotic translation initiation factor 5A from Methanococcus jannaschii at 1.8 A resolution.
K.K.Kim, L.W.Hung, H.Yokota, R.Kim, S.H.Kim.
 
  ABSTRACT  
 
Eukaryotic translation initiation factor 5A (eIF-5A) is a ubiquitous protein found in all eukaryotic cells. The protein is closely associated with cell proliferation in the G1-S stage of the cell cycle. Recent findings show that the eIF-5A proteins are highly expressed in tumor cells and act as a cofactor of the Rev protein in HIV-1-infected cells. The mature eIF is the only protein known to have the unusual amino acid hypusine, a post-translationally modified lysine. The crystal structure of eIF-5A from Methanococcus jannaschii (MJ eIF-5A) has been determined at 1.9 A and 1.8 A resolution in two crystal forms by using the multiple isomorphous replacement method and the multiwavelength anomalous diffraction method for the first crystal form and the molecular replacement method for the second crystal form. The structure consists of two folding domains, one of which is similar to the oligonucleotide-binding domain found in the prokaryotic cold shock protein and the translation initiation factor IF1 despite the absence of any significant sequence similarities. The 12 highly conserved amino acid residues found among eIF-5As include the hypusine site and form a long protruding loop at one end of the elongated molecule.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. (A) Topology diagram of the MJ eIF-5A structure. The arrows represent -strands and the short cylinder represents a 3[10] helix. The lysine modification site is represented by a gray circle. (B) Ribbon diagram of MJ eIF-5A structure in C2 crystal form. The arrows represent -strands. The secondary structures were assigned by the method of Kabsch and Sander (31). Two domains are colored magenta and blue and connected by a green linker. The side chain of Lys-40 is shown as a ball-and-stick model. This figure was made with MOLSCRIPT (32). 		Figure 6.
Fig. 6. Two different views of the surface charge distribution of MJ eIF-5A as calculated by program GRASP (39). The red and blue colors represent negatively and positively charged surfaces, respectively. The lysine modification site (Lys-40) is labeled.
 
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21451136 A.Henderson, and J.W.Hershey (2011).
Eukaryotic translation initiation factor (eIF) 5A stimulates protein synthesis in Saccharomyces cerevisiae.
  Proc Natl Acad Sci U S A, 108, 6415-6419.  
21365687 S.Choi, and J.Choe (2011).
Crystal structure of elongation factor P from Pseudomonas aeruginosa at 1.75 å resolution.
  Proteins, 79, 1688-1693.  
20492553 F.Ma, Z.Liu, T.W.Wang, M.T.Hopkins, C.A.Peterson, and J.E.Thompson (2010).
Arabidopsis eIF5A3 influences growth and the response to osmotic and nutrient stress.
  Plant Cell Environ, 33, 1682-1696.  
20091748 M.Mihailovich, C.Militti, T.Gabaldón, and F.Gebauer (2010).
Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression.
  Bioessays, 32, 109-118.  
20807213 Y.Ma, E.Miura, B.K.Ham, H.W.Cheng, Y.J.Lee, and W.J.Lucas (2010).
Pumpkin eIF5A isoforms interact with components of the translational machinery in the cucurbit sieve tube system.
  Plant J, 64, 536-550.  
19120453 P.M.Gentz, G.L.Blatch, and R.A.Dorrington (2009).
Dimerization of the yeast eukaryotic translation initiation factor 5A requires hypusine and is RNA dependent.
  FEBS J, 276, 695-706.  
18341589 C.A.Dias, V.S.Cano, S.M.Rangel, L.H.Apponi, M.C.Frigieri, J.R.Muniz, W.Garcia, M.H.Park, R.C.Garratt, C.F.Zanelli, and S.R.Valentini (2008).
Structural modeling and mutational analysis of yeast eukaryotic translation initiation factor 5A reveal new critical residues and reinforce its involvement in protein synthesis.
  FEBS J, 275, 1874-1888.  
18067580 V.S.Cano, G.A.Jeon, H.E.Johansson, C.A.Henderson, J.H.Park, S.R.Valentini, J.W.Hershey, and M.H.Park (2008).
Mutational analyses of human eIF5A-1--identification of amino acid residues critical for eIF5A activity and hypusine modification.
  FEBS J, 275, 44-58.  
17578650 C.F.Zanelli, and S.R.Valentini (2007).
Is there a role for eIF5A in translation?
  Amino Acids, 33, 351-358.  
17213197 K.R.Kang, Y.S.Kim, E.C.Wolff, and M.H.Park (2007).
Specificity of the deoxyhypusine hydroxylase-eukaryotic translation initiation factor (eIF5A) interaction: identification of amino acid residues of the enzyme required for binding of its substrate, deoxyhypusine-containing eIF5A.
  J Biol Chem, 282, 8300-8308.  
16215987 D.L.Jao, and K.Y.Chen (2006).
Tandem affinity purification revealed the hypusine-dependent binding of eukaryotic initiation factor 5A to the translating 80S ribosomal complex.
  J Cell Biochem, 97, 583-598.  
16408210 I.Chatterjee, S.R.Gross, T.G.Kinzy, and K.Y.Chen (2006).
Rapid depletion of mutant eukaryotic initiation factor 5A at restrictive temperature reveals connections to actin cytoskeleton and cell cycle progression.
  Mol Genet Genomics, 275, 264-276.  
16371467 J.H.Park, L.Aravind, E.C.Wolff, J.Kaevel, Y.S.Kim, and M.H.Park (2006).
Molecular cloning, expression, and structural prediction of deoxyhypusine hydroxylase: a HEAT-repeat-containing metalloenzyme.
  Proc Natl Acad Sci U S A, 103, 51-56.  
16452303 M.H.Park (2006).
The post-translational synthesis of a polyamine-derived amino acid, hypusine, in the eukaryotic translation initiation factor 5A (eIF5A).
  J Biochem, 139, 161-169.  
16550432 M.Saeftel, R.S.Sarite, T.Njuguna, U.Holzgrabe, D.Ulmer, A.Hoerauf, and A.Kaiser (2006).
Piperidones with activity against Plasmodium falciparum.
  Parasitol Res, 99, 281-286.  
15755955 B.S.Laursen, H.P.Sørensen, K.K.Mortensen, and H.U.Sperling-Petersen (2005).
Initiation of protein synthesis in bacteria.
  Microbiol Mol Biol Rev, 69, 101-123.  
16148304 J.Eichler, and M.W.Adams (2005).
Posttranslational protein modification in Archaea.
  Microbiol Mol Biol Rev, 69, 393-425.  
15808741 P.Londei (2005).
Evolution of translational initiation: new insights from the archaea.
  FEMS Microbiol Rev, 29, 185-200.  
15063867 J.E.Thompson, M.T.Hopkins, C.Taylor, and T.W.Wang (2004).
Regulation of senescence by eukaryotic translation initiation factor 5A: implications for plant growth and development.
  Trends Plant Sci, 9, 174-179.  
15210970 K.Hanawa-Suetsugu, S.Sekine, H.Sakai, C.Hori-Takemoto, T.Terada, S.Unzai, J.R.Tame, S.Kuramitsu, M.Shirouzu, and S.Yokoyama (2004).
Crystal structure of elongation factor P from Thermus thermophilus HB8.
  Proc Natl Acad Sci U S A, 101, 9595-9600.
PDB code: 1ueb
15572767 T.C.Terwilliger (2004).
Using prime-and-switch phasing to reduce model bias in molecular replacement.
  Acta Crystallogr D Biol Crystallogr, 60, 2144-2149.  
12581660 N.Sonenberg, and T.E.Dever (2003).
Eukaryotic translation initiation factors and regulators.
  Curr Opin Struct Biol, 13, 56-63.  
14622290 P.M.Clement, C.A.Henderson, Z.A.Jenkins, Z.Smit-McBride, E.C.Wolff, J.W.Hershey, M.H.Park, and H.E.Johansson (2003).
Identification and characterization of eukaryotic initiation factor 5A-2.
  Eur J Biochem, 270, 4254-4263.  
12640443 P.Yuan, G.Jedd, D.Kumaran, S.Swaminathan, H.Shio, D.Hewitt, N.H.Chua, and K.Swaminathan (2003).
A HEX-1 crystal lattice required for Woronin body function in Neurospora crassa.
  Nat Struct Biol, 10, 264-270.
PDB code: 1khi
12210765 D.L.Jao, and K.Yu Chen (2002).
Subcellular localization of the hypusine-containing eukaryotic initiation factor 5A by immunofluorescent staining and green fluorescent protein tagging.
  J Cell Biochem, 86, 590-600.  
12209000 M.C.Ganoza, M.C.Kiel, and H.Aoki (2002).
Evolutionary conservation of reactions in translation.
  Microbiol Mol Biol Rev, 66, 460.  
  11861547 S.R.Valentini, J.M.Casolari, C.C.Oliveira, P.A.Silver, and A.E.McBride (2002).
Genetic interactions of yeast eukaryotic translation initiation factor 5A (eIF5A) reveal connections to poly(A)-binding protein and protein kinase C signaling.
  Genetics, 160, 393-405.  
11406387 S.A.Teichmann, A.G.Murzin, and C.Chothia (2001).
Determination of protein function, evolution and interactions by structural genomics.
  Curr Opin Struct Biol, 11, 354-363.  
11714910 W.Li, and D.W.Hoffman (2001).
Structure and dynamics of translation initiation factor aIF-1A from the archaeon Methanococcus jannaschii determined by NMR spectroscopy.
  Protein Sci, 10, 2426-2438.
PDB code: 1jt8
10944119 G.Lipowsky, F.R.Bischoff, P.Schwarzmaier, R.Kraft, S.Kostka, E.Hartmann, U.Kutay, and D.Görlich (2000).
Exportin 4: a mediator of a novel nuclear export pathway in higher eukaryotes.
  EMBO J, 19, 4362-4371.  
10958635 L.Aravind, and E.V.Koonin (2000).
Eukaryote-specific domains in translation initiation factors: implications for translation regulation and evolution of the translation system.
  Genome Res, 10, 1172-1184.  
10987361 M.C.Ganoza, and H.Aoki (2000).
Peptide bond synthesis: function of the efp gene product.
  Biol Chem, 381, 553-559.  
10075918 A.Nakagawa, T.Nakashima, M.Taniguchi, H.Hosaka, M.Kimura, and I.Tanaka (1999).
The three-dimensional structure of the RNA-binding domain of ribosomal protein L2; a protein at the peptidyl transferase center of the ribosome.
  EMBO J, 18, 1459-1467.
PDB code: 1rl2
10508726 T.Gaasterland (1999).
Archaeal genomics.
  Curr Opin Microbiol, 2, 542-547.  
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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