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PDBsum entry 1ecx

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1ecx
Jmol
Contents
Protein chains
364 a.a. *
Ligands
PLP ×2
CYS ×2
Waters ×179
* Residue conservation analysis
PDB id:
1ecx
Name: Transferase
Title: Nifs-like protein
Structure: Aminotransferase. Chain: a, b. Engineered: yes. Other_details: nifs-like protein
Source: Thermotoga maritima. Organism_taxid: 2336. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.70Å     R-factor:   0.207     R-free:   0.256
Authors: J.T.Kaiser,T.C.Clausen,G.P.Bourenkow,H.-D.Bartunik,S.Steinba R.Huber
Key ref:
J.T.Kaiser et al. (2000). Crystal structure of a NifS-like protein from Thermotoga maritima: implications for iron sulphur cluster assembly. J Mol Biol, 297, 451-464. PubMed id: 10715213 DOI: 10.1006/jmbi.2000.3581
Date:
26-Jan-00     Release date:   20-Mar-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9X218  (Q9X218_THEMA) -  Aminotransferase, class V
Seq:
Struc:
384 a.a.
364 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.8.1.7  - Cysteine desulfurase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-cysteine + acceptor = L-alanine + S-sulfanyl-acceptor
L-cysteine
+ acceptor
= L-alanine
+ S-sulfanyl-acceptor
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.2000.3581 J Mol Biol 297:451-464 (2000)
PubMed id: 10715213  
 
 
Crystal structure of a NifS-like protein from Thermotoga maritima: implications for iron sulphur cluster assembly.
J.T.Kaiser, T.Clausen, G.P.Bourenkow, H.D.Bartunik, S.Steinbacher, R.Huber.
 
  ABSTRACT  
 
NifS-like proteins are ubiquitous, homodimeric, proteins which belong to the alpha-family of pyridoxal-5'-phoshate dependent enzymes. They are proposed to donate elementary sulphur, generated from cysteine, via a cysteinepersulphide intermediate during iron sulphur cluster biosynthesis, an important albeit not well understood process. Here, we report on the crystal structure of a NifS-like protein from the hyperthermophilic bacterium Thermotoga maritima (tmNifS) at 2.0 A resolution. The tmNifS is structured into two domains, the larger bearing the pyridoxal-5'-phosphate-binding active site, the smaller hosting the active site cysteine in the middle of a highly flexible loop, 12 amino acid residues in length. Once charged with sulphur the loop could possibly deliver S(0) directly to regions far remote from the protein. Based on the three-dimensional structures of the native as well as the substrate complexed form and on spectrophotometric results, a mechanism of sulphur activation is proposed. The His99, which stacks on top of the pyridoxal-5'-phosphate co-factor, is assigned a crucial role during the catalytic cycle by acting as an acid-base catalyst and is believed to have a pK(a) value depending on the co-factor redox state.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Stereo drawing of the active site of the substrate free model at 2.0 Å resolution. The final 2F[o] -F[c] electron density covering the co-factor, the Lys203 and the sulphate ion is overlaid. Protein residues are depicted in blue, the PLP-co-factor in yellow and the substrate in red. The Figure was prepared with BOBSCRIPT [Esnouf 1997] and Raster3D [Merritt and Murphy 1994].
Figure 5.
Figure 5. Stereo drawing of the active site of reductively inactivated, substrate-complexed tmNifS at 2.7 Å resolution overlaid with the 2F[o] -F[c] electron density map computed with the cysteine omitted. Protein residues are depicted in blue, the PLP-co-factor (yellow); substrate (red). The Figure was prepared with BOBSCRIPT [Esnouf 1997] and Raster3D [Merritt and Murphy 1994].
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 297, 451-464) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21226084 S.Rawat, and T.L.Stemmler (2011).
Key players and their role during mitochondrial iron-sulfur cluster biosynthesis.
  Chemistry, 17, 746-753.  
19308466 M.Nuth, and J.A.Cowan (2009).
Iron-sulfur cluster biosynthesis: characterization of IscU-IscS complex formation and a structural model for sulfide delivery to the [2Fe-2S] assembly site.
  J Biol Inorg Chem, 14, 829-839.  
19675643 R.Lill (2009).
Function and biogenesis of iron-sulphur proteins.
  Nature, 460, 831-838.  
18562278 E.C.Raulfs, I.P.O'Carroll, P.C.Dos Santos, M.C.Unciuleac, and D.R.Dean (2008).
In vivo iron-sulfur cluster formation.
  Proc Natl Acad Sci U S A, 105, 8591-8596.  
18425540 J.Huang, E.Dizin, and J.A.Cowan (2008).
Mapping iron binding sites on human frataxin: implications for cluster assembly on the ISU Fe-S cluster scaffold protein.
  J Biol Inorg Chem, 13, 825-836.  
18093968 O.M.Ganichkin, X.M.Xu, B.A.Carlson, H.Mix, D.L.Hatfield, V.N.Gladyshev, and M.C.Wahl (2008).
Structure and catalytic mechanism of eukaryotic selenocysteine synthase.
  J Biol Chem, 283, 5849-5865.
PDB codes: 3bc8 3bca 3bcb
18366324 R.Lill, and U.Mühlenhoff (2008).
Maturation of iron-sulfur proteins in eukaryotes: mechanisms, connected processes, and diseases.
  Annu Rev Biochem, 77, 669-700.  
17653385 Y.Liu, and J.A.Cowan (2007).
Iron sulfur cluster biosynthesis. Human NFU mediates sulfide delivery to ISU in the final step of [2Fe-2S] cluster assembly.
  Chem Commun (Camb), (), 3192-3194.  
16847322 A.Biederbick, O.Stehling, R.Rösser, B.Niggemeyer, Y.Nakai, H.P.Elsässer, and R.Lill (2006).
Role of human mitochondrial Nfs1 in cytosolic iron-sulfur protein biogenesis and iron regulation.
  Mol Cell Biol, 26, 5675-5687.  
17020883 B.Campanini, F.Schiaretti, S.Abbruzzetti, D.Kessler, and A.Mozzarelli (2006).
Sulfur mobilization in cyanobacteria: the catalytic mechanism of L-cystine C-S lyase (C-DES) from synechocystis.
  J Biol Chem, 281, 38769-38780.  
17064282 D.Kessler (2006).
Enzymatic activation of sulfur for incorporation into biomolecules in prokaryotes.
  FEMS Microbiol Rev, 30, 825-840.  
16547008 N.Shigi, Y.Sakaguchi, T.Suzuki, and K.Watanabe (2006).
Identification of two tRNA thiolation genes required for cell growth at extremely high temperatures.
  J Biol Chem, 281, 14296-14306.  
16824008 R.Lill, and U.Mühlenhoff (2006).
Iron-sulfur protein biogenesis in eukaryotes: components and mechanisms.
  Annu Rev Cell Dev Biol, 22, 457-486.  
17064285 S.B.Conners, E.F.Mongodin, M.R.Johnson, C.I.Montero, K.E.Nelson, and R.M.Kelly (2006).
Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species.
  FEMS Microbiol Rev, 30, 872-905.  
15952888 D.C.Johnson, D.R.Dean, A.D.Smith, and M.K.Johnson (2005).
Structure, function, and formation of biological iron-sulfur clusters.
  Annu Rev Biochem, 74, 247-281.  
16380427 P.O'Donoghue, A.Sethi, C.R.Woese, and Z.A.Luthey-Schulten (2005).
The evolutionary history of Cys-tRNACys formation.
  Proc Natl Acad Sci U S A, 102, 19003-19008.  
15727041 R.J.Wilson (2005).
Parasite plastids: approaching the endgame.
  Biol Rev Camb Philos Soc, 80, 129-153.  
15498941 A.Paiardini, F.Bossa, and S.Pascarella (2004).
Evolutionarily conserved regions and hydrophobic contacts at the superfamily level: The case of the fold-type I, pyridoxal-5'-phosphate-dependent enzymes.
  Protein Sci, 13, 2992-3005.  
14978044 C.T.Lauhon, E.Skovran, H.D.Urbina, D.M.Downs, and L.E.Vickery (2004).
Substitutions in an active site loop of Escherichia coli IscS result in specific defects in Fe-S cluster and thionucleoside biosynthesis in vivo.
  J Biol Chem, 279, 19551-19558.  
15300825 J.Balk, and R.Lill (2004).
The cell's cookbook for iron--sulfur clusters: recipes for fool's gold?
  Chembiochem, 5, 1044-1049.  
15466556 M.A.Pysz, S.B.Conners, C.I.Montero, K.R.Shockley, M.R.Johnson, D.E.Ward, and R.M.Kelly (2004).
Transcriptional analysis of biofilm formation processes in the anaerobic, hyperthermophilic bacterium Thermotoga maritima.
  Appl Environ Microbiol, 70, 6098-6112.  
15040816 M.van der Giezen, S.Cox, and J.Tovar (2004).
The iron-sulfur cluster assembly genes iscS and iscU of Entamoeba histolytica were acquired by horizontal gene transfer.
  BMC Evol Biol, 4, 7.  
14688265 S.S.Mansy, S.P.Wu, and J.A.Cowan (2004).
Iron-sulfur cluster biosynthesis: biochemical characterization of the conformational dynamics of Thermotoga maritima IscU and the relevance for cellular cluster assembly.
  J Biol Chem, 279, 10469-10475.  
15220327 U.Mühlenhoff, J.Balk, N.Richhardt, J.T.Kaiser, K.Sipos, G.Kispal, and R.Lill (2004).
Functional characterization of the eukaryotic cysteine desulfurase Nfs1p from Saccharomyces cerevisiae.
  J Biol Chem, 279, 36906-36915.  
14757765 V.Ali, Y.Shigeta, U.Tokumoto, Y.Takahashi, and T.Nozaki (2004).
An intestinal parasitic protist, Entamoeba histolytica, possesses a non-redundant nitrogen fixation-like system for iron-sulfur cluster assembly under anaerobic conditions.
  J Biol Chem, 279, 16863-16874.  
14675553 E.Settembre, T.P.Begley, and S.E.Ealick (2003).
Structural biology of enzymes of the thiamin biosynthesis pathway.
  Curr Opin Struct Biol, 13, 739-747.  
12912902 G.Capitani, D.De Biase, C.Aurizi, H.Gut, F.Bossa, and M.G.Grütter (2003).
Crystal structure and functional analysis of Escherichia coli glutamate decarboxylase.
  EMBO J, 22, 4027-4037.
PDB codes: 1pmm 1pmo
12386155 J.T.Kaiser, S.Bruno, T.Clausen, R.Huber, F.Schiaretti, A.Mozzarelli, and D.Kessler (2003).
Snapshots of the cystine lyase C-DES during catalysis. Studies in solution and in the crystalline state.
  J Biol Chem, 278, 357-365.
PDB codes: 1n2t 1n31
12876288 L.Loiseau, S.Ollagnier-de-Choudens, L.Nachin, M.Fontecave, and F.Barras (2003).
Biogenesis of Fe-S cluster by the bacterial Suf system: SufS and SufE form a new type of cysteine desulfurase.
  J Biol Chem, 278, 38352-38359.  
12077450 H.D.Urbina, J.R.Cupp-Vickery, and L.E.Vickery (2002).
Preliminary crystallographic analysis of the cysteine desulfurase IscS from Escherichia coli.
  Acta Crystallogr D Biol Crystallogr, 58, 1224-1225.  
11972033 S.Kato, H.Mihara, T.Kurihara, Y.Takahashi, U.Tokumoto, T.Yoshimura, and N.Esaki (2002).
Cys-328 of IscS and Cys-63 of IscU are the sites of disulfide bridge formation in a covalently bound IscS/IscU complex: implications for the mechanism of iron-sulfur cluster assembly.
  Proc Natl Acad Sci U S A, 99, 5948-5952.  
11934893 S.S.Mansy, G.Wu, K.K.Surerus, and J.A.Cowan (2002).
Iron-sulfur cluster biosynthesis. Thermatoga maritima IscU is a structured iron-sulfur cluster assembly protein.
  J Biol Chem, 277, 21397-21404.  
11555280 K.E.Ellis, B.Clough, J.W.Saldanha, and R.J.Wilson (2001).
Nifs and Sufs in malaria.
  Mol Microbiol, 41, 973-981.  
10971575 H.Beinert (2000).
A tribute to sulfur.
  Eur J Biochem, 267, 5657-5664.  
10891064 J.N.Agar, C.Krebs, J.Frazzon, B.H.Huynh, D.R.Dean, and M.K.Johnson (2000).
IscU as a scaffold for iron-sulfur cluster biosynthesis: sequential assembly of [2Fe-2S] and [4Fe-4S] clusters in IscU.
  Biochemistry, 39, 7856-7862.  
11029694 L.Amrani, J.Primus, A.Glatigny, L.Arcangeli, C.Scazzocchio, and V.Finnerty (2000).
Comparison of the sequences of the Aspergillus nidulans hxB and Drosophila melanogaster ma-l genes with nifS from Azotobacter vinelandii suggests a mechanism for the insertion of the terminal sulphur atom in the molybdopterin cofactor.
  Mol Microbiol, 38, 114-125.  
10916152 R.Lill, and G.Kispal (2000).
Maturation of cellular Fe-S proteins: an essential function of mitochondria.
  Trends Biochem Sci, 25, 352-356.  
11004453 U.Mühlenhoff, and R.Lill (2000).
Biogenesis of iron-sulfur proteins in eukaryotes: a novel task of mitochondria that is inherited from bacteria.
  Biochim Biophys Acta, 1459, 370-382.  
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.