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PDBsum entry 1r30

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1r30
Jmol
Contents
Protein chains
312 a.a. *
Ligands
SAM ×2
SF4 ×2
FES ×2
DTB ×2
TRS
* Residue conservation analysis
PDB id:
1r30
Name: Transferase
Title: The crystal structure of biotin synthase, an s- adenosylmethionine-dependent radical enzyme
Structure: Biotin synthase. Chain: a, b. Synonym: biotin synthetase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: biob. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
3.40Å     R-factor:   0.256     R-free:   0.300
Authors: F.Berkovitch,Y.Nicolet,J.T.Wan,J.T.Jarrett,C.L.Drennan
Key ref:
F.Berkovitch et al. (2004). Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme. Science, 303, 76-79. PubMed id: 14704425 DOI: 10.1126/science.1088493
Date:
30-Sep-03     Release date:   13-Jan-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P12996  (BIOB_ECOLI) -  Biotin synthase
Seq:
Struc:
346 a.a.
312 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.8.1.6  - Biotin synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Dethiobiotin + sulfur-(sulfur carrier) + 2 S-adenosyl-L-methionine + 2 reduced [2Fe-2S] ferredoxin = biotin + (sulfur carrier) + 2 L-methionine + 2 5'-deoxyadenosine + 2 oxidized [2Fe-2S] ferredoxin
Dethiobiotin
Bound ligand (Het Group name = DTB)
corresponds exactly
+ sulfur-(sulfur carrier)
+
2 × S-adenosyl-L-methionine
Bound ligand (Het Group name = SAM)
corresponds exactly
+ 2 × reduced [2Fe-2S] ferredoxin
=
biotin
Bound ligand (Het Group name = TRS)
matches with 41.00% similarity
+ (sulfur carrier)
+ 2 × L-methionine
+ 2 × 5'-deoxyadenosine
+ 2 × oxidized [2Fe-2S] ferredoxin
      Cofactor: Iron-sulfur
Iron-sulfur
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     biotin biosynthetic process   1 term 
  Biochemical function     catalytic activity     9 terms  

 

 
    reference    
 
 
DOI no: 10.1126/science.1088493 Science 303:76-79 (2004)
PubMed id: 14704425  
 
 
Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme.
F.Berkovitch, Y.Nicolet, J.T.Wan, J.T.Jarrett, C.L.Drennan.
 
  ABSTRACT  
 
The crystal structure of biotin synthase from Escherichia coli in complex with S-adenosyl-L-methionine and dethiobiotin has been determined to 3.4 angstrom resolution. This structure addresses how "AdoMet radical" or "radical SAM" enzymes use Fe4S4 clusters and S-adenosyl-L-methionine to generate organic radicals. Biotin synthase catalyzes the radical-mediated insertion of sulfur into dethiobiotin to form biotin. The structure places the substrates between the Fe4S4 cluster, essential for radical generation, and the Fe2S2 cluster, postulated to be the source of sulfur, with both clusters in unprecedented coordination environments.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. (A) Structure of BioB, FeS clusters, and bound AdoMet and DTB. BioB exists as a homodimer in solution (11) and we find two possible dimeric relationships between BioB monomers in the crystal. The dimer shown here buries 17.6% of the monomer surface area (13,249 Å2) and is likely to be physiologically relevant. An anomalous Fourier electron density map, calculated with data collected at the Fe absorption peak wavelength (1.73827 Å) and phases from the polypeptide portion of the model, is contoured at 3 in black mesh. These electron density peaks represent the positions of the four FeS clusters in this dimeric structure. There are no other features of a similar size in the electron density map. The FeS clusters are shown as ball-and-stick representations, with brown Fe atoms and yellow S atoms. In addition, we find one AdoMet (red) and one DTB (green) per subunit. Figures 1A and 2 were prepared with PyMOL (42). (B) Topology diagram of the BioB TIM barrel showing the location of important residues with respect to the ß strands (arrows, numbered 1 to 8). The numbers to the left of each ß strand correspond to the N-terminal residue of that secondary structure element. Ligands to the Fe[4]S[4] cluster are in black, ligands to the Fe[2]S[2] cluster are in red, and residues that contact the Fe[2]S[2] cluster ligand Arg260 are in pink. AdoMet contacts (blue) include Ala^100, Trp102, and Arg173, which form hydrogen bonds to the amino acid moiety; Asp155 and Asn153, which form hydrogen bonds to the ribose hydroxyl groups (Fig. 2A); Tyr59 and Ile^192, which stack against the adenine ring (Fig. 2A); and Val225, which forms backbone hydrogen bonds to the adenine ring. Residues in position to form hydrogen bonds to DTB (brown) include Asn151, Asn153, and Asn222, which contact the DTB ureido ring (Fig. 2C), and Thr292 and Thr293, which contact the carboxylate tail. Asterisks denote main-chain interactions.
Figure 2.
Fig. 2. (A) Stereo view of the Fe[4]S[4] cluster with AdoMet bound. Conserved side-chain contacts between BioB and AdoMet are indicated, and AdoMet is shown in a simulated annealing omit map contoured at 4.5 (orange). DTB is omitted for clarity. Color code: C, gray; O, red; N, blue; S, yellow; Fe, brown. (B) Stereo view of the active site, focusing on the Fe[2]S[2] cluster and its ligands. The unusual Arg260 ligand is shown in a simulated annealing omit map contoured at 4.5 . In addition to the Fe[2]S[2] cluster, Arg260 interacts with Ser43, Ser218, Ser283, and Arg95. Also shown are the positions of the Fe[4]S[4] cluster, AdoMet, and DTB with respect to the Fe[2]S[2] cluster. (C) Stereo view of DTB interacting with AdoMet and conserved residues Asn222, Asn151, and Asn153 in the active site. Potential hydrogen bonds between Asn222 and DTB are drawn as dashed lines. The stacking of the carboxylate tail of DTB and the adenine ring of AdoMet is visible in the orientation, although contacts with Thr292 and Thr293 are not. DTB is shown in a simulated annealing omit map contoured at 4.0 .
 
  The above figures are reprinted from an Open Access publication published by the AAAs: Science (2004, 303, 76-79) copyright 2004.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21527702 J.Stubbe (2011).
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Generation of adenosyl radical from S-adenosylmethionine (SAM) in biotin synthase.
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20559373 J.B.Broderick (2010).
Biochemistry: A radically different enzyme.
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19768473 M.G.Fuchs, F.Meyer, and U.Ryde (2010).
A combined computational and experimental investigation of the [2Fe-2S] cluster in biotin synthase.
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Post-translational modification of ribosomal proteins: structural and functional characterization of RimO from Thermotoga maritima, a radical S-adenosylmethionine methylthiotransferase.
  J Biol Chem, 285, 5792-5801.
PDB code: 2qgq
20405152 S.C.Silver, T.Chandra, E.Zilinskas, S.Ghose, W.E.Broderick, and J.B.Broderick (2010).
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Diphthamide biosynthesis requires an organic radical generated by an iron-sulphur enzyme.
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PDB codes: 3lzc 3lzd
19348578 C.T.Jurgenson, T.P.Begley, and S.E.Ealick (2009).
The structural and biochemical foundations of thiamin biosynthesis.
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19269883 K.S.Duschene, S.E.Veneziano, S.C.Silver, and J.B.Broderick (2009).
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19744927 M.Del Vecchio, R.Pogni, M.C.Baratto, A.Nobbs, R.Rappuoli, M.Pizza, and E.Balducci (2009).
Identification of an iron-sulfur cluster that modulates the enzymatic activity in NarE, a Neisseria meningitidis ADP-ribosyltransferase.
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Anaerobic functionalization of unactivated C-H bonds.
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Bioinformatic Identification of Novel Methyltransferases.
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19706452 Y.Nicolet, P.Amara, J.M.Mouesca, and J.C.Fontecilla-Camps (2009).
Unexpected electron transfer mechanism upon AdoMet cleavage in radical SAM proteins.
  Proc Natl Acad Sci U S A, 106, 14867-14871.
PDB codes: 3iix 3iiz
19771344 Y.Shimazaki, M.Takani, and O.Yamauchi (2009).
Metal complexes of amino acids and amino acid side chain groups. Structures and properties.
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18953358 A.Chatterjee, Y.Li, Y.Zhang, T.L.Grove, M.Lee, C.Krebs, S.J.Booker, T.P.Begley, and S.E.Ealick (2008).
Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily.
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PDB codes: 3epm 3epn 3epo
18086897 C.Gelling, I.W.Dawes, N.Richhardt, R.Lill, and U.Mühlenhoff (2008).
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PDB codes: 3c8f 3cb8
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In vitro characterization of AtsB, a radical SAM formylglycine-generating enzyme that contains three [4Fe-4S] clusters.
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Iron-sulfur proteins as initiators of radical chemistry.
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Electron paramagnetic resonance and Mössbauer spectroscopy of intact mitochondria from respiring Saccharomyces cerevisiae.
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17483229 D.Nakunst, C.Larisch, A.T.Hüser, A.Tauch, A.Pühler, and J.Kalinowski (2007).
The extracytoplasmic function-type sigma factor SigM of Corynebacterium glutamicum ATCC 13032 is involved in transcription of disulfide stress-related genes.
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17222594 F.J.Ruzicka, and P.A.Frey (2007).
Glutamate 2,3-aminomutase: a new member of the radical SAM superfamily of enzymes.
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16738799 M.A.Grillo, and S.Colombatto (2007).
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BluB cannibalizes flavin to form the lower ligand of vitamin B12.
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PDB codes: 2isj 2isk 2isl
17898899 P.H.Buist (2007).
Exotic biomodification of fatty acids.
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Structural snapshots along the reaction pathway of ferredoxin-thioredoxin reductase.
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PDB codes: 2pu9 2puk 2puo 2pvd 2pvg 2pvo
17377573 S.E.Ealick, and T.P.Begley (2007).
Biochemistry: molecular cannibalism.
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17881823 S.Goto-Ito, R.Ishii, T.Ito, R.Shibata, E.Fusatomi, S.I.Sekine, Y.Bessho, and S.Yokoyama (2007).
Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis.
  Acta Crystallogr D Biol Crystallogr, 63, 1059-1068.
PDB code: 2yx0
17936058 S.J.Booker, R.M.Cicchillo, and T.L.Grove (2007).
Self-sacrifice in radical S-adenosylmethionine proteins.
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17259550 U.Mühlenhoff, M.J.Gerl, B.Flauger, H.M.Pirner, S.Balser, N.Richhardt, R.Lill, and J.Stolz (2007).
The ISC [corrected] proteins Isa1 and Isa2 are required for the function but not for the de novo synthesis of the Fe/S clusters of biotin synthase in Saccharomyces cerevisiae.
  Eukaryot Cell, 6, 495-504.  
16420352 C.Paraskevopoulou, S.A.Fairhurst, D.J.Lowe, P.Brick, and S.Onesti (2006).
The Elongator subunit Elp3 contains a Fe4S4 cluster and binds S-adenosylmethionine.
  Mol Microbiol, 59, 795-806.  
16430685 J.A.Imlay (2006).
Iron-sulphur clusters and the problem with oxygen.
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17010373 J.Chartron, K.S.Carroll, C.Shiau, H.Gao, J.A.Leary, C.R.Bertozzi, and C.D.Stout (2006).
Substrate recognition, protein dynamics, and iron-sulfur cluster in Pseudomonas aeruginosa adenosine 5'-phosphosulfate reductase.
  J Mol Biol, 364, 152-169.
PDB code: 2goy
16981206 L.Di Costanzo, L.V.Flores, and D.W.Christianson (2006).
Stereochemistry of guanidine-metal interactions: implications for L-arginine-metal interactions in protein structure and function.
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16688781 L.Sun, and K.Warncke (2006).
Comparative model of EutB from coenzyme B12-dependent ethanolamine ammonia-lyase reveals a beta8alpha8, TIM-barrel fold and radical catalytic site structural features.
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16547473 M.Fontecave (2006).
Iron-sulfur clusters: ever-expanding roles.
  Nat Chem Biol, 2, 171-174.  
16632608 P.Hänzelmann, and H.Schindelin (2006).
Binding of 5'-GTP to the C-terminal FeS cluster of the radical S-adenosylmethionine enzyme MoaA provides insights into its mechanism.
  Proc Natl Acad Sci U S A, 103, 6829-6834.
PDB codes: 2fb2 2fb3
16453120 P.M.Rodrigues, A.L.Macedo, B.J.Goodfellow, I.Moura, and J.J.Moura (2006).
Desulfovibrio gigas ferredoxin II: redox structural modulation of the [3Fe-4S] cluster.
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Functional studies of [FeFe] hydrogenase maturation in an Escherichia coli biosynthetic system.
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17115711 R.B.Broach, and J.T.Jarrett (2006).
Role of the [2Fe-2S]2+ cluster in biotin synthase: mutagenesis of the atypical metal ligand arginine 260.
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16788911 R.K.Szilagyi, and M.A.Winslow (2006).
On the accuracy of density functional theory for iron-sulfur clusters.
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16453030 T.P.Begley (2006).
Cofactor biosynthesis: an organic chemist's treasure trove.
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16704345 W.Buckel, and B.T.Golding (2006).
Radical enzymes in anaerobes.
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16166264 B.W.Lepore, F.J.Ruzicka, P.A.Frey, and D.Ringe (2005).
The x-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale.
  Proc Natl Acad Sci U S A, 102, 13819-13824.
PDB code: 2a5h
16154351 B.Zheng, C.J.Gerdts, and R.F.Ismagilov (2005).
Using nanoliter plugs in microfluidics to facilitate and understand protein crystallization.
  Curr Opin Struct Biol, 15, 548-555.  
15952888 D.C.Johnson, D.R.Dean, A.D.Smith, and M.K.Johnson (2005).
Structure, function, and formation of biological iron-sulfur clusters.
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15911379 E.Choi-Rhee, and J.E.Cronan (2005).
A nucleosidase required for in vivo function of the S-adenosyl-L-methionine radical enzyme, biotin synthase.
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16218869 G.Layer, E.Kervio, G.Morlock, D.W.Heinz, D.Jahn, J.Retey, and W.D.Schubert (2005).
Structural and functional comparison of HemN to other radical SAM enzymes.
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15951221 J.Balk, and S.Lobréaux (2005).
Biogenesis of iron-sulfur proteins in plants.
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16178037 S.Gambarelli, F.Luttringer, D.Padovani, E.Mulliez, and M.Fontecave (2005).
Activation of the anaerobic ribonucleotide reductase by S-adenosylmethionine.
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Removing a bottleneck in the Bacillus subtilis biotin pathway: bioA utilizes lysine rather than S-adenosylmethionine as the amino donor in the KAPA-to-DAPA reaction.
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16218870 T.Selmer, A.J.Pierik, and J.Heider (2005).
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16216579 W.Shi, C.Zhan, A.Ignatov, B.A.Manjasetty, N.Marinkovic, M.Sullivan, R.Huang, and M.R.Chance (2005).
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A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase.
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PDB code: 1xrs
15317939 P.Hänzelmann, and H.Schindelin (2004).
Crystal structure of the S-adenosylmethionine-dependent enzyme MoaA and its implications for molybdenum cofactor deficiency in humans.
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PDB codes: 1tv7 1tv8
15181002 S.Agarwalla, R.M.Stroud, and B.J.Gaffney (2004).
Redox reactions of the iron-sulfur cluster in a ribosomal RNA methyltransferase, RumA: optical and EPR studies.
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15278785 S.Ollagnier-de-Choudens, Y.Sanakis, and M.Fontecave (2004).
SufA/IscA: reactivity studies of a class of scaffold proteins involved in [Fe-S] cluster assembly.
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15289575 Y.Nicolet, and C.L.Drennan (2004).
AdoMet radical proteins--from structure to evolution--alignment of divergent protein sequences reveals strong secondary structure element conservation.
  Nucleic Acids Res, 32, 4015-4025.  
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.