PDBsum entry 1r30

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Transferase PDB id
Protein chains
312 a.a. *
SAM ×2
SF4 ×2
FES ×2
DTB ×2
* Residue conservation analysis
PDB id:
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)
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
30-Sep-03     Release date:   13-Jan-04    
Go to PROCHECK summary

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

 Enzyme reactions 
   Enzyme class: E.C.  - 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
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
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
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  


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.
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

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PDB code: 2qgq
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PDB codes: 3lzc 3lzd
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PDB codes: 3iix 3iiz
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PDB codes: 3epm 3epn 3epo
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PDB codes: 2isj 2isk 2isl
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PDB codes: 2pu9 2puk 2puo 2pvd 2pvg 2pvo
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PDB code: 2yx0
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Substrate recognition, protein dynamics, and iron-sulfur cluster in Pseudomonas aeruginosa adenosine 5'-phosphosulfate reductase.
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PDB code: 2goy
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Stereochemistry of guanidine-metal interactions: implications for L-arginine-metal interactions in protein structure and function.
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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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Binding of 5'-GTP to the C-terminal FeS cluster of the radical S-adenosylmethionine enzyme MoaA provides insights into its mechanism.
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PDB codes: 2fb2 2fb3
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On the accuracy of density functional theory for iron-sulfur clusters.
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Cofactor biosynthesis: an organic chemist's treasure trove.
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The x-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale.
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PDB code: 2a5h
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Using nanoliter plugs in microfluidics to facilitate and understand protein crystallization.
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A nucleosidase required for in vivo function of the S-adenosyl-L-methionine radical enzyme, biotin synthase.
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Biogenesis of iron-sulfur proteins in plants.
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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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PDB code: 1xrs
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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
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AdoMet radical proteins--from structure to evolution--alignment of divergent protein sequences reveals strong secondary structure element conservation.
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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.