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PDBsum entry 1bib

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protein ligands links
Transcription regulation PDB id
1bib
Jmol
Contents
Protein chain
294 a.a. *
Ligands
BTN
Waters ×19
* Residue conservation analysis
PDB id:
1bib
Name: Transcription regulation
Title: The e. Coli biotin holoenzyme synthetase(slash)bio repressor crystal structure delineates the biotin and DNA- binding domains
Structure: Bir a. Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562
Resolution:
2.80Å     R-factor:   0.173    
Authors: K.P.Wilson,L.M.Shewchuk,B.W.Matthews
Key ref: K.P.Wilson et al. (1992). Escherichia coli biotin holoenzyme synthetase/bio repressor crystal structure delineates the biotin- and DNA-binding domains. Proc Natl Acad Sci U S A, 89, 9257-9261. PubMed id: 1409631 DOI: 10.1073/pnas.89.19.9257
Date:
06-Jul-92     Release date:   31-Oct-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06709  (BIRA_ECOLI) -  Bifunctional ligase/repressor BirA
Seq:
Struc:
321 a.a.
294 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.3.4.15  - Biotin--[acetyl-CoA-carboxylase] ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + biotin + apo-[acetyl-CoA:carbon-dioxide ligase (ADP-forming)] = AMP + diphosphate + [acetyl-CoA:carbon-dioxide ligase (ADP-forming)]
ATP
+
biotin
Bound ligand (Het Group name = BTN)
corresponds exactly
+ apo-[acetyl-CoA:carbon-dioxide ligase (ADP-forming)]
= AMP
+ diphosphate
+ [acetyl-CoA:carbon-dioxide ligase (ADP-forming)]
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     biotin biosynthetic process   5 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.89.19.9257 Proc Natl Acad Sci U S A 89:9257-9261 (1992)
PubMed id: 1409631  
 
 
Escherichia coli biotin holoenzyme synthetase/bio repressor crystal structure delineates the biotin- and DNA-binding domains.
K.P.Wilson, L.M.Shewchuk, R.G.Brennan, A.J.Otsuka, B.W.Matthews.
 
  ABSTRACT  
 
The three-dimensional structure of BirA, the repressor of the Escherichia coli biotin biosynthetic operon, has been determined by x-ray crystallography and refined to a crystallographic residual of 19.0% at 2.3-A resolution. BirA is a sequence-specific DNA-binding protein that also catalyzes the formation of biotinyl-5'-adenylate from biotin and ATP and transfers the biotin moiety to other proteins. The level of biotin biosynthetic enzymes in the cell is controlled by the amount of biotinyl-5'-adenylate, which is the BirA corepressor. The structure provides an example of a transcription factor that is also an enzyme. The structure of BirA is highly asymmetric and consists of three domains. The N-terminal domain is mostly alpha-helical, contains a helix-turn-helix DNA-binding motif, and is loosely connected to the remainder of the molecule. The central domain consists of a seven-stranded mixed beta-sheet with alpha-helices covering one face. The other side of the sheet is largely solvent-exposed and contains the active site. The C-terminal domain comprises a six-stranded, antiparallel beta-sheet sandwich. The location of biotin binding is consistent with mutations that affect enzymatic activity. A nearby loop has a sequence that has been associated with phosphate binding in other proteins. It is inferred that ATP binds in this region, adjacent to the biotin. It is proposed that the binding of corepressor to monomeric BirA may promote DNA binding by facilitating the formation of a multimeric BirA-corepressor-DNA complex. The structural details of this complex remain an open question, however.
 

Literature references that cite this PDB file's key reference

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PDB code: 1dpr
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Searching protein structure databases has come of age.
  Proteins, 19, 165-173.  
  8076591 R.H.Fogh, G.Ottleben, H.Rüterjans, M.Schnarr, R.Boelens, and R.Kaptein (1994).
Solution structure of the LexA repressor DNA binding domain determined by 1H NMR spectroscopy.
  EMBO J, 13, 3936-3944.
PDB codes: 1lea 1leb
7881904 R.T.Clubb, J.G.Omichinski, H.Savilahti, K.Mizuuchi, A.M.Gronenborn, and G.M.Clore (1994).
A novel class of winged helix-turn-helix protein: the DNA-binding domain of Mu transposase.
  Structure, 2, 1041-1048.
PDB codes: 1tns 1tnt
  7687536 M.E.Noble, A.Musacchio, M.Saraste, S.A.Courtneidge, and R.K.Wierenga (1993).
Crystal structure of the SH3 domain in human Fyn; comparison of the three-dimensional structures of SH3 domains in tyrosine kinases and spectrin.
  EMBO J, 12, 2617-2624.
PDB code: 1shf
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.