1QJ5

Crystal structure of 7,8-diaminopelargonic acid synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal Structure of Diaminopelargonic Acid Synthase; Evolutionary Relationships between Pyridoxal-5'-Phosphate Dependent Enzymes

Kack, H.Sandmark, J.Gibson, K.J.Schneider, G.Lindqvist, Y.

(1999) J.Mol.Biol. 291: 857

  • DOI: 10.1006/jmbi.1999.2997
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The three-dimensional structure of diaminopelargonic acid synthase, a vitamin B6-dependent enzyme in the pathway of the biosynthesis of biotin, has been determined to 1.8 A resolution by X-ray crystallography. The structure was solved by multi-wavele ...

    The three-dimensional structure of diaminopelargonic acid synthase, a vitamin B6-dependent enzyme in the pathway of the biosynthesis of biotin, has been determined to 1.8 A resolution by X-ray crystallography. The structure was solved by multi-wavelength anomalous diffraction techniques using a crystal derivatized with mercury ions. The protein model has been refined to a crystallographic R -value of 17.5% (R -free 22.6%). Each enzyme subunit consists of two domains, a large domain (residues 50-329) containing a seven-stranded predominantly parallel beta-sheet, surrounded by alpha-helices, and a small domain comprising residues 1-49 and 330-429. Two subunits, related by a non-crystallographic dyad in the crystals, form the homodimeric molecule, which contains two equal active sites. Pyridoxal-5'-phosphate is bound in a cleft formed by both domains of one subunit and the large domain of the second subunit. The cofactor is anchored to the enzyme by a covalent linkage to the side-chain of the invariant residue Lys274. The phosphate group interacts with main-chain nitrogen atoms and the side-chain of Ser113, located at the N terminus of an alpha-helix. The pyridine nitrogen forms a hydrogen bond to the side-chain of the invariant residue Asp245. Electron density corresponding to a metal ion, most likely Na(+), was found in a tight turn at the surface of the enzyme. Structure analysis reveals that diaminopelargonic acid synthase belongs to the family of vitamin B6-dependent aminotransferases with the same fold as originally observed in aspartate aminotransferase. A multiple structure alignment of enzymes in this family indicated that they form at least six different subclasses. Striking differences in the fold of the N-terminal part of the polypeptide chain are one of the hallmarks of these subclasses. Diaminopelargonic acid synthase is a member of the aminotransferase subclass III. From the structure of the non-productive complex of the holoenzyme with the substrate 7-keto-8-aminopelargonic acid the location of the active site and residues involved in substrate binding have been identified.


    Organizational Affiliation

    Division of Structural Biology Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Doktorsringen 9, Stockholm, S-171 77, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
7,8-DIAMINOPELARGONIC ACID SYNTHASE
A, B
429Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: bioA
EC: 2.6.1.62
Find proteins for P12995 (Escherichia coli (strain K12))
Go to UniProtKB:  P12995
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, B
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 58.338α = 90.00
b = 55.556β = 96.97
c = 120.884γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
CCP4phasing
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-06-22
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-10-24
    Type: Data collection, Source and taxonomy
  • Version 1.4: 2019-07-10
    Type: Data collection, Derived calculations