2rbb

X-ray diffraction
1.82Å resolution

Crystal structure of a glyoxalase/bleomycin resistance protein/dioxygenase family enzyme from Burkholderia phytofirmans PsJN

Released:
Entry authors: Rao KN, Sauder JM, Burley SK, Swaminathan S, New York SGX Research Center for Structural Genomics (NYSGXRC)

Function and Biology Details

Reactions catalysed:
dUTP + H(2)O = dUMP + diphosphate
L-lysine + NADPH + O(2) = N(6)-hydroxy-L-lysine + NADP(+) + H(2)O
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
5-hydroxyisourate + H(2)O = 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate
NTP + H(2)O = NDP + phosphate
ATP + H(2)O = ADP + phosphate
Acts on substrates that are at least partially unfolded. The cleavage site P1 residue is normally between a pair of hydrophobic residues, such as Val-|-Val
(S)-3-hydroxyacyl-CoA + NAD(+) = 3-oxoacyl-CoA + NADH
Isocitrate = succinate + glyoxylate
(3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O
D-xylopyranose = D-xylulose
(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)(+) + H(2)O = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H
2 nitric oxide + 2 O(2) + NAD(P)H = 2 nitrate + NAD(P)(+) + H(+)
ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
Selective hydrolysis of -Xaa-Xaa-|-Yaa- bonds in which each of the Xaa can be either Arg or Lys and Yaa can be either Ser or Ala.
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
(S)-dihydroorotate + fumarate = orotate + succinate
ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
S-adenosyl-L-methionine + a catechol = S-adenosyl-L-homocysteine + a guaiacol
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glyoxalase_6 domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 141 amino acids
Theoretical weight: 16.33 KDa
Source organism: Paraburkholderia phytofirmans PsJN
Expression system: Escherichia coli
UniProt:
  • Canonical: B2TEV0 (Residues: 1-128; Coverage: 99%)
Gene name: Bphyt_4242
Sequence domains: Glyoxalase-like domain
Structure domains: 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

Ligands and Environments

No bound ligands
1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P42212
Unit cell:
a: 83.23Å b: 83.23Å c: 99.59Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.239 0.239 0.259
Expression system: Escherichia coli