5hv0

X-ray diffraction
1.63Å resolution

Structural Analysis of Cofactor Binding of a Prolyl 4-Hydroxylase from the Pathogenic Bacterium Bacillus anthracis

Released:
Source organism: Bacillus anthracis

Function and Biology Details

Reactions catalysed:
Triacylglycerol + H(2)O = diacylglycerol + a carboxylate
2 bilirubin + O(2) = 2 biliverdin + 2 H(2)O
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
Acetyl-CoA + a 2-deoxystreptamine antibiotic = CoA + N(3)-acetyl-2-deoxystreptamine antibiotic
(S)-lactate + NAD(+) = pyruvate + NADH
Myo-inositol phosphate + H(2)O = myo-inositol + phosphate
(1a) S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [HECT-type E3 ubiquitin transferase]-L-cysteine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + S-ubiquitinyl-[HECT-type E3 ubiquitin transferase]-L-cysteine
Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides
Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)- glycosidic linkages of terminal sialic acid residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
L-glutamate + H(2)O + NAD(+) = 2-oxoglutarate + NH(3) + NADH
Autocatalytic release of the core protein from the N-terminus of the togavirus structural polyprotein by hydrolysis of a -Trp-|-Ser- bond.
Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
Hydrolyzes glutaminyl bonds, and activity is further restricted by preferences for the amino acids in P6 - P1' that vary with the species of potyvirus, e.g. Glu-Xaa-Xaa-Tyr-Xaa-Gln-|-(Ser or Gly) for the enzyme from tobacco etch virus. The natural substrate is the viral polyprotein, but other proteins and oligopeptides containing the appropriate consensus sequence are also cleaved.
Hydrolyzes a Gly-|-Gly bond at its own C-terminus, commonly in the sequence -Tyr-Xaa-Val-Gly-|-Gly, in the processing of the potyviral polyprotein.
2 glutathione + ROOH = glutathione disulfide + H(2)O + ROH
ATP + a protein = ADP + a phosphoprotein
Hydrolysis of terminal, non-reducing branched (1->3)-alpha-D-galactosidic residues, producing free D-galactose
Cutin + H(2)O = cutin monomers
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.
Release of N-terminal proline from a peptide.
Hydrolysis of --Pro-|- and to a lesser extent --Ala-|- in oligopeptides.
NTP + H(2)O = NDP + phosphate
An aldehyde + NAD(P)(+) + H(2)O = a carboxylate + NAD(P)H
Selective cleavage of Tyr-|-Gly bond in picornavirus polyprotein.
Acetyl-CoA + L-serine = CoA + O-acetyl-L-serine
Diphosphate + H(2)O = 2 phosphate
(R)-3-hydroxybutanoate + NAD(+) = acetoacetate + NADH
Release of an N-terminal amino acid, Xaa-|-Yaa-, in which Xaa is preferably Leu, but may be other amino acids including Pro although not Arg or Lys, and Yaa may be Pro. Amino acid amides and methyl esters are also readily hydrolyzed, but rates on arylamides are exceedingly low.
(1a) (2R,3S)-3-isopropylmalate = 2-isopropylmaleate + H(2)O
ATP + AMP = 2 ADP
Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
ADP-alpha-D-glucose + D-glucose 6-phosphate = ADP + alpha,alpha-trehalose 6-phosphate
Hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactolipids
Hydrolysis of terminal, non-reducing beta-D-mannose residues in beta-D-mannosides
ATP + H(2)O = ADP + phosphate
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
(R)-pantoate + NADP(+) = 2-dehydropantoate + NADPH
A beta-lactam + H(2)O = a substituted beta-amino acid
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
6-phospho-D-gluconate + NADP(+) = D-ribulose 5-phosphate + CO(2) + NADPH
2 3-phospho-D-glycerate + 2 H(+) = D-ribulose 1,5-bisphosphate + CO(2) + H(2)O
(1a) L-cysteine + [enzyme]-cysteine = L-alanine + [enzyme]-S-sulfanylcysteine
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Fe2OG dioxygenase domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 217 amino acids
Theoretical weight: 24.71 KDa
Source organism: Bacillus anthracis
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A4Y1WAP5 (Residues: 2-216; Coverage: 100%)
Gene name: GBAA_4459
Sequence domains: 2OG-Fe(II) oxygenase superfamily
Structure domains: q2cbj1_9rhob like domain

Ligands and Environments

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 4.2.2
Spacegroup: P3
Unit cell:
a: 90.336Å b: 90.336Å c: 51.423Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.176 0.174 0.215
Expression system: Escherichia coli