5ond

X-ray diffraction
2.1Å resolution

Function and Biology Details

Reactions catalysed:
(R)-2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + NADH
L-arginine + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-arginine + succinate + CO(2)
A phenyl acetate + H(2)O = a phenol + acetate
AMP + H(2)O = D-ribose 5-phosphate + adenine
(R)-mandelonitrile = cyanide + benzaldehyde
Acyl-[acyl-carrier-protein] + malonyl-[acyl-carrier-protein] = 3-oxoacyl-[acyl-carrier-protein] + CO(2) + [acyl-carrier-protein]
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
RX + glutathione = HX + R-S-glutathione
An alpha-L-fucoside + H(2)O = L-fucose + an alcohol
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
Peptidylproline (omega=180) = peptidylproline (omega=0)
ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Hydrolysis of four peptide bonds in the viral precursor polyprotein, commonly with Asp or Glu in the P6 position, Cys or Thr in P1 and Ser or Ala in P1'.
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
UDP-alpha-D-glucose = UDP-alpha-D-galactose
NH(3) + 2 H(2)O + 6 ferricytochrome c = nitrite + 6 ferrocytochrome c + 7 H(+)
ATP + glycerol = ADP + sn-glycerol 3-phosphate
3-phospho-D-glycerate + NAD(+) = 3-phosphonooxypyruvate + NADH
2 H(2)O(2) = O(2) + 2 H(2)O
(S)-dihydroorotate + fumarate = orotate + succinate
S-adenosyl-L-methionine + adenine in DNA = S-adenosyl-L-homocysteine + N-6-methyladenine in DNA 
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
ATP-dependent breakage, passage and rejoining of double-stranded DNA
(R)-propane-1,2-diol + NAD(+) = (R)-lactaldehyde + NADH
Hydrolyzes poly(ADP-D-ribose) at glycosidic (1''-2') linkage of ribose-ribose bond to produce free ADP-D-ribose
NTP + H(2)O = NDP + phosphate
4 benzenediol + O(2) = 4 benzosemiquinone + 2 H(2)O
D-glyceraldehyde 3-phosphate + phosphate + NAD(+) = 3-phospho-D-glyceroyl phosphate + NADH
1-haloalkane + H(2)O = a primary alcohol + halide
Palmitoyl-CoA + H(2)O = CoA + palmitate
2-lysophosphatidylcholine + H(2)O = glycerophosphocholine + a carboxylate
Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. Alpha-Casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec; and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also occurs).
Oleoyl-[acyl-carrier-protein] + H(2)O = [acyl-carrier-protein] + oleate
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
Cleavage of peptide bonds with very broad specificity.
ATP-dependent cleavage of peptide bonds with broad specificity.
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.
A 2'-deoxyribonucleoside 5'-monophosphate + H(2)O = a 2'-deoxyribonucleoside + phosphate
5-methyltetrahydrofolate + NAD(P)(+) = 5,10-methylenetetrahydrofolate + NAD(P)H
L-lysine + NADPH + O(2) = N(6)-hydroxy-L-lysine + NADP(+) + H(2)O
Selective cleavage of Tyr-|-Gly bond in picornavirus polyprotein.
ATP + H(2)O = ADP + phosphate
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
L-glutaminyl-peptide = 5-oxoprolyl-peptide + NH(3)
Biochemical function:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Transcription antitermination protein RfaH Chains: A, B
Molecule details ›
Chains: A, B
Length: 162 amino acids
Theoretical weight: 18.32 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0AFW0 (Residues: 1-162; Coverage: 100%)
Gene names: JW3818, b3842, hlyT, rfaH, sfrB
Sequence domains: Transcription termination factor nusG
DNA (5'-D(*GP*CP*GP*GP*TP*AP*GP*TP*C)-3') Chains: C, D
Molecule details ›
Chains: C, D
Length: 9 nucleotides
Theoretical weight: 2.77 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P1
Unit cell:
a: 36.31Å b: 43.19Å c: 61.86Å
α: 80.45° β: 75.48° γ: 75.39°
R-values:
R R work R free
0.189 0.186 0.233
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided