3h9n

X-ray diffraction
2.7Å resolution

Crystal structure of the ribosome maturation factor rimm (hi0203) from h.influenzae. northeast structural genomics consortium target IR66.

Released:
Source organism: Haemophilus influenzae
Entry authors: Kuzin A, Su M, Seetharaman J, Mao M, Xiao R, Maglaqui M, Zhao L, Everett JK, Nair R, Acton TB, Rost B, Montelione GT, Hunt JF, Tong L, Northeast Structural Genomics Consortium (NESG)

Function and Biology Details

Reactions catalysed:
L-arginine + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-arginine + succinate + CO(2)
Autocatalytic release of the core protein from the N-terminus of the togavirus structural polyprotein by hydrolysis of a -Trp-|-Ser- bond.
Acyl-[acyl-carrier-protein] + malonyl-[acyl-carrier-protein] = 3-oxoacyl-[acyl-carrier-protein] + CO(2) + [acyl-carrier-protein]
ATP = 3',5'-cyclic AMP + diphosphate
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.
D-xylopyranose = D-xylulose
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
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).
ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
Random hydrolysis of (1->4)-beta-D-mannosidic linkages in mannans, galactomannans and glucomannans
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins
1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = ATP + 5-phospho-alpha-D-ribose 1-diphosphate
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
D-glucarate = 5-dehydro-4-deoxy-D-glucarate + H(2)O
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
GDP-beta-L-fucose + NADP(+) = GDP-4-dehydro-alpha-D-rhamnose + NADPH
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'.
Naphthalene + NADH + O(2) = (1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD(+)
(S)-dihydroorotate + fumarate = orotate + succinate
Selective cleavage of Tyr-|-Gly bond in picornavirus polyprotein.
5-methyltetrahydrofolate + NAD(P)(+) = 5,10-methylenetetrahydrofolate + NAD(P)H
2 bilirubin + O(2) = 2 biliverdin + 2 H(2)O
ATP + H(2)O = ADP + phosphate
Acyl-CoA + H(2)O = CoA + a carboxylate
NTP + H(2)O = NDP + phosphate
Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans
4 benzenediol + O(2) = 4 benzosemiquinone + 2 H(2)O
(S)-3-hydroxyacyl-CoA + NAD(+) = 3-oxoacyl-CoA + NADH
L-aspartate 4-semialdehyde + phosphate + NADP(+) = L-4-aspartyl phosphate + NADPH
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
AMP + H(2)O = D-ribose 5-phosphate + adenine
dUTP + H(2)O = dUMP + diphosphate
Cleavage of peptide bonds with very broad specificity.
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
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.
ATP + thymidine = ADP + thymidine 5'-phosphate
4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
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).
A beta-lactam + H(2)O = a substituted beta-amino acid
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
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.
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
2 3-phospho-D-glycerate + 2 H(+) = D-ribulose 1,5-bisphosphate + CO(2) + H(2)O
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo trimer
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribosome maturation factor RimM Chain: A
Molecule details ›
Chain: A
Length: 177 amino acids
Theoretical weight: 20.64 KDa
Source organism: Haemophilus influenzae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P44568 (Residues: 8-178; Coverage: 96%)
Gene names: HI_0203, rimM
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4A
Spacegroup: I213
Unit cell:
a: 129.642Å b: 129.642Å c: 129.642Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.211 0.211 0.237
Expression system: Escherichia coli BL21(DE3)