4iuf

X-ray diffraction
2.75Å resolution

Crystal Structure of Human TDP-43 RRM1 Domain in Complex with a Single-stranded DNA

Released:

Function and Biology Details

Reactions catalysed:
Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine
L-arginine + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-arginine + succinate + CO(2)
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
Random hydrolysis of (1->4)-beta-D-mannosidic linkages in mannans, galactomannans and glucomannans
D-mannose = D-fructose
D-galactose + O(2) = D-galacto-hexodialdose + H(2)O(2)
L-alanine + H(2)O + NAD(+) = pyruvate + NH(3) + NADH
IMP + diphosphate = hypoxanthine + 5-phospho-alpha-D-ribose 1-diphosphate
Autocatalytic release of the core protein from the N-terminus of the togavirus structural polyprotein by hydrolysis of a -Trp-|-Ser- bond.
RX + glutathione = HX + R-S-glutathione
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).
L-glutamate + H(2)O + NADP(+) = 2-oxoglutarate + NH(3) + NADPH
ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
CoA-(4'-phosphopantetheine) + apo-[acyl-carrier-protein] = adenosine 3',5'-bisphosphate + holo-[acyl-carrier-protein]
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
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'.
Trans,octacis-decaprenylphospho-beta-D-ribofuranose + FAD = trans,octacis-decaprenylphospho-beta-D-erythro-pentofuranosid-2-ulose + FADH(2)
tRNA uridine(55) = tRNA pseudouridine(55)
A (3R)-3-hydroxyacyl-[acyl-carrier-protein] + a UDP-3-O-((3R)-hydroxyacyl)-alpha-D-glucosamine = a UDP-2-N,3-O-bis((3R)-3-hydroxyacyl)-alpha-D-glucosamine + a holo-[acyl-carrier-protein]
ATP + (R)-pantoate + beta-alanine = AMP + diphosphate + (R)-pantothenate
ATP + a protein = ADP + a phosphoprotein
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
ATP + (R)-pantothenate = ADP + (R)-4'-phosphopantothenate
ATP + glycerol = ADP + sn-glycerol 3-phosphate
7,8-dihydroneopterin + O(2) = 7,8-dihydroxanthopterin + formate + glycolaldehyde
Isocitrate = succinate + glyoxylate
Hydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose and cellotetraose, releasing cellobiose from the non-reducing ends of the chains
NTP + H(2)O = NDP + phosphate
Succinate + a quinone = fumarate + a quinol
Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans
N(2)-acetyl-L-ornithine + L-glutamate = L-ornithine + N-acetyl-L-glutamate
Selective cleavage of Tyr-|-Gly bond in picornavirus polyprotein.
Acetyl-CoA + L-serine = CoA + O-acetyl-L-serine
S-adenosyl-L-methionine + guanosine(2251) in 23S rRNA = S-adenosyl-L-homocysteine + 2'-O-methylguanosine(2251) in 23S rRNA 
ATP-dependent breakage, passage and rejoining of double-stranded DNA
ATP = 3',5'-cyclic AMP + diphosphate
Isochorismate = salicylate + pyruvate
Release of N-terminal proline from a peptide.
Phosphonoacetaldehyde + H(2)O = acetaldehyde + phosphate
Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H(2)O
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.
7,8-dihydroneopterin = 7,8-dihydromonapterin
2-iminobutanoate + H(2)O = 2-oxobutanoate + NH(3)
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
7,8-dihydroneopterin = 6-hydroxymethyl-7,8-dihydropterin + glycolaldehyde
A primary alcohol + NAD(+) = an aldehyde + NADH
H(2)CO(3) = CO(2) + H(2)O
dUTP + H(2)O = dUMP + diphosphate
Cleavage of peptide bonds with very broad specificity.
Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.
Carbamoyl phosphate + L-aspartate = phosphate + N-carbamoyl-L-aspartate
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.
S-adenosyl-L-homocysteine + H(2)O = L-homocysteine + adenosine
Diphosphate + H(2)O = 2 phosphate
L-lysine + NADPH + O(2) = N(6)-hydroxy-L-lysine + NADP(+) + H(2)O
(1a) L-glutamine + H(2)O = L-glutamate + NH(3)
Hydrolysis of terminal, non-reducing beta-D-mannose residues in beta-D-mannosides
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.
ATP + H(2)O = ADP + phosphate
4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
Isochorismate + H(2)O = (2S,3S)-2,3-dihydroxy-2,3-dihydrobenzoate + pyruvate
(GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala))(n)-diphosphoundecaprenol + GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol = (GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala))(n+1)-diphosphoundecaprenol + undecaprenyl diphosphate
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).
2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + NADPH
Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate
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.
1-deoxy-L-glycero-tetrulose 4-phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(D-ribityl)lumazine + 2 H(2)O + phosphate
Chorismate = isochorismate
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
ATP + protoporphyrin IX + Mg(2+) + H(2)O = ADP + phosphate + Mg-protoporphyrin IX + 2 H(+)
Chorismate = prephenate
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
(1a) L-cysteine + [enzyme]-cysteine = L-alanine + [enzyme]-S-sulfanylcysteine
Biochemical function:
Biological process:
  • not assigned
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):
TAR DNA-binding protein 43 Chain: A
Molecule details ›
Chain: A
Length: 77 amino acids
Theoretical weight: 8.99 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13148 (Residues: 103-179; Coverage: 19%)
Gene names: TARDBP, TDP43
Sequence domains: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
Structure domains: Alpha-Beta Plaits
5'-D(*GP*TP*TP*GP*(XUA)P*GP*CP*GP*T)-3' Chain: B
Molecule details ›
Chain: B
Length: 9 nucleotides
Theoretical weight: 2.88 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL13C1
Spacegroup: P6522
Unit cell:
a: 71.11Å b: 71.11Å c: 101.663Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.212 0.206 0.259
Expression systems:
  • Escherichia coli
  • Not provided