1u8c

X-ray diffraction
3.1Å resolution

A novel adaptation of the integrin PSI domain revealed from its crystal structure

Released:
Source organism: Homo sapiens

Function and Biology Details

Reactions catalysed:
2 ATP = 2 diphosphate + cyclic di-3',5'-adenylate
RX + glutathione = HX + R-S-glutathione
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
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.
(1a) L-cysteine + [enzyme]-cysteine = L-alanine + [enzyme]-S-sulfanylcysteine
Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil
Shikimate + NADP(+) = 3-dehydroshikimate + NADPH
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.
(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
Autocatalytic release of the core protein from the N-terminus of the togavirus structural polyprotein by hydrolysis of a -Trp-|-Ser- bond.
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.
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
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
2'-deoxycytidine + H(2)O = 2'-deoxyuridine + NH(3)
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.
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
ATP + RNA(n) = diphosphate + RNA(n+1)
TSAVLQ-|-SGFRK-NH(2) and SGVTFQ-|-GKFKK the two peptides corresponding to the two self-cleavage sites of the SARS 3C-like proteinase are the two most reactive peptide substrates. The enzyme exhibits a strong preference for substrates containing Gln at P1 position and Leu at P2 position.
ATP + glycerol = ADP + sn-glycerol 3-phosphate
Cutin + H(2)O = cutin monomers
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
Release of N-terminal proline from a peptide.
ATP + [protein]-L-threonine = diphosphate + [protein]-O(4)-(5'-adenylyl)-L-threonine
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.
Selective cleavage of Tyr-|-Gly bond in picornavirus polyprotein.
Acetyl-CoA + L-serine = CoA + O-acetyl-L-serine
ADP-alpha-D-glucose + D-glucose 6-phosphate = ADP + alpha,alpha-trehalose 6-phosphate
(2E,6E)-farnesyl diphosphate + isopentenyl diphosphate = diphosphate + geranylgeranyl diphosphate
NTP + H(2)O = NDP + phosphate
4 benzenediol + O(2) = 4 benzosemiquinone + 2 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.
L-lysine + NADPH + O(2) = N(6)-hydroxy-L-lysine + NADP(+) + H(2)O
17-alpha-hydroxypregnenolone + [reduced NADPH--hemoprotein reductase] + O(2) = 3-beta-hydroxyandrost-5-en-17-one + acetate + [oxidized NADPH--hemoprotein reductase] + H(2)O
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
Myo-inositol phosphate + H(2)O = myo-inositol + phosphate
A C(21)-steroid + [reduced NADPH--hemoprotein reductase] + O(2) = a 17-alpha-hydroxy-C(21)-steroid + [oxidized NADPH--hemoprotein reductase] + H(2)O
Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Diphosphate + H(2)O = 2 phosphate
Hydrolysis of terminal, non-reducing beta-D-glucosyl residues with release of beta-D-glucose
L-aspartate = D-aspartate
ATP + H(2)O = ADP + phosphate
Geranylgeranyl diphosphate = (+)-copalyl diphosphate
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)
L-histidine-[translation elongation factor 2] + S-adenosyl-L-methionine = 2-((3S)-3-amino-3-carboxypropyl)-L-histidine-[translation elongation factor 2] + S-methyl-5'-thioadenosine
Alpha-D-glucose = beta-D-glucose
Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
Glutarate + 2-oxoglutarate + O(2) = (S)-2-hydroxyglutarate + succinate + CO(2)
D-mannose 6-phosphate = D-fructose 6-phosphate
GTP = 3',5'-cyclic GMP + diphosphate
(1a) L-cystathionine = L-cysteine + 2-aminobut-2-enoate
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
D-xylopyranose = D-xylulose
L-arginine + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-arginine + succinate + CO(2)
Sucrose + ((1->6)-alpha-D-glucosyl)(n) = D-fructose + ((1->6)-alpha-D-glucosyl)(n+1)
ATP + a protein = ADP + a phosphoprotein
N-acetyl-O-acetylneuraminate + H(2)O = N-acetylneuraminate + acetate
An aldehyde + NAD(+) + H(2)O = a carboxylate + NADH
L-cystathionine + H(2)O = L-homocysteine + NH(3) + pyruvate
L-aspartate 4-semialdehyde + phosphate + NADP(+) = L-4-aspartyl phosphate + NADPH
ATP + AMP = 2 ADP
2 3-phospho-D-glycerate + 2 H(+) = D-ribulose 1,5-bisphosphate + CO(2) + H(2)O
Arsenate + glutathione + glutaredoxin = arsenite + a glutaredoxin-glutathione disulfide + H(2)O
Peptidylproline (omega=180) = peptidylproline (omega=0)
(3R)-3-hydroxyacyl-[acyl-carrier-protein] + NADP(+) = 3-oxoacyl-[acyl-carrier-protein] + NADPH
1-haloalkane + H(2)O = a primary alcohol + halide
ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
Chorismate = prephenate
ATP + [DNA-directed RNA polymerase] = ADP + [DNA-directed RNA polymerase] phosphate
Eliminative cleavage of alginate to give oligosaccharides with 4-deoxy-alpha-L-erythro-hex-4-enuronosyl groups at their non-reducing ends and beta-D-mannuronate at their reducing end.
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (4 distinct):
Integrin alpha-V Chain: A
Molecule details ›
Chain: A
Length: 957 amino acids
Theoretical weight: 105.88 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P06756 (Residues: 31-987; Coverage: 94%)
Gene names: ITGAV, MSK8, VNRA, VTNR
Sequence domains:
Structure domains:
Integrin beta-3 Chain: B
Molecule details ›
Chain: B
Length: 692 amino acids
Theoretical weight: 76.65 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P05106 (Residues: 27-718; Coverage: 91%)
Gene names: GP3A, ITGB3
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer : NEW Components: NAG, NDG
2 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P3221
Unit cell:
a: 130Å b: 130Å c: 307.3Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.293 0.293 0.367
Expression system: Spodoptera frugiperda