4xdx

X-ray diffraction
0.95Å resolution

The crystal structure of soluble human interleukin 8 expressed in Pichia pastoris

Released:
Source organism: Homo sapiens
Entry authors: Ostrov DA, Pompeu YA, Jakoncic JJ

Function and Biology Details

Reactions catalysed:
2-lysophosphatidylcholine + H(2)O = glycerophosphocholine + a carboxylate
A phenyl acetate + H(2)O = a phenol + acetate
ATP = 3',5'-cyclic AMP + diphosphate
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.
Acetyl-CoA + [protein]-L-lysine = CoA + [protein]-N(6)-acetyl-L-lysine
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.
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
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.
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = ATP + 5-phospho-alpha-D-ribose 1-diphosphate
D-tagatose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate
NH(3) + 2 H(2)O + 6 ferricytochrome c = nitrite + 6 ferrocytochrome c + 7 H(+)
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
(R)-2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + NADH
3-phospho-D-glycerate + NAD(+) = 3-phosphonooxypyruvate + NADH
ATP + propanoyl-CoA + HCO(3)(-) = ADP + phosphate + (S)-methylmalonyl-CoA
N-acetyl-O-acetylneuraminate + H(2)O = N-acetylneuraminate + acetate
Reduced riboflavin + NAD(P)(+) = riboflavin + NAD(P)H
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.
Diphosphate + H(2)O = 2 phosphate
ATP-dependent breakage, passage and rejoining of double-stranded DNA
ATP + H(2)O = ADP + phosphate
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
ATP + succinate + CoA = ADP + phosphate + succinyl-CoA
NTP + H(2)O = NDP + phosphate
ATP + H(2)O + cellular protein(Side 1) = ADP + phosphate + cellular protein(Side 2)
Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H(2)O
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
Autocatalytically cleaves itself from the polyprotein of the foot-and-mouth disease virus by hydrolysis of a Lys-|-Gly bond, but then cleaves host cell initiation factor eIF-4G at bonds -Gly-|-Arg- and -Lys-|-Arg-.
ATP + acetyl-CoA + HCO(3)(-) = ADP + phosphate + malonyl-CoA
Palmitoyl-CoA + H(2)O = CoA + palmitate
AMP + H(2)O = D-ribose 5-phosphate + adenine
L-methionine + thioredoxin disulfide + H(2)O = L-methionine (S)-S-oxide + thioredoxin
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
ATP + H(2)O + vitamin B12-[cobalamin-binding protein](Side 1) = ADP + phosphate + vitamin B12(Side 2) + [cobalamin-binding protein](Side 1)
5'-deoxyadenosine + H(2)O = 5-deoxy-D-ribose + adenine
Maltose = alpha,alpha-trehalose
A 2'-deoxyribonucleoside 5'-monophosphate + H(2)O = a 2'-deoxyribonucleoside + phosphate
Blasticidin S + H(2)O = deaminohydroxyblasticidin S + NH(3)
L-lysine + NADPH + O(2) = N(6)-hydroxy-L-lysine + NADP(+) + H(2)O
Eliminative cleavage of (1->4)-alpha-D-galacturonan to give oligosaccharides with 4-deoxy-alpha-D-galact-4-enuronosyl groups at their non-reducing ends
ATP + thymidine = ADP + thymidine 5'-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
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.
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).
Preferential cleavage at the carboxyl of hydrophobic amino acids, but fails to cleave 15-Leu-|-Tyr-16, 16-Tyr-|-Leu-17 and 24-Phe-|-Phe-25 of insulin B chain. Activates trypsinogen, and degrades keratin.
4 benzenediol + O(2) = 4 benzosemiquinone + 2 H(2)O
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Oleoyl-[acyl-carrier-protein] + H(2)O = [acyl-carrier-protein] + oleate
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
IL-8(8-77) Chain: A
Molecule details ›
Chain: A
Length: 70 amino acids
Theoretical weight: 8.24 KDa
Source organism: Homo sapiens
Expression system: Komagataella pastoris
UniProt:
  • Canonical: P10145 (Residues: 30-99; Coverage: 89%)
Gene names: CXCL8, IL8
Sequence domains: Small cytokines (intecrine/chemokine), interleukin-8 like
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X6A
Spacegroup: P3121
Unit cell:
a: 40.093Å b: 40.093Å c: 89.269Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.122 0.121 0.136
Expression system: Komagataella pastoris