4xn3

X-ray diffraction
1.65Å resolution

Tailspike protein mutant E372A of E. coli bacteriophage HK620 in complex with hexasaccharide

Released:
Source organism: Salmonella virus HK620
Entry authors: Gohlke U, Broeker NK, Heinemann U, Seckler R, Barbirz S

Function and Biology Details

Reactions catalysed:
L-cystathionine + H(2)O = L-homocysteine + NH(3) + pyruvate
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate = (S)-allantoin + CO(2)
Acyl-[acyl-carrier-protein] + malonyl-[acyl-carrier-protein] = 3-oxoacyl-[acyl-carrier-protein] + CO(2) + [acyl-carrier-protein]
ATP = 3',5'-cyclic AMP + diphosphate
Acetyl-CoA + H(2)O + oxaloacetate = citrate + CoA
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.
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
L-alanine + H(2)O + NAD(+) = pyruvate + NH(3) + NADH
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).
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
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.
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
ATP-dependent cleavage of peptide bonds with broad specificity.
Nicotinate + 5-phospho-alpha-D-ribose 1-diphosphate + ATP + H(2)O = beta-nicotinate D-ribonucleotide + diphosphate + ADP + phosphate
Thioredoxin + ROOH = thioredoxin disulfide + H(2)O + ROH
Trans,octacis-decaprenylphospho-beta-D-ribofuranose + FAD = trans,octacis-decaprenylphospho-beta-D-erythro-pentofuranosid-2-ulose + FADH(2)
NADH + ROOH + H(+) = NAD(+) + H(2)O + ROH
2 H(2)O(2) = O(2) + 2 H(2)O
ATP + a protein = ADP + a phosphoprotein
Endopeptidase with a preference for cleavage when the P1 position is occupied by Glu-|- and the P1' position is occupied by Gly-|-
NAD(+) + diphthamide-[translation elongation factor 2] = nicotinamide + N-(ADP-D-ribosyl)diphthamide-[translation elongation factor 2]
D-glucarate = 5-dehydro-4-deoxy-D-glucarate + H(2)O
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
N-(5-phospho-D-ribosyl)-anthranilate + diphosphate = anthranilate + 5-phospho-alpha-D-ribose 1-diphosphate
NTP + H(2)O = NDP + phosphate
Maleate = fumarate
Orotidine 5'-phosphate = UMP + CO(2)
5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole = 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate
(1a) L-cystathionine = L-cysteine + 2-aminobut-2-enoate
ATP + H(2)O + cellular protein(Side 1) = ADP + phosphate + cellular protein(Side 2)
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.
Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates
UDP-alpha-D-galactopyranose = UDP-alpha-D-galactofuranose
5-methyltetrahydrofolate + NAD(P)(+) = 5,10-methylenetetrahydrofolate + NAD(P)H
N-acetyl-L-glutamate 5-semialdehyde + NADP(+) + phosphate = N-acetyl-L-glutamyl 5-phosphate + NADPH
ATP-dependent breakage, passage and rejoining of double-stranded DNA
ATP + H(2)O = ADP + phosphate
2-hydroxy-4-oxobutane-1,2,4-tricarboxylate = oxaloacetate + pyruvate
RH + [reduced NADPH--hemoprotein reductase] + O(2) = ROH + [oxidized NADPH--hemoprotein reductase] + H(2)O
Creatinine + H(2)O = creatine
Release of N-terminal proline from a peptide.
Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans
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.
(3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O
3-deoxy-D-manno-octulosonate 8-phosphate + H(2)O = 3-deoxy-D-manno-octulosonate + phosphate
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
(+)-muconolactone = 5-oxo-4,5-dihydrofuran-2-acetate
3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate = urocanate + H(2)O
O-phospho-L(or D)-serine + H(2)O = L(or D)-serine + phosphate
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.
Leu is conserved at position P1 for all four cleavage sites. Alanine is found at position P1' of the NS4A-NS4B cleavage site, whereas serine is found at position P1' of the NS3-NS4A, NS4B-NS5A and NS5A-NS5B cleavage sites
Cleavage of hydrophobic, N-terminal signal or leader sequences from secreted and periplasmic proteins.
ATP + benzoate + CoA = AMP + diphosphate + benzoyl-CoA
Hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactolipids
Hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides
Acetyl-CoA + malonyl-[acyl-carrier-protein] = acetoacetyl-[acyl-carrier-protein] + CoA + CO(2) 
Exolytic cleavage of the (1->4)-beta-glycosidic linkage between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) residues in peptidoglycan, from either the reducing or the non-reducing ends of the peptidoglycan chains, with concomitant formation of a 1,6-anhydrobond in the MurNAc residue.
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
(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
Release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.
A beta-lactam + H(2)O = a substituted beta-amino acid
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
1-O-(2-acetamido-2-deoxy-alpha-D-glucopyranosyl)-1D-myo-inositol + H(2)O = 1-O-(2-amino-2-deoxy-alpha-D-glucopyranosyl)-1D-myo-inositol + acetate
(1a) 2 Fe(2+) + O(2) + 4 H(2)O = 2 (FeO(OH)) + 4 H(+) + H(2)O(2)
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
ATP + [DNA-directed RNA polymerase] = ADP + [DNA-directed RNA polymerase] phosphate
ATP + L-aspartate = ADP + 4-phospho-L-aspartate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Head_binding domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 596 amino acids
Theoretical weight: 64.19 KDa
Source organism: Salmonella virus HK620
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9AYY6 (Residues: 115-710; Coverage: 84%)
Gene name: 9
Sequence domains: Phage spike trimer
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, NDG, GLA, GLC, RAM
3 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P321
Unit cell:
a: 74.413Å b: 74.413Å c: 174.612Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.143 0.141 0.179
Expression system: Escherichia coli BL21(DE3)