2izw

X-ray diffraction
2.9Å resolution

Crystal structure of Ryegrass Mottle Virus

Released:

Function and Biology Details

Reactions catalysed:
(2S)-2-amino-4-deoxychorismate + H(2)O = (5S,6S)-6-amino-5-hydroxycyclohexa-1,3-diene-1-carboxylate + pyruvate
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
Phosphoenolpyruvate + protein L-histidine = pyruvate + protein N(pi)-phospho-L-histidine
D-galactose + O(2) = D-galacto-hexodialdose + H(2)O(2)
IMP + diphosphate = hypoxanthine + 5-phospho-alpha-D-ribose 1-diphosphate
dUTP + H(2)O = dUMP + diphosphate
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
(8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate = cyclic pyranopterin phosphate + diphosphate
Carbamoyl phosphate + L-ornithine = phosphate + L-citrulline
2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + CMP
S-adenosyl-L-methionine + guanine(1405) in 16S rRNA = S-adenosyl-L-homocysteine + N(7)-methylguanine(1405) in 16S rRNA 
ATP + a protein = ADP + a phosphoprotein
(R)-2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + NADH
Beta-nicotinate D-ribonucleotide + diphosphate + CO(2) = pyridine-2,3-dicarboxylate + 5-phospho-alpha-D-ribose 1-diphosphate
N-(5-phospho-D-ribosyl)-anthranilate + diphosphate = anthranilate + 5-phospho-alpha-D-ribose 1-diphosphate
S-adenosyl-L-methionine + phospholipid olefinic fatty acid = S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid
3-phospho-D-glycerate + NAD(+) = 3-phosphonooxypyruvate + NADH
Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates
ATP-dependent breakage, passage and rejoining of double-stranded DNA
ATP = 3',5'-cyclic AMP + diphosphate
(1a) ATP + a long-chain fatty acid = diphosphate + a long-chain acyl-adenylate ester
Release of N-terminal proline from a peptide.
10-formyltetrahydrofolate + H(2)O = formate + tetrahydrofolate
GTP + H(2)O = GDP + phosphate
7,8-dihydroneopterin = 7,8-dihydromonapterin
Isochorismate + H(2)O = (2S,3S)-2,3-dihydroxy-2,3-dihydrobenzoate + pyruvate
A phosphate monoester + H(2)O = an alcohol + phosphate
O-phospho-L(or D)-serine + H(2)O = L(or D)-serine + phosphate
Cleavage of peptide bonds with very broad specificity.
ATP-dependent cleavage of peptide bonds with broad specificity.
Carbamoyl phosphate + L-aspartate = phosphate + N-carbamoyl-L-aspartate
N(2)-acetyl-L-ornithine + L-glutamate = L-ornithine + N-acetyl-L-glutamate
Diphosphate + H(2)O = 2 phosphate
L-lysine + NADPH + O(2) = N(6)-hydroxy-L-lysine + NADP(+) + H(2)O
Selective cleavage of Tyr-|-Gly bond in picornavirus polyprotein.
A nucleoside triphosphate + H(2)O = a nucleotide + diphosphate
4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
4 benzenediol + O(2) = 4 benzosemiquinone + 2 H(2)O
N-substituted aminoacyl-tRNA + H(2)O = N-substituted amino acid + tRNA
(1a) L-tyrosine + 1/2 O(2) = L-dopa
Chorismate = prephenate
L-asparagine + H(2)O = L-aspartate + NH(3)
2-lysophosphatidylcholine + H(2)O = glycerophosphocholine + a carboxylate
A phenyl acetate + H(2)O = a phenol + acetate
Acyl-[acyl-carrier-protein] + malonyl-[acyl-carrier-protein] = 3-oxoacyl-[acyl-carrier-protein] + CO(2) + [acyl-carrier-protein]
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.
Acetyl-CoA + [protein]-L-lysine = CoA + [protein]-N(6)-acetyl-L-lysine
(1a) S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [HECT-type E3 ubiquitin transferase]-L-cysteine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + S-ubiquitinyl-[HECT-type E3 ubiquitin transferase]-L-cysteine
4-phosphonooxy-L-threonine + 2-oxoglutarate = (3R)-3-hydroxy-2-oxo-4-phosphonooxybutanoate + L-glutamate
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
Acetyl-CoA + alpha-D-glucosamine 1-phosphate = CoA + N-acetyl-alpha-D-glucosamine 1-phosphate
CoA-(4'-phosphopantetheine) + apo-[acyl-carrier-protein] = adenosine 3',5'-bisphosphate + holo-[acyl-carrier-protein]
Hydrolyzes poly(ADP-D-ribose) at glycosidic (1''-2') linkage of ribose-ribose bond to produce free ADP-D-ribose
Protein N(6)-(dihydrolipoyl)lysine + NAD(+) = protein N(6)-(lipoyl)lysine + NADH
Cyclo(L-tyrosyl-L-tyrosyl) + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H(+) + O(2) = mycocyclosin + 2 oxidized ferredoxin [iron-sulfur] cluster + 2 H(2)O
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
ATP + shikimate = ADP + shikimate 3-phosphate
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.
Endopeptidase with a preference for cleavage when the P1 position is occupied by Glu-|- and the P1' position is occupied by Gly-|-
Sucrose + ((1->6)-alpha-D-glucosyl)(n) = D-fructose + ((1->6)-alpha-D-glucosyl)(n+1)
A [lipoyl-carrier protein]-N(6)-((R)-dihydrolipoyl)-L-lysine + ROOH = a [lipoyl-carrier protein]-N(6)-((R)-lipoyl)-L-lysine + H(2)O + ROH
3-dehydroquinate = 3-dehydroshikimate + H(2)O
N-acetyl-O-acetylneuraminate + H(2)O = N-acetylneuraminate + acetate
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
Isochorismate = salicylate + pyruvate
Prephenate = phenylpyruvate + H(2)O + CO(2)
(R)-10-hydroxystearate = oleate + H(2)O
NTP + H(2)O = NDP + phosphate
A 5'-phosphopolynucleotide + H(2)O = a polynucleotide + phosphate
Succinate semialdehyde + NADP(+) + H(2)O = succinate + NADPH
Trans,octacis-decaprenylphospho-beta-D-ribofuranose + FAD = trans,octacis-decaprenylphospho-beta-D-erythro-pentofuranosid-2-ulose + FADH(2)
ATP + L-glutamate + NH(3) = ADP + phosphate + L-glutamine
5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole = 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
(+)-muconolactone = 5-oxo-4,5-dihydrofuran-2-acetate
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
[Biotin carboxyl-carrier protein]-N(6)-carboxybiotinyl-L-lysine + acetyl-CoA = [biotin carboxyl-carrier protein]-N(6)-biotinyl-L-lysine + malonyl-CoA
UTP + N-acetyl-alpha-D-glucosamine 1-phosphate = diphosphate + UDP-N-acetyl-alpha-D-glucosamine
(1a) ATP + [DNA ligase]-L-lysine = [DNA ligase]-N(6)-(5'-adenylyl)-L-lysine + diphosphate
5,10-methylenetetrahydrofolate + dUMP + NADPH = dTMP + tetrahydrofolate + NADP(+)
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.
Isocitrate = succinate + glyoxylate
Endonucleolytic cleavage to 5'-phosphodinucleotide and 5'-phosphooligonucleotide end-products
A beta-lactam + H(2)O = a substituted beta-amino acid
Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate
2-carboxy-2,5-dihydro-5-oxofuran-2-acetate = cis,cis-butadiene-1,2,4-tricarboxylate
3-deoxy-D-manno-octulosonate 8-phosphate + H(2)O = 3-deoxy-D-manno-octulosonate + phosphate
RX + glutathione = HX + R-S-glutathione
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
D-glucarate = 5-dehydro-4-deoxy-D-glucarate + H(2)O
L-arginine + H(2)O = L-ornithine + urea
D-glyceraldehyde 3-phosphate = glycerone phosphate
(1a) 2 cob(II)alamin + 2 [corrinoid adenosyltransferase] = 2 [corrinoid adenosyltransferase]-cob(II)alamin
L-aspartate = D-aspartate
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).
Autocatalytic release of the core protein from the N-terminus of the togavirus structural polyprotein by hydrolysis of a -Trp-|-Ser- bond.
D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate
ATP + pantetheine 4'-phosphate = diphosphate + 3'-dephospho-CoA
Hydrolysis of terminal, non-reducing beta-D-mannose residues in beta-D-mannosides
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'.
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 + [I-kappa-B protein] = ADP + [I-kappa-B phosphoprotein]
(2Z,6E)-farnesyl diphosphate + 7 isopentenyl diphosphate = 7 diphosphate + (2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E)-decaprenyl diphosphate
(2E,6E)-farnesyl diphosphate + n isopentenyl diphosphate = n diphosphate + ditrans,polycis-polyprenyl diphosphate (n = 10-55)
2 phenolic donor + H(2)O(2) = 2 phenoxyl radical of the donor + 2 H(2)O
Peptidylproline (omega=180) = peptidylproline (omega=0)
5-methyltetrahydrofolate + NAD(P)(+) = 5,10-methylenetetrahydrofolate + NAD(P)H
S-adenosyl-L-methionine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(ribonucleotide)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-ribonucleotide)-[mRNA]
S-adenosyl-L-methionine + a 5'-(5'-triphosphoguanosine)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA]
(2E,6E)-farnesyl diphosphate + isopentenyl diphosphate = diphosphate + geranylgeranyl diphosphate
(R)-3-hydroxybutanoate + NAD(+) = acetoacetate + NADH
L-histidinol phosphate + H(2)O = L-histidinol + phosphate
Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units
(S)-3-hydroxyacyl-CoA + NAD(+) = 3-oxoacyl-CoA + NADH
D-fructose 1,6-bisphosphate + H(2)O = D-fructose 6-phosphate + phosphate
ATP + (R)-pantoate + beta-alanine = AMP + diphosphate + (R)-pantothenate
Succinate semialdehyde + NAD(P)(+) + H(2)O = succinate + 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.
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
S-methyl-5'-thioadenosine + phosphate = adenine + S-methyl-5-thio-alpha-D-ribose 1-phosphate
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 + thymidine = ADP + thymidine 5'-phosphate
Geranylgeranyl diphosphate = (+)-copalyl 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).
ATP + H(2)O = ADP + phosphate
Acetyl-CoA + H(2)O + glyoxylate = (S)-malate + CoA
CTP + N-acylneuraminate = diphosphate + CMP-N-acylneuraminate
Chorismate = isochorismate
L-threonylcarbamoyladenylate + adenine(37) in tRNA = AMP + N(6)-L-threonylcarbamoyladenine(37) in tRNA
Oleoyl-[acyl-carrier-protein] + H(2)O = [acyl-carrier-protein] + oleate
Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
A primary alcohol + 2 cytochrome c(L) = an aldehyde + 2 reduced cytochrome c(L) + 2 H(+)
Acetyl-CoA + a 2-deoxystreptamine antibiotic = CoA + N(3)-acetyl-2-deoxystreptamine antibiotic
(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate = fumarate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide
Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides
ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
Protein L-glutamine + H(2)O = protein L-glutamate + NH(3)
An aldehyde + H(2)O + 2 oxidized ferredoxin = a carboxylate + 2 H(+) + 2 reduced ferredoxin
(1E,2Z)-3-hydroxy-5,9,17-trioxo-4,5:9,10-disecoandrosta-1(10),2-dien-4-oate + H(2)O = 3-((3aS,4S,7aS)-7a-methyl-1,5-dioxo-octahydro-1H-inden-4-yl)propanoate + (2Z,4Z)-2-hydroxyhexa-2,4-dienoate
ATP + L-serine + tRNA(Sec) = AMP + diphosphate + L-seryl-tRNA(Sec)
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]
5-hydroxyisourate + H(2)O = 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate
ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly)
Beta-D-ribopyranose = beta-D-ribofuranose
7,8-dihydroneopterin + O(2) = 7,8-dihydroxanthopterin + formate + glycolaldehyde
(S)-4-hydroxy-2-oxopentanoate = acetaldehyde + pyruvate
GTP + a 5'-diphospho-[mRNA] = diphosphate + a 5'-(5'-triphosphoguanosine)-[mRNA]
tRNA(n+1) + phosphate = tRNA(n) + a nucleoside diphosphate
Succinate + a quinone = fumarate + a quinol
An aldehyde + NAD(P)(+) + H(2)O = a carboxylate + NAD(P)H
Adenosine + H(2)O = inosine + NH(3)
4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H(2)O
Thioredoxin + ROOH = thioredoxin disulfide + H(2)O + ROH
7,8-dihydroneopterin = 6-hydroxymethyl-7,8-dihydropterin + glycolaldehyde
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.
Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H(2)O
ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu)
(3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O
Palmitoyl-CoA + H(2)O = CoA + palmitate
A primary alcohol + NAD(+) = an aldehyde + NADH
AMP + H(2)O = D-ribose 5-phosphate + adenine
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu)
Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.
ATP + D-glucose = ADP + D-glucose 6-phosphate
Hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides
Acetyl-CoA + L-serine = CoA + O-acetyl-L-serine
Acetyl-CoA + malonyl-[acyl-carrier-protein] = acetoacetyl-[acyl-carrier-protein] + CoA + CO(2) 
N(6)-prenyladenine + acceptor + H(2)O = adenine + 3-methylbut-2-enal + reduced acceptor
NH(3) + 2 H(2)O + 6 ferricytochrome c = nitrite + 6 ferrocytochrome c + 7 H(+)
(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
Desacetylmycothiol + acetyl-CoA = CoA + mycothiol
2,6-dioxo-6-phenylhexa-3-enoate + H(2)O = benzoate + 2-oxopent-4-enoate
Tuberculosinyl diphosphate + adenosine = 1-tuberculosinyladenosine + diphosphate
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
CTP + 2-C-methyl-D-erythritol 4-phosphate = diphosphate + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol
NADPH + NAD(+) + H(+)(Side 1) = NADP(+) + H(+)(Side 2) + NADH
Release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.
(S)-4-hydroxy-2-oxohexanoate = propanal + pyruvate
Biochemical function:
Biological process:
  • not assigned
Cellular component:

Structure analysis Details

Assemblies composition:
homo 180-mer (preferred)
homo trimer
homo pentadecamer
homo octadecamer
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Capsid protein Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 234 amino acids
Theoretical weight: 25.52 KDa
Source organism: Ryegrass mottle virus
UniProt:
  • Canonical: Q9E962 (Residues: 2-235; Coverage: 100%)
Gene names: CP, ORF4
Sequence domains: Viral coat protein (S domain)
Structure domains: Jelly Rolls

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P21
Unit cell:
a: 277.641Å b: 298.719Å c: 392.485Å
α: 90° β: 92.74° γ: 90°
R-values:
R R work R free
0.294 0.294 not available