1im5

X-ray diffraction
1.65Å resolution

Crystal Structure of Pyrazinamidase of Pyrococcus horikoshii in Complex with Zinc

Released:

Function and Biology Details

Reactions catalysed:
ATP + L-arginine = ADP + N(omega)-phospho-L-arginine
Diphosphate + D-fructose 6-phosphate = phosphate + D-fructose 1,6-bisphosphate
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 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
1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = ATP + 5-phospho-alpha-D-ribose 1-diphosphate
Hydrolysis of (1->4)-beta-D-xylans, to remove successive D-xylose residues from the non-reducing termini
Random hydrolysis of (1->4)-linkages between N-acetyl-beta-D-glucosamine and D-glucuronate residues in hyaluronate
Hydrolysis of (1->3)-beta-D-glucosidic linkages in (1->3)-beta-D-glucans
Endonucleolytic cleavage of RNA, removing 21 and 42 nucleotides, respectively, from the 5'- and 3'-termini of a 5S-rRNA precursor.
UDP-N-acetyl-alpha-D-glucosamine + H(2)O = N-acetyl-D-mannosamine + UDP
(9Z)-(13S)-12,13-epoxyoctadeca-9,11,15-trienoate = (15Z)-12-oxophyto-10,15-dienoate
4-O-(beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline + H(2)O = 4-O-(beta-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline + beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranose
Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates
Chloride + O(2) = chlorite
(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate = fumarate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide
Oligoglycosylglucosyl-(1<->1)-ceramide + H(2)O = ceramide + oligoglycosylglucose
Release of N-terminal proline from a peptide.
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.
A (3R)-3-hydroxyacyl-[acyl-carrier-protein] + UDP-N-acetyl-alpha-D-glucosamine = an [acyl-carrier-protein] + a UDP-3-O-(3-hydroxyacylyl)-N-acetyl-alpha-D-glucosamine
O-phospho-L(or D)-serine + H(2)O = L(or D)-serine + phosphate
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
D-allothreonine = glycine + acetaldehyde
Diphosphate + H(2)O = 2 phosphate
Selective cleavage of Tyr-|-Gly bond in picornavirus polyprotein.
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
6-phospho-beta-D-glucosyl-(1,4)-D-glucose + H(2)O = D-glucose + D-glucose 6-phosphate
Urea + H(2)O = CO(2) + 2 NH(3)
L-serine + L-homocysteine = L-cystathionine + H(2)O
Xyloglucan + H(2)O = xyloglucan oligosaccharides
A carboxylic ester + H(2)O = an alcohol + a carboxylate
L-alanine = D-alanine
L-glutamate = D-glutamate
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 (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins
Thioredoxin + ROOH = thioredoxin disulfide + H(2)O + ROH
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
An acyl-[acyl-carrier protein] + NADP(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADPH
Sucrose + ((1->6)-alpha-D-glucosyl)(n) = D-fructose + ((1->6)-alpha-D-glucosyl)(n+1)
Thioredoxin + NADP(+) = thioredoxin disulfide + NADPH
Formyl-L-methionyl peptide + H(2)O = formate + methionyl peptide
Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H(2)O
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
Prephenate = phenylpyruvate + H(2)O + CO(2)
NTP + H(2)O = NDP + phosphate
An aliphatic amide = a nitrile + H(2)O
6-phospho-D-gluconate + NADP(+) = D-ribulose 5-phosphate + CO(2) + NADPH
S-adenosyl-L-methionine + guanine(37) in tRNA = S-adenosyl-L-homocysteine + N(1)-methylguanine(37) in tRNA
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
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.
An aryl sulfate + a phenol = a phenol + an aryl sulfate
A beta-lactam + H(2)O = a substituted beta-amino acid
Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate
2 3-phospho-D-glycerate + 2 H(+) = D-ribulose 1,5-bisphosphate + CO(2) + H(2)O
(1a) isocitrate + NADP(+) = 2-oxalosuccinate + NADPH
Transfers a segment of a (1->4)-alpha-D-glucan to a new position in an acceptor, which may be glucose or a (1->4)-alpha-D-glucan
N-acetyl-D-glucosamine 6-phosphate + H(2)O = D-glucosamine 6-phosphate + acetate
D-glucose 6-phosphate = D-fructose 6-phosphate
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate = (S)-allantoin + CO(2)
D-glucarate = 5-dehydro-4-deoxy-D-glucarate + H(2)O
L-arginine + H(2)O = L-ornithine + urea
ATP = 3',5'-cyclic AMP + diphosphate
D-ribose 5-phosphate = D-ribulose 5-phosphate
6-hydroxymethyl-7,8-dihydropterin diphosphate + 4-aminobenzoate = diphosphate + dihydropteroate
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.
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
A (Z)-hexadec-9-enoyl-[acyl-carrier protein] + a malonyl-[acyl-carrier protein] = a (Z)-3-oxooctadec-11-enoyl-[acyl-carrier protein] + CO(2) + an [acyl-carrier protein]
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-.
Reduced plastocyanin + oxidized ferredoxin + light = oxidized plastocyanin + reduced ferredoxin
Peptidylproline (omega=180) = peptidylproline (omega=0)
Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans
Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans
2 superoxide + 2 H(+) = O(2) + H(2)O(2)
N,N-dimethylformamide + H(2)O = dimethylamine + formate
ATP + UDP-N-acetyl-alpha-D-muramoyl-L-alanine + D-glutamate = ADP + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate
RH + Cl(-) + H(2)O(2) = RCl + 2 H(2)O
GTP + IMP + L-aspartate = GDP + phosphate + N(6)-(1,2-dicarboxyethyl)-AMP
1D-chiro-inositol + NAD(+) = 2D-2,3,5/4,6-pentahydroxycyclohexanone + NADH
S-adenosyl-L-homocysteine + H(2)O = L-homocysteine + adenosine
(1a) L-glutamine + H(2)O = L-glutamate + NH(3)
A 4-O-methyl-D-glucopyranuronate ester + H(2)O = 4-O-methyl-D-glucuronic acid + an alcohol
A glutathione-S-conjugate + H(2)O = an (L-cysteinylglycine)-S-conjugate + L-glutamate
(R)-pantoate + NADP(+) = 2-dehydropantoate + NADPH
Hydrolysis of proteins and small molecule substrates at -Asn-|-Xaa- bonds.
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.
L-arginine + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-arginine + succinate + CO(2)
L-carnitine + NAD(P)H + O(2) = (3R)-3-hydroxy-4-oxobutanoate + trimethylamine + NAD(P)(+) + H(2)O
L-histidinol + H(2)O + 2 NAD(+) = L-histidine + 2 NADH
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides
L-glutamate + H(2)O + NADP(+) = 2-oxoglutarate + NH(3) + NADPH
Methyl-CoM + CoB = CoM-S-S-CoB + methane
4-amino-5-aminomethyl-2-methylpyrimidine + H(2)O = 4-amino-5-hydroxymethyl-2-methylpyrimidine + ammonia
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
Beta-D-ribopyranose = beta-D-ribofuranose
4 ferrocytochrome c + O(2) + 4 H(+) = 4 ferricytochrome c + 2 H(2)O
Betaine aldehyde + NAD(+) + H(2)O = betaine + NADH
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.
CoB + CoM + methanophenazine = CoM-S-S-CoB + dihydromethanophenazine
D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H(2)O
Myo-inositol + NAD(+) = 2,4,6/3,5-pentahydroxycyclohexanone + NADH
Tetradecanoyl-CoA + an N-terminal-glycyl-[protein] = CoA + an N-terminal-N-tetradecanoylglycyl-[protein]
ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu)
(3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O
L-homoserine + NAD(P)(+) = L-aspartate 4-semialdehyde + NAD(P)H
Hydrolysis of terminal, non-reducing (1->4)-linked alpha-D-glucose residues with release of alpha-D-glucose
Hydrolysis of terminal, non-reducing beta-D-glucosyl residues with release of beta-D-glucose
Hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides
4-trimethylammoniobutanoate + 2-oxoglutarate + O(2) = 3-hydroxy-4-trimethylammoniobutanoate + succinate + CO(2) 
O-phospho-L-homoserine + H(2)O = L-threonine + phosphate
Acetyl-CoA + malonyl-[acyl-carrier-protein] = acetoacetyl-[acyl-carrier-protein] + CoA + CO(2) 
ATP + H(2)O = ADP + phosphate
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
Inosine 5'-phosphate + NAD(+) + H(2)O = xanthosine 5'-phosphate + NADH
(R)-lactate + N-acetyl-D-glucosamine 6-phosphate = N-acetylmuramate 6-phosphate + H(2)O
D-ribulose 5-phosphate = D-xylulose 5-phosphate
A (5-L-glutamyl)-peptide + an amino acid = a peptide + a 5-L-glutamyl amino acid
Release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Isochorismatase domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 180 amino acids
Theoretical weight: 20.22 KDa
Source organism: Pyrococcus horikoshii
Expression system: Escherichia coli
UniProt:
  • Canonical: O58727 (Residues: 1-180; Coverage: 100%)
Gene name: PH0999
Sequence domains: Isochorismatase family
Structure domains: Isochorismatase-like

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P21
Unit cell:
a: 32.978Å b: 43.266Å c: 55.553Å
α: 90° β: 101.34° γ: 90°
R-values:
R R work R free
0.153 0.153 0.232
Expression system: Escherichia coli