2ej5

X-ray diffraction
2Å resolution

Crystal structure of GK2038 protein (enoyl-CoA hydratase subunit II) from Geobacillus kaustophilus

Released:
Source organism: Geobacillus kaustophilus
Entry authors: Okazaki N, Agari Y, Ebihara A, Chen L, Fu ZQ, Chrzas J, Wang BC, Kuramitsu S, Yamamoto M, Yokoyama S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Function and Biology Details

Reactions catalysed:
Thioredoxin + NADP(+) = thioredoxin disulfide + NADPH
UMP + diphosphate = uracil + 5-phospho-alpha-D-ribose 1-diphosphate
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
1-(5-phospho-beta-D-ribosyl)-5-((5-phospho-beta-D-ribosylamino)methylideneamino)imidazole-4-carboxamide = 5-((5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino)-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide
1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = ATP + 5-phospho-alpha-D-ribose 1-diphosphate
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
(R)-2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + NADH
ATP + molybdopterin = diphosphate + adenylyl-molybdopterin
N-(5-phospho-D-ribosyl)-anthranilate + diphosphate = anthranilate + 5-phospho-alpha-D-ribose 1-diphosphate
3-phospho-D-glycerate + NAD(+) = 3-phosphonooxypyruvate + NADH
ATP-dependent breakage, passage and rejoining of double-stranded DNA
ATP = 3',5'-cyclic AMP + diphosphate
7,8-dihydroneopterin = 7,8-dihydromonapterin
ATP + H(2)O + cellular protein(Side 1) = ADP + phosphate + cellular protein(Side 2)
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
Cleavage of peptide bonds with very broad specificity.
Carbamoyl phosphate + L-ornithine = phosphate + L-citrulline
D-tagatose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate
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.
Diphosphate + H(2)O = 2 phosphate
Blasticidin S + H(2)O = deaminohydroxyblasticidin S + NH(3)
L-lysine + NADPH + O(2) = N(6)-hydroxy-L-lysine + NADP(+) + H(2)O
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
(1a) L-tyrosine + 1/2 O(2) = L-dopa
Chorismate = prephenate
2-lysophosphatidylcholine + H(2)O = glycerophosphocholine + a carboxylate
A phenyl acetate + H(2)O = a phenol + acetate
Acetyl-CoA + [protein]-L-lysine = CoA + [protein]-N(6)-acetyl-L-lysine
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
NH(3) + 2 H(2)O + 6 ferricytochrome c = nitrite + 6 ferrocytochrome c + 7 H(+)
3-oxoadipate + NAD(P)(+) = 2-maleylacetate + NAD(P)H
N-acetyl-O-acetylneuraminate + H(2)O = N-acetylneuraminate + acetate
Reduced riboflavin + NAD(P)(+) = riboflavin + NAD(P)H
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
Isochorismate = salicylate + pyruvate
NTP + H(2)O = NDP + phosphate
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-.
N-(5-phospho-beta-D-ribosyl)anthranilate = 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate
Oleoyl-[acyl-carrier-protein] + H(2)O = [acyl-carrier-protein] + oleate
ATP + 7,8-diaminononanoate + CO(2) = ADP + phosphate + dethiobiotin
Maltose = alpha,alpha-trehalose
ATP + deamido-NAD(+) + L-glutamine + H(2)O = AMP + diphosphate + NAD(+) + L-glutamate
ATP + succinate + CoA = ADP + phosphate + succinyl-CoA
ATP + 3-methylbut-3-en-1-yl phosphate = ADP + 3-methylbut-3-en-1-yl 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.
Aceneneuramate = N-acetyl-D-mannosamine + pyruvate
Isocitrate = succinate + glyoxylate
A beta-lactam + H(2)O = a substituted beta-amino acid
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-methionine + thioredoxin disulfide + H(2)O = L-methionine (S)-S-oxide + thioredoxin
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).
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)
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Trans,octacis-decaprenylphospho-beta-D-ribofuranose + FAD = trans,octacis-decaprenylphospho-beta-D-erythro-pentofuranosid-2-ulose + FADH(2)
D-glucose 6-phosphate + oxidized coenzyme F420 = D-glucono-1,5-lactone 6-phosphate + reduced coenzyme F420
L-lysine + 2-oxoglutarate = (S)-2-amino-6-oxohexanoate + L-glutamate
(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 bilirubin + O(2) = 2 biliverdin + 2 H(2)O
D-fructose 1,6-bisphosphate + H(2)O = D-fructose 6-phosphate + phosphate
ATP + (R)-pantoate + beta-alanine = AMP + diphosphate + (R)-pantothenate
ATP + H(2)O + vitamin B12-[cobalamin-binding protein](Side 1) = ADP + phosphate + vitamin B12(Side 2) + [cobalamin-binding protein](Side 1)
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
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
ATP + NAD(+) = ADP + NADP(+)
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.
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).
Chorismate = isochorismate
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.
Acetyl-CoA + a 2-deoxystreptamine antibiotic = CoA + N(3)-acetyl-2-deoxystreptamine antibiotic
An ultra-long-chain mono-unsaturated acyl-[acyl-carrier protein] + a malonyl-[acyl-carrier protein] = an ultra-long-chain mono-unsaturated 3-oxo-fatty acyl-[acyl-carrier protein] + CO(2) + a holo-[acyl-carrier protein]
ATP + AMP = 2 ADP
L-alanine + H(2)O + NAD(+) = pyruvate + NH(3) + NADH
L-glutamate + H(2)O + NADP(+) = 2-oxoglutarate + NH(3) + NADPH
ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
Nucleoside 3',5'-cyclic phosphate + H(2)O = nucleoside 5'-phosphate
Nucleoside 2',3'-cyclic phosphate + H(2)O = nucleoside 3'-phosphate
5-hydroxyisourate + H(2)O = 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate
7,8-dihydroneopterin + O(2) = 7,8-dihydroxanthopterin + formate + glycolaldehyde
N(2)-acetyl-L-ornithine + L-glutamate = L-ornithine + N-acetyl-L-glutamate
Selective cleavage of Tyr-|-Gly bond in picornavirus polyprotein.
O-phospho-L-serine + [CysO sulfur-carrier protein]-Gly-NH-CH(2)-C(O)SH = [CysO sulfur-carrier protein]-Gly-NH-CH(2)-C(O)-S-L-cysteine + phosphate
4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H(2)O
Pyridoxamine 5'-phosphate + H(2)O + O(2) = pyridoxal 5'-phosphate + NH(3) + H(2)O(2)
7,8-dihydroneopterin = 6-hydroxymethyl-7,8-dihydropterin + glycolaldehyde
Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H(2)O
Palmitoyl-CoA + H(2)O = CoA + palmitate
AMP + H(2)O = D-ribose 5-phosphate + adenine
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.
5'-deoxyadenosine + H(2)O = 5-deoxy-D-ribose + adenine
A 2'-deoxyribonucleoside 5'-monophosphate + H(2)O = a 2'-deoxyribonucleoside + 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
ATP + [DNA-directed RNA polymerase] = ADP + [DNA-directed RNA polymerase] phosphate
2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + NADPH
2 superoxide + 2 H(+) = O(2) + H(2)O(2)
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
ATP + acetyl-CoA + HCO(3)(-) = ADP + phosphate + malonyl-CoA
ATP + propanoyl-CoA + HCO(3)(-) = ADP + phosphate + (S)-methylmalonyl-CoA
NADPH + NAD(+) + H(+)(Side 1) = NADP(+) + H(+)(Side 2) + NADH
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:
homo trimer (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Enoyl-CoA hydratase subunit II (Phenylacetic acid catabolism) Chains: A, B
Molecule details ›
Chains: A, B
Length: 257 amino acids
Theoretical weight: 28.21 KDa
Source organism: Geobacillus kaustophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5KYB3 (Residues: 1-257; Coverage: 100%)
Gene name: GK2038
Sequence domains: Enoyl-CoA hydratase/isomerase
Structure domains:

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B2, APS BEAMLINE 22-BM
Spacegroup: P213
Unit cell:
a: 117.008Å b: 117.008Å c: 117.008Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.192 0.242
Expression system: Escherichia coli