3epy

X-ray diffraction
2Å resolution

Crystal Structure of human acyl-CoA binding domain 7 complexed with palmitoyl-Coa

Released:
Source organism: Homo sapiens
Entry authors: Kavanagh KL, Salah E, Yue WW, Savitsky P, Murray JW, Arrowsmith CH, Weigelt J, Edwards AM, Bountra C, von Delft F, Oppermann U, Structural Genomics Consortium (SGC)

Function and Biology Details

Reactions catalysed:
Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine
Phosphoenolpyruvate + D-erythrose 4-phosphate + H(2)O = 3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate + phosphate
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
ATP + deamido-NAD(+) + L-glutamine + H(2)O = AMP + diphosphate + NAD(+) + L-glutamate
AMP + diphosphate = adenine + 5-phospho-alpha-D-ribose 1-diphosphate
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
ATP + D-xylulose = ADP + D-xylulose 5-phosphate
D-glycero-beta-D-manno-heptose 1-phosphate + ATP = ADP-D-glycero-beta-D-manno-heptose + diphosphate
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
L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H(2)O
GTP + a 5'-diphospho-[mRNA] = diphosphate + a 5'-(5'-triphosphoguanosine)-[mRNA]
6-phospho-D-glucono-1,5-lactone + H(2)O = 6-phospho-D-gluconate
ATP-dependent breakage, passage and rejoining of double-stranded DNA
(S)-ureidoglycolate = glyoxylate + urea
2 alpha,alpha'-trehalose 6-mycolate = alpha,alpha'-trehalose + alpha,alpha'-trehalose 6,6'-bismycolate
Release of N-terminal proline from a peptide.
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
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.
GTP + H(2)O = GDP + phosphate
ATP + L-methionine + H(2)O = phosphate + diphosphate + S-adenosyl-L-methionine
1-haloalkane + H(2)O = a primary alcohol + halide
A phosphate monoester + H(2)O = an alcohol + phosphate
(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)(+) + H(2)O = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H
Cleavage of peptide bonds with very broad specificity.
Carbamoyl phosphate + L-aspartate = phosphate + N-carbamoyl-L-aspartate
S-adenosyl-L-methionine + 8-amino-7-oxononanoate = S-adenosyl-4-methylthio-2-oxobutanoate + 7,8-diaminononanoate
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
UDP-alpha-D-galactopyranose = UDP-alpha-D-galactofuranose
4 benzenediol + O(2) = 4 benzosemiquinone + 2 H(2)O
Chorismate = prephenate
2-lysophosphatidylcholine + H(2)O = glycerophosphocholine + a carboxylate
A phenyl acetate + H(2)O = a phenol + acetate
Triacylglycerol + H(2)O = diacylglycerol + a carboxylate
Hydrogen sulfide + 6 oxidized ferredoxin [iron-sulfur] cluster + 3 H(2)O = sulfite + 6 reduced ferredoxin [iron-sulfur] cluster + 6 H(+)
(2S)-2-hydroxy-3,4-dioxopentyl phosphate = 3-hydroxy-2,4-dioxopentyl 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.
CoA-(4'-phosphopantetheine) + apo-[acyl-carrier-protein] = adenosine 3',5'-bisphosphate + holo-[acyl-carrier-protein]
NDP-glucose + 3-phospho-D-glycerate = NDP + 2-O-(alpha-D-glucopyranosyl)-3-phospho-D-glycerate
Random endo-hydrolysis of N-acetyl-beta-D-glucosaminide (1->4)-beta-linkages in chitin and chitodextrins
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
NADH + ROOH + H(+) = NAD(+) + H(2)O + ROH
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
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-|-
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
dTDP-beta-L-rhamnose + NADP(+) = dTDP-4-dehydro-beta-L-rhamnose + NADPH
5-methyltetrahydrofolate + L-homocysteine = tetrahydrofolate + L-methionine
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
Endonucleolytic cleavage to 5'-phosphomononucleotide and 5'-phosphooligonucleotide end-products
Isochorismate = salicylate + pyruvate
Prephenate = phenylpyruvate + H(2)O + CO(2)
NTP + H(2)O = NDP + phosphate
(Polyphosphate)(n) + H(2)O = (polyphosphate)(n-1) + phosphate
dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-beta-L-rhamnose
5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole = 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate
Oleoyl-[acyl-carrier-protein] + H(2)O = [acyl-carrier-protein] + oleate
(+)-muconolactone = 5-oxo-4,5-dihydrofuran-2-acetate
Maltose = alpha,alpha-trehalose
[Biotin carboxyl-carrier protein]-N(6)-carboxybiotinyl-L-lysine + acetyl-CoA = [biotin carboxyl-carrier protein]-N(6)-biotinyl-L-lysine + malonyl-CoA
ATP + UMP = ADP + UDP
(1a) L-glutamine + H(2)O = L-glutamate + NH(3)
ATP + a protein = ADP + a phosphoprotein
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
A beta-lactam + H(2)O = a substituted beta-amino acid
3'-phosphoadenylyl sulfate + a phenol = adenosine 3',5'-bisphosphate + an aryl sulfate
Phosphoenolpyruvate + 3-phosphoshikimate = phosphate + 5-O-(1-carboxyvinyl)-3-phosphoshikimate
RX + glutathione = HX + R-S-glutathione
(1a) cholest-4-en-3-one + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H(+) + O(2) = (25S)-26-hydroxycholest-4-en-3-one + 2 oxidized ferredoxin [iron-sulfur] cluster + H(2)O
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
ATP = 3',5'-cyclic AMP + diphosphate
L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate
6-hydroxymethyl-7,8-dihydropterin diphosphate + 4-aminobenzoate = diphosphate + dihydropteroate
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.
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.
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'.
L-glutamate 5-semialdehyde + NAD(+) + H(2)O = L-glutamate + NADH
S-adenosyl-L-methionine + phospholipid olefinic fatty acid = S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid
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-.
Hydrolysis of the bonds linking certain hydrophobic residues in hemoglobin or globin. Also cleaves small molecules substrates such as Ala-Leu-Glu-Arg-Thr-Phe-|-Phe(NO(2))-Ser-Phe-Pro-Thr.
ATP + 5-formyltetrahydrofolate = ADP + phosphate + 5,10-methenyltetrahydrofolate
ATP + (R)-pantoate + beta-alanine = AMP + diphosphate + (R)-pantothenate
Acetyl-CoA + an alkane-alpha,omega-diamine = CoA + an N-acetyldiamine
5-methyltetrahydrofolate + NAD(P)(+) = 5,10-methylenetetrahydrofolate + NAD(P)H
2 bilirubin + O(2) = 2 biliverdin + 2 H(2)O
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]
Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans
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
Hydrolysis of terminal (1->4)-linked alpha-D-glucose residues successively from non-reducing ends of the chains with release of beta-D-glucose
L-aspartate 4-semialdehyde + phosphate + NADP(+) = L-4-aspartyl phosphate + NADPH
2 superoxide + 2 H(+) = O(2) + H(2)O(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.
4-phosphonooxy-L-threonine + 2-oxoglutarate = (3R)-3-hydroxy-2-oxo-4-phosphonooxybutanoate + L-glutamate
ATP + adenosine = ADP + AMP
ATP + thymidine = ADP + thymidine 5'-phosphate
L-proline + a quinone = (S)-1-pyrroline-5-carboxylate + a quinol
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).
Acetyl-CoA + H(2)O + glyoxylate = (S)-malate + CoA
CTP + N-acylneuraminate = diphosphate + CMP-N-acylneuraminate
Chorismate = isochorismate
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Acyl-CoA + 1,2-diacylglycerol = CoA + triacylglycerol
Hydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose and similar substrates, releasing cellobiose from the reducing ends of the chains.
S-adenosyl-L-methionine + cytidine(1402) in 16S rRNA = S-adenosyl-L-homocysteine + 2'-O-methylcytidine(1402) in 16S rRNA 
(S)-lactate + NAD(+) = pyruvate + NADH
5,10-methenyltetrahydrofolate + H(2)O = 10-formyltetrahydrofolate
Protein L-glutamine + H(2)O = protein L-glutamate + NH(3)
Arsenate + mycothiol = arseno-mycothiol + H(2)O
ATP + thiamine = AMP + thiamine diphosphate
ATP + 6-hydroxymethyl-7,8-dihydropterin = AMP + 6-hydroxymethyl-7,8-dihydropterin diphosphate
NAD(P)H + O(2) = NAD(P)(+) + H(2)O(2)
Creatinine + H(2)O = creatine
5-hydroxyisourate + H(2)O = 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate
Succinate + a quinone = fumarate + a quinol
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
10-formyltetrahydrofolate + H(2)O = formate + tetrahydrofolate
Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H(2)O
(3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O
Limited hydrolysis of proteins of the neuroexocytosis apparatus, synaptobrevin (also known as neuronal vesicle-associated membrane protein, VAMP), synaptosome-associated protein of 25 kDa (SNAP25) or syntaxin. No detected action on small molecule substrates.
Palmitoyl-CoA + H(2)O = CoA + palmitate
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.
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-galactose residues in beta-D-galactosides
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
5,10-methylenetetrahydrofolate + NADP(+) = 5,10-methenyltetrahydrofolate + 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
2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + NADPH
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
(1a) L-serine = 2-aminoprop-2-enoate + H(2)O
CTP + 2-C-methyl-D-erythritol 4-phosphate = diphosphate + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol
2-iminobutanoate + H(2)O = 2-oxobutanoate + NH(3)
4-fumarylacetoacetate + H(2)O = acetoacetate + fumarate
NADPH + NAD(+) + H(+)(Side 1) = NADP(+) + H(+)(Side 2) + NADH
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assemblies composition:
homo tetramer
homo dimer (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Acyl-CoA-binding domain-containing protein 7 Chains: A, B
Molecule details ›
Chains: A, B
Length: 89 amino acids
Theoretical weight: 9.89 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8N6N7 (Residues: 1-88; Coverage: 100%)
Gene name: ACBD7
Sequence domains: Acyl CoA binding protein
Structure domains: Acyl-CoA Binding Protein

Ligands and Environments


Cofactor: Ligand COA 2 x COA
1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: C2
Unit cell:
a: 114.515Å b: 27.922Å c: 60.437Å
α: 90° β: 102.79° γ: 90°
R-values:
R R work R free
0.206 0.203 0.257
Expression system: Escherichia coli