1r8j

X-ray diffraction
2.03Å resolution

Crystal Structure of Circadian Clock Protein KaiA from Synechococcus elongatus

Released:

Function and Biology Details

Reactions catalysed:
D-galactose + O(2) = D-galacto-hexodialdose + H(2)O(2)
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
D-arabinose 5-phosphate = D-ribulose 5-phosphate
5-phospho-beta-D-ribosylamine + diphosphate + L-glutamate = L-glutamine + 5-phospho-alpha-D-ribose 1-diphosphate + H(2)O
ATP + a protein = ADP + a phosphoprotein
N-(5-phospho-D-ribosyl)-anthranilate + diphosphate = anthranilate + 5-phospho-alpha-D-ribose 1-diphosphate
UDP-N-acetyl-alpha-D-glucosamine = UDP-2-acetamido-2,6-dideoxy-alpha-D-xylo-hex-4-ulose + H(2)O
7,8-dihydroneopterin 3'-triphosphate + H(2)O = 6-carboxy-5,6,7,8-tetrahydropterin + acetaldehyde + triphosphate
2-(N(omega)-L-arginino)succinate = fumarate + L-arginine
ATP = 3',5'-cyclic AMP + diphosphate
Isochorismate + H(2)O = (2S,3S)-2,3-dihydroxy-2,3-dihydrobenzoate + pyruvate
1-(5-phospho-beta-D-ribosyl)-ATP + H(2)O = 1-(5-phospho-beta-D-ribosyl)-AMP + diphosphate
Cleavage of peptide bonds with very broad specificity.
N(2)-acetyl-L-ornithine + L-glutamate = L-ornithine + N-acetyl-L-glutamate
2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine
Diphosphate + H(2)O = 2 phosphate
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
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).
Chorismate = prephenate
L-asparagine + H(2)O = L-aspartate + NH(3)
Acyl-[acyl-carrier-protein] + malonyl-[acyl-carrier-protein] = 3-oxoacyl-[acyl-carrier-protein] + CO(2) + [acyl-carrier-protein]
D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate
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
Acetyl-CoA + D-glucosamine 6-phosphate = CoA + N-acetyl-D-glucosamine 6-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.
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
Thioredoxin + ROOH = thioredoxin disulfide + H(2)O + ROH
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
dCTP + 2 H(2)O = dUMP + diphosphate + NH(3)
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.
Mycoredoxin + ROOH = mycoredoxin disulfide + H(2)O + ROH
Hydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose and cellotetraose, releasing cellobiose from the non-reducing ends of the chains
N-acetyl-O-acetylneuraminate + H(2)O = N-acetylneuraminate + acetate
(S)-dihydroorotate + fumarate = orotate + succinate
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
Isochorismate = salicylate + pyruvate
NTP + H(2)O = NDP + phosphate
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 + 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
ATP + 7,8-diaminononanoate + CO(2) = ADP + phosphate + dethiobiotin
ATP + 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine = ADP + phosphate + 5-amino-1-(5-phospho-D-ribosyl)imidazole
ATP + deamido-NAD(+) + L-glutamine + H(2)O = AMP + diphosphate + NAD(+) + L-glutamate
ATP + UMP = ADP + UDP
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
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
2 reduced ferredoxin + NADP(+) + H(+) = 2 oxidized ferredoxin + NADPH
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
3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate = urocanate + H(2)O
(R)-mandelonitrile = cyanide + benzaldehyde
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)
ATP + dTMP = ADP + dTDP
Trans,octacis-decaprenylphospho-beta-D-ribofuranose + FAD = trans,octacis-decaprenylphospho-beta-D-erythro-pentofuranosid-2-ulose + FADH(2)
Pyruvate + [dihydrolipoyllysine-residue acetyltransferase] lipoyllysine = [dihydrolipoyllysine-residue acetyltransferase] S-acetyldihydrolipoyllysine + CO(2)
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]
[a protein]-serine/threonine phosphate + H(2)O = [a protein]-serine/threonine + phosphate
(S)-3-hydroxyacyl-CoA + NAD(+) = 3-oxoacyl-CoA + NADH
ATP + (R)-pantoate + beta-alanine = AMP + diphosphate + (R)-pantothenate
(S)-malate = fumarate + H(2)O
H(2)CO(3) = CO(2) + H(2)O
S-adenosyl-L-homocysteine + H(2)O = L-homocysteine + adenosine
Acetyl-CoA + L-glutamate = CoA + N-acetyl-L-glutamate
ATP + thymidine = ADP + thymidine 5'-phosphate
ATP + adenylyl sulfate = ADP + 3'-phosphoadenylyl sulfate
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
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
DNA (containing 4-O-methylthymine) + protein L-cysteine = DNA (without 4-O-methylthymine) + protein S-methyl-L-cysteine
Reduced plastocyanin + oxidized ferredoxin + light = oxidized plastocyanin + reduced ferredoxin
(S)-lactate + NAD(+) = pyruvate + NADH
L-alanine + H(2)O + NAD(+) = pyruvate + NH(3) + NADH
ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
ATP + (R)-pantothenate = ADP + (R)-4'-phosphopantothenate
(1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate = 2-succinylbenzoate + H(2)O
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.
An aldehyde + NAD(+) + H(2)O = a carboxylate + NADH
4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H(2)O
ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + L-tyrosyl-tRNA(Tyr)
AMP + H(2)O = D-ribose 5-phosphate + adenine
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
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
ATP + N-acetyl-L-glutamate = ADP + N-acetyl-L-glutamate 5-phosphate
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
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
2-iminobutanoate + H(2)O = 2-oxobutanoate + NH(3)
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Circadian clock protein KaiA Chains: A, B
Molecule details ›
Chains: A, B
Length: 289 amino acids
Theoretical weight: 33.14 KDa
Source organism: Synechococcus elongatus PCC 7942
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q79PF6 (Residues: 2-284; Coverage: 100%)
Gene names: Synpcc7942_1218, kaiA, see0009
Sequence domains: KaiA C-terminal domain
Structure domains:

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21
Unit cell:
a: 47.111Å b: 125.818Å c: 56.818Å
α: 90° β: 114.9° γ: 90°
R-values:
R R work R free
0.213 0.21 0.271
Expression system: Escherichia coli BL21