1v8k

X-ray diffraction
2.25Å resolution

The Crystal Structure of the Minimal Functional Domain of the Microtubule Destabilizer KIF2C Complexed with Mg-AMPPNP

Released:

Function and Biology Details

Reactions catalysed:
Phosphatidylinositol 3,4,5-trisphosphate + H(2)O = phosphatidylinositol 4,5-bisphosphate + phosphate
Hydrolysis of proteins in presence of ATP.
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
(1a) (5')pppAACA-[mRNA] + (protein L)-L-histidine = diphosphate + (protein L)-L-histidyl-(5')phosphonato-AACA-[mRNA] + H(2)O
(1a) isocitrate + NADP(+) = 2-oxalosuccinate + NADPH
IMP + diphosphate = hypoxanthine + 5-phospho-alpha-D-ribose 1-diphosphate
Nitrite + acceptor = nitrate + reduced acceptor
dUTP + H(2)O = dUMP + diphosphate
7,8-dihydroneopterin 3'-triphosphate + H(2)O = 6-carboxy-5,6,7,8-tetrahydropterin + acetaldehyde + triphosphate
Uridine + phosphate = uracil + alpha-D-ribose 1-phosphate 
NADPH + n oxidized hemoprotein = NADP(+) + n reduced hemoprotein
ATP + a protein = ADP + a phosphoprotein
D-glycero-beta-D-manno-heptose 1-phosphate + ATP = ADP-D-glycero-beta-D-manno-heptose + diphosphate
4-hydroxy-2-oxohexanoate = (2Z,4Z)-2-hydroxyhexa-2,4-dienoate + H(2)O
(1a) [acetyl-CoA C-acyltransferase]-S-acyl-L-cyteine + acetyl-CoA = 3-oxoacyl-CoA + [acetyl-CoA C-acyltransferase]-L-cyteine
D-glucose + O(2) = 2-dehydro-D-glucose + H(2)O(2)
Quercetin + O(2) = 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate + CO + H(+)
dTDP-beta-L-rhamnose + NADP(+) = dTDP-4-dehydro-beta-L-rhamnose + NADPH
Chloride + O(2) = chlorite
ATP-dependent breakage, passage and rejoining of double-stranded DNA
Acyl-CoA + H(2)O = CoA + a carboxylate
RH + [reduced NADPH--hemoprotein reductase] + O(2) = ROH + [oxidized NADPH--hemoprotein reductase] + H(2)O
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.
17-alpha-hydroxypregnenolone + [reduced NADPH--hemoprotein reductase] + O(2) = 3-beta-hydroxyandrost-5-en-17-one + acetate + [oxidized NADPH--hemoprotein reductase] + H(2)O
Cleavage of peptide bonds with very broad specificity.
A glycerophosphodiester + H(2)O = an alcohol + sn-glycerol 3-phosphate
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
Diphosphate + H(2)O = 2 phosphate
L-lysine + NADPH + O(2) = N(6)-hydroxy-L-lysine + NADP(+) + H(2)O
2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde
4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O
Methylamine + H(2)O + 2 oxidized [amicyanin] = formaldehyde + NH(3) + 2 reduced [amicyanin]
(S)-4-hydroxy-2-oxopentanoate = (2Z)-2-hydroxypenta-2,4-dienoate + H(2)O
UDP-alpha-D-galactopyranose = UDP-alpha-D-galactofuranose
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
N-substituted aminoacyl-tRNA + H(2)O = N-substituted amino acid + tRNA
Acetyl-CoA + L-serine = CoA + O-acetyl-L-serine
Cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA)
Urea + H(2)O = CO(2) + 2 NH(3)
L-serine + L-homocysteine = L-cystathionine + H(2)O
A carboxylic ester + H(2)O = an alcohol + a carboxylate
Propane-1,2-diol = propanal + H(2)O
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
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.
Trypanothione + NADP(+) = trypanothione disulfide + NADPH
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO(3)(-) = ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
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
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
Endopeptidase with a preference for cleavage when the P1 position is occupied by Glu-|- and the P1' position is occupied by Gly-|-
((1->4)-alpha-D-glucosyl)(n) + phosphate = ((1->4)-alpha-D-glucosyl)(n-1) + alpha-D-glucose 1-phosphate
Orotidine 5'-phosphate = UMP + CO(2)
L-tyrosine = tyramine + CO(2)
Hydrolysis of Xaa-|-Pro dipeptides. Also acts on aminoacyl-hydroxyproline analogs. No action on Pro-|-Pro.
Acetyl-CoA + L-2,4-diaminobutanoate = CoA + N(4)-acetyl-L-2,4-diaminobutanoate
Tetradecanoyl-CoA + an N-terminal-glycyl-[protein] = CoA + an N-terminal-N-tetradecanoylglycyl-[protein]
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
L-glutamate 5-semialdehyde + NAD(+) + H(2)O = L-glutamate + NADH
Prephenate = phenylpyruvate + H(2)O + CO(2)
NTP + H(2)O = NDP + phosphate
4 benzenediol + O(2) = 4 benzosemiquinone + 2 H(2)O
A (3R)-3-hydroxyacyl-[acyl-carrier protein] = a trans-2-enoyl-[acyl-carrier protein] + H(2)O
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
L-leucine + 2-oxoglutarate = 4-methyl-2-oxopentanoate + L-glutamate
S-adenosyl-L-methionine + guanine(37) in tRNA = S-adenosyl-L-homocysteine + N(1)-methylguanine(37) in tRNA
ATP + pyruvate = ADP + phosphoenolpyruvate
D-fructose 6-phosphate + phosphate = acetyl phosphate + D-erythrose 4-phosphate + H(2)O
(+)-muconolactone = 5-oxo-4,5-dihydrofuran-2-acetate
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
(1a) ATP + [DNA ligase]-L-lysine = [DNA ligase]-N(6)-(5'-adenylyl)-L-lysine + diphosphate
ATP + 3-methylbut-3-en-1-yl phosphate = ADP + 3-methylbut-3-en-1-yl diphosphate
dTTP + alpha-D-glucose 1-phosphate = diphosphate + dTDP-alpha-D-glucose
(4Z)-2-oxohept-4-enedioate + H(2)O = (4S)-4-hydroxy-2-oxoheptanedioate
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.
(3R)-3-hydroxyacyl-[acyl-carrier-protein] + NADP(+) = 3-oxoacyl-[acyl-carrier-protein] + NADPH
An alcohol + NADP(+) = an aldehyde + NADPH
A beta-lactam + H(2)O = a substituted beta-amino acid
An alpha-amino acid ester + H(2)O = an alpha-amino acid + an alcohol
Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate
Cellobiose + phosphate = alpha-D-glucose 1-phosphate + D-glucose
Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.
2 reduced [2Fe-2S] ferredoxin + NAD(+) + H(+) = 2 oxidized [2Fe-2S] ferredoxin + NADH
5,6,7,8-tetrahydrobiopterin + 2 NADP(+) = biopterin + 2 NADPH
3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholan-24-oylglycine + H(2)O = 3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholanate + glycine
RX + glutathione = HX + R-S-glutathione
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
L-arginine + H(2)O = L-ornithine + urea
Geranyl diphosphate + isopentenyl diphosphate = diphosphate + (2E,6E)-farnesyl diphosphate
S-adenosyl 3-(methylthio)propylamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine
6-hydroxymethyl-7,8-dihydropterin diphosphate + 4-aminobenzoate = diphosphate + dihydropteroate
Succinyl-CoA + acetyl-CoA = CoA + 3-oxoadipyl-CoA
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]
ATP + sulfate = diphosphate + adenylyl sulfate
Hydrolyzes glutaminyl bonds, and activity is further restricted by preferences for the amino acids in P6 - P1' that vary with the species of potyvirus, e.g. Glu-Xaa-Xaa-Tyr-Xaa-Gln-|-(Ser or Gly) for the enzyme from tobacco etch virus. The natural substrate is the viral polyprotein, but other proteins and oligopeptides containing the appropriate consensus sequence are also cleaved.
Hydrolyzes a Gly-|-Gly bond at its own C-terminus, commonly in the sequence -Tyr-Xaa-Val-Gly-|-Gly, in the processing of the potyviral polyprotein.
Maltose = alpha,alpha-trehalose
ATP + [I-kappa-B protein] = ADP + [I-kappa-B phosphoprotein]
2 H(2)O(2) = O(2) + 2 H(2)O
Peptidylproline (omega=180) = peptidylproline (omega=0)
Acetyl-CoA + an alkane-alpha,omega-diamine = CoA + an N-acetyldiamine
2 bilirubin + O(2) = 2 biliverdin + 2 H(2)O
CO + H(2)O + 2 oxidized ferredoxin = CO(2) + 2 reduced ferredoxin + 2 H(+)
(R)-3-hydroxybutanoate + NAD(+) = acetoacetate + NADH
Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans
Hydrolysis of terminal (1->4)-linked alpha-D-glucose residues successively from non-reducing ends of the chains with release of beta-D-glucose
(1a) 2 farnesyl diphosphate = diphosphate + presqualene diphosphate
2 superoxide + 2 H(+) = O(2) + H(2)O(2)
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate = ADP + phosphate + (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate
N,N-dimethylformamide + H(2)O = dimethylamine + formate
H(2)CO(3) = CO(2) + H(2)O
4-aminobutanal + NAD(+) + H(2)O = 4-aminobutanoate + NADH
Sarcosine + H(2)O + O(2) = glycine + formaldehyde + H(2)O(2)
ATP + acetate + CoA = AMP + diphosphate + acetyl-CoA
(1a) acetyl-CoA + [acetyl-CoA C-acetyltransferase]-L-cysteine = [acetyl-CoA C-acetyltransferase]-S-acetyl-L-cysteine + CoA
S-adenosyl-L-methionine + adenine in DNA = S-adenosyl-L-homocysteine + N-6-methyladenine in DNA 
S-methyl-5'-thioadenosine + phosphate = adenine + S-methyl-5-thio-alpha-D-ribose 1-phosphate
S-adenosyl-L-homocysteine + H(2)O = L-homocysteine + adenosine
(1a) L-glutamine + H(2)O = L-glutamate + NH(3)
ATP + adenosine = ADP + AMP
ATP + adenylyl sulfate = ADP + 3'-phosphoadenylyl sulfate
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).
ATP + H(2)O = ADP + phosphate
Prenyl phosphate + FMNH(2) = prenylated FMNH(2) + phosphate
Acetyl-CoA + glycine = CoA + 2-amino-3-oxobutanoate
ATP + protoporphyrin IX + Mg(2+) + H(2)O = ADP + phosphate + Mg-protoporphyrin IX + 2 H(+)
S-formylglutathione + H(2)O = glutathione + formate
S-adenosyl-L-methionine + uracil(1498) in 16S rRNA = S-adenosyl-L-homocysteine + N(3)-methyluracil(1498) in 16S rRNA 
L-arginine + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-arginine + succinate + CO(2)
Acetyl-CoA + H(2)O + oxaloacetate = citrate + CoA
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
Acetyl-CoA + a 2-deoxystreptamine antibiotic = CoA + N(3)-acetyl-2-deoxystreptamine antibiotic
ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides
ATP + 6-hydroxymethyl-7,8-dihydropterin = AMP + 6-hydroxymethyl-7,8-dihydropterin diphosphate
2'-deoxycytidine + H(2)O = 2'-deoxyuridine + NH(3)
Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans
Creatinine + H(2)O = creatine
ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-methionyl-tRNA(Met)
Beta-D-ribopyranose = beta-D-ribofuranose
Oxalate + O(2) + 2 H(+) = 2 CO(2) + H(2)O(2)
ATP + glycerol = ADP + sn-glycerol 3-phosphate
4-aminobutanoate + 2-oxoglutarate = succinate semialdehyde + L-glutamate
[a protein]-serine/threonine phosphate + H(2)O = [a protein]-serine/threonine + phosphate
Succinate + a quinone = fumarate + a quinol
Malonyl-CoA + an [acyl-carrier-protein] = CoA + a malonyl-[acyl-carrier-protein]
Betaine aldehyde + NAD(+) + H(2)O = betaine + NADH
(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = pyruvate + succinate
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.
IMP + H(2)O = inosine + phosphate
Pyridoxamine 5'-phosphate + H(2)O + O(2) = pyridoxal 5'-phosphate + NH(3) + H(2)O(2)
ATP + L-aspartate + tRNA(Asp) = AMP + diphosphate + L-aspartyl-tRNA(Asp)
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.
Protoheme + 3 [reduced NADPH--hemoprotein reductase] + 3 O(2) = biliverdin + Fe(2+) + CO + 3 [oxidized NADPH--hemoprotein reductase] + 3 H(2)O
A C(21)-steroid + [reduced NADPH--hemoprotein reductase] + O(2) = a 17-alpha-hydroxy-C(21)-steroid + [oxidized NADPH--hemoprotein reductase] + H(2)O
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
Propanoyl-CoA + phosphate = CoA + propanoyl phosphate
Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.
D-fructose 1,6-bisphosphate + H(2)O = D-fructose 6-phosphate + phosphate
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 alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactolipids
Hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides
(3E)-2-oxohex-3-enedioate = 2-oxopent-4-enoate + CO(2)
L-proline + NAD(P)(+) = 1-pyrroline-5-carboxylate + NAD(P)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.
(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
Quinol + 2 ferricytochrome c(Side 2) = quinone + 2 ferrocytochrome c(Side 2) + 2 H(+)(Side 2)
Inosine 5'-phosphate + NAD(+) + H(2)O = xanthosine 5'-phosphate + NADH
NADH + ubiquinone + 5 H(+)(Side 1) = NAD(+) + ubiquinol + 4 H(+)(Side 2)
ATP + pyruvate + HCO(3)(-) = ADP + phosphate + oxaloacetate
(R)-2-hydroxyglutarate + acceptor = 2-oxoglutarate + reduced acceptor
D-ribulose 5-phosphate = D-xylulose 5-phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo tetramer
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Kinesin-like protein KIF2C Chain: A
Molecule details ›
Chain: A
Length: 410 amino acids
Theoretical weight: 46.8 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q922S8 (Residues: 183-585; Coverage: 56%)
Gene name: Kif2c
Sequence domains: Kinesin motor domain
Structure domains: Kinesin motor domain

Ligands and Environments

2 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: C222
Unit cell:
a: 61.068Å b: 191.475Å c: 74.627Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.238 0.215 0.252
Expression system: Escherichia coli