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show all sequences of 1.1.1.12

Structure and engineering of L-arabinitol 4-dehydrogenase from Neurospora crassa

Bae, B.; Sullivan, R.P.; Zhao, H.; Nair, S.K.; J. Mol. Biol. 402, 230-240 (2010)

Data extracted from this reference:

Crystallization (Commentary)
Crystallization
Organism
molecular replacement method using the coordinates of human sorbitol dehydrogenase, PDB ID 1PL8. Each monomer contains a bidomain architecture composed of a large catalytic domain of residues Ala5 through Val167, and residues Arg308 through Leu362, and a smaller cofactor-binding domain with residues Ala168 through Tyr307, with a large cleft separating the two domains
Neurospora crassa
Engineering
Amino acid exchange
Commentary
Organism
D211S
strong decrease in activity
Neurospora crassa
D211S/I212R
strong decrease in activity, increase in activity with cofactor NADP+
Neurospora crassa
D211S/I212R/D213N
strong decrease in activity, increase in activity with cofactor NADP+
Neurospora crassa
D211S/I212R/S348T
strong decrease in activity, increase in activity with cofactor NADP+
Neurospora crassa
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.14
-
NAD+
wild-type, pH 8.0, 25°C
Neurospora crassa
0.48
-
NADP+
mutant D211S/I212R, pH 8.0, 25°C
Neurospora crassa
0.55
-
NADP+
mutant D211S/I212R/S348T, pH 8.0, 25°C
Neurospora crassa
1.45
-
NADP+
mutant D211S/I212R/D213N, pH 8.0, 25°C
Neurospora crassa
2.9
-
NAD+
mutant D211S, pH 8.0, 25°C
Neurospora crassa
3.6
-
NAD+
mutant D211S/I212R, pH 8.0, 25°C
Neurospora crassa
5
-
NAD+
or above, mutant D211S/I212R/D213N, pH 8.0, 25°C; or above, mutant D211S/I212R/S348T, pH 8.0, 25°C
Neurospora crassa
5
-
NADP+
or above, mutant D211S, pH 8.0, 25°C
Neurospora crassa
8
-
NADP+
or above, wild-type, pH 8.0, 25°C
Neurospora crassa
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Zn2+
a structural zinc ion is situated at a loop region located adjacent to the catalytic domain, where it is ligated by enzyme residues Cys108, Cys111, Cys114, and Cys122. The catalytically requisite zinc ion constitutes the second metal found in each monomer of LAD. This metal is coordinated by residues Cys53, His78, and Glu79, with a water molecule completing a near-tetrahedral coordination sphere
Neurospora crassa
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Neurospora crassa
Q7SI09
-
-
Purification (Commentary)
Commentary
Organism
-
Neurospora crassa
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
adonitol + NAD+
-
712767
Neurospora crassa
? + NADH + H+
-
-
-
?
L-arabinitol + NAD+
-
712767
Neurospora crassa
L-xylulose + NADH + H+
-
-
-
?
L-arabinitol + NADP+
no activity with cofactor NADP+ for wild-type
712767
Neurospora crassa
L-xylulose + NADPH + H+
-
-
-
?
additional information
no substrate: D-arabinitol. The promiscuity of LAD towards different substrates is restricted to five-carbon sugars, and no activity is observed towards either D-sorbitol or D-mannitol
712767
Neurospora crassa
?
-
-
-
-
xylitol + NAD+
-
712767
Neurospora crassa
D-xylulose + NADH + H+
-
-
-
?
Turnover Number [1/s]
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
3.18
-
NAD+
mutant D211S/I212R, pH 8.0, 25°C
Neurospora crassa
8.23
-
NADP+
mutant D211S/I212R, pH 8.0, 25°C
Neurospora crassa
8.58
-
NAD+
mutant D211S, pH 8.0, 25°C
Neurospora crassa
10.83
-
NAD+
wild-type, pH 8.0, 25°C
Neurospora crassa
11.9
-
NADP+
mutant D211S/I212R/D213N, pH 8.0, 25°C
Neurospora crassa
20.16
-
NADP+
mutant D211S/I212R/S348T, pH 8.0, 25°C
Neurospora crassa
Cofactor
Cofactor
Commentary
Organism
Structure
NAD+
electron density corresponding to the bound NAD+ cofactor is observed within the smaller nucleotide-binding domain, along a crevice between the two domains. The adenine ring is nestled in a shallow pocket created by numerous hydrophobic residues, including Ile212, Val232, Thr260, and Val262. The nicotinamide is adjacent to the catalytic zinc ion, where it is poised for hydride transfer to the C2 atom of the substrate
Neurospora crassa
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
NAD+
electron density corresponding to the bound NAD+ cofactor is observed within the smaller nucleotide-binding domain, along a crevice between the two domains. The adenine ring is nestled in a shallow pocket created by numerous hydrophobic residues, including Ile212, Val232, Thr260, and Val262. The nicotinamide is adjacent to the catalytic zinc ion, where it is poised for hydride transfer to the C2 atom of the substrate
Neurospora crassa
Crystallization (Commentary) (protein specific)
Crystallization
Organism
molecular replacement method using the coordinates of human sorbitol dehydrogenase, PDB ID 1PL8. Each monomer contains a bidomain architecture composed of a large catalytic domain of residues Ala5 through Val167, and residues Arg308 through Leu362, and a smaller cofactor-binding domain with residues Ala168 through Tyr307, with a large cleft separating the two domains
Neurospora crassa
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
D211S
strong decrease in activity
Neurospora crassa
D211S/I212R
strong decrease in activity, increase in activity with cofactor NADP+
Neurospora crassa
D211S/I212R/D213N
strong decrease in activity, increase in activity with cofactor NADP+
Neurospora crassa
D211S/I212R/S348T
strong decrease in activity, increase in activity with cofactor NADP+
Neurospora crassa
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.14
-
NAD+
wild-type, pH 8.0, 25°C
Neurospora crassa
0.48
-
NADP+
mutant D211S/I212R, pH 8.0, 25°C
Neurospora crassa
0.55
-
NADP+
mutant D211S/I212R/S348T, pH 8.0, 25°C
Neurospora crassa
1.45
-
NADP+
mutant D211S/I212R/D213N, pH 8.0, 25°C
Neurospora crassa
2.9
-
NAD+
mutant D211S, pH 8.0, 25°C
Neurospora crassa
3.6
-
NAD+
mutant D211S/I212R, pH 8.0, 25°C
Neurospora crassa
5
-
NAD+
or above, mutant D211S/I212R/D213N, pH 8.0, 25°C; or above, mutant D211S/I212R/S348T, pH 8.0, 25°C
Neurospora crassa
5
-
NADP+
or above, mutant D211S, pH 8.0, 25°C
Neurospora crassa
8
-
NADP+
or above, wild-type, pH 8.0, 25°C
Neurospora crassa
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Zn2+
a structural zinc ion is situated at a loop region located adjacent to the catalytic domain, where it is ligated by enzyme residues Cys108, Cys111, Cys114, and Cys122. The catalytically requisite zinc ion constitutes the second metal found in each monomer of LAD. This metal is coordinated by residues Cys53, His78, and Glu79, with a water molecule completing a near-tetrahedral coordination sphere
Neurospora crassa
Purification (Commentary) (protein specific)
Commentary
Organism
-
Neurospora crassa
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
adonitol + NAD+
-
712767
Neurospora crassa
? + NADH + H+
-
-
-
?
L-arabinitol + NAD+
-
712767
Neurospora crassa
L-xylulose + NADH + H+
-
-
-
?
L-arabinitol + NADP+
no activity with cofactor NADP+ for wild-type
712767
Neurospora crassa
L-xylulose + NADPH + H+
-
-
-
?
additional information
no substrate: D-arabinitol. The promiscuity of LAD towards different substrates is restricted to five-carbon sugars, and no activity is observed towards either D-sorbitol or D-mannitol
712767
Neurospora crassa
?
-
-
-
-
xylitol + NAD+
-
712767
Neurospora crassa
D-xylulose + NADH + H+
-
-
-
?
Turnover Number [1/s] (protein specific)
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
3.18
-
NAD+
mutant D211S/I212R, pH 8.0, 25°C
Neurospora crassa
8.23
-
NADP+
mutant D211S/I212R, pH 8.0, 25°C
Neurospora crassa
8.58
-
NAD+
mutant D211S, pH 8.0, 25°C
Neurospora crassa
10.83
-
NAD+
wild-type, pH 8.0, 25°C
Neurospora crassa
11.9
-
NADP+
mutant D211S/I212R/D213N, pH 8.0, 25°C
Neurospora crassa
20.16
-
NADP+
mutant D211S/I212R/S348T, pH 8.0, 25°C
Neurospora crassa
KCat/KM [mM/s]
kcat/KM Value [1/mMs-1]
kcat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
0.88
-
NAD+
mutant D211S/I212R, pH 8.0, 25°C
Neurospora crassa
2.92
-
NAD+
mutant D211S, pH 8.0, 25°C
Neurospora crassa
8.27
-
NADP+
mutant D211S/I212R/D213N, pH 8.0, 25°C
Neurospora crassa
17.17
-
NADP+
mutant D211S/I212R, pH 8.0, 25°C
Neurospora crassa
36.6
-
NADP+
mutant D211S/I212R/S348T, pH 8.0, 25°C
Neurospora crassa
79
-
NAD+
wild-type, pH 8.0, 25°C
Neurospora crassa
KCat/KM [mM/s] (protein specific)
KCat/KM Value [1/mMs-1]
KCat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
0.88
-
NAD+
mutant D211S/I212R, pH 8.0, 25°C
Neurospora crassa
2.92
-
NAD+
mutant D211S, pH 8.0, 25°C
Neurospora crassa
8.27
-
NADP+
mutant D211S/I212R/D213N, pH 8.0, 25°C
Neurospora crassa
17.17
-
NADP+
mutant D211S/I212R, pH 8.0, 25°C
Neurospora crassa
36.6
-
NADP+
mutant D211S/I212R/S348T, pH 8.0, 25°C
Neurospora crassa
79
-
NAD+
wild-type, pH 8.0, 25°C
Neurospora crassa
Other publictions for EC 1.1.1.12
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
710970
Kim
Cloning, characterization, and ...
Aspergillus niger, Penicillium chrysogenum, Penicillium chrysogenum Wisconsin 54-1255, Trichoderma reesei
Appl. Microbiol. Biotechnol.
87
1407-1414
2010
-
-
-
-
3
-
-
6
-
-
-
-
-
4
-
-
-
-
-
-
3
-
4
-
3
-
-
6
-
-
-
6
-
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-
-
-
-
6
-
3
-
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-
-
6
-
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-
-
-
-
3
-
4
-
3
-
-
6
-
-
-
-
-
-
-
-
6
6
711121
Fernandes
Cloning, heterologous expressi ...
Rasamsonia emersonii
Biochem. Genet.
48
480-495
2010
-
-
1
-
-
-
-
4
-
1
2
-
-
1
-
-
-
-
-
-
-
-
3
1
-
1
-
4
1
1
-
2
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1
2
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-
-
-
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4
-
1
2
-
-
-
-
-
-
-
-
-
3
1
-
1
-
4
1
1
-
-
-
-
-
-
4
4
712767
Bae
Structure and engineering of L ...
Neurospora crassa
J. Mol. Biol.
402
230-240
2010
-
-
-
1
4
-
-
9
-
1
-
-
-
2
-
-
1
-
-
-
-
-
5
-
-
-
-
6
-
-
-
1
-
-
-
-
-
-
1
1
4
-
-
-
-
9
-
1
-
-
-
-
-
1
-
-
-
-
5
-
-
-
-
6
-
-
-
-
-
-
-
-
6
6
712797
Tiwari
Molecular modeling studies of ...
Trichoderma reesei
J. Mol. Graph. Model.
28
707-713
2010
-
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-
1
-
-
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-
1
-
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4
-
-
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1
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1
1
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-
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1
-
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-
-
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-
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-
-
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-
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-
-
-
-
-
-
-
-
-
-
-
696988
Rutten
A single amino acid change (Y3 ...
Aspergillus niger
BMC Microbiol.
9
166
2009
-
-
1
1
2
-
-
10
-
-
-
-
-
3
-
-
1
-
-
-
-
-
6
-
-
-
-
12
-
-
-
1
-
-
-
-
-
1
1
1
2
-
-
-
-
10
-
-
-
-
-
-
-
1
-
-
-
-
6
-
-
-
-
12
-
-
-
-
-
-
-
-
-
-
711877
Akel
Molecular regulation of arabin ...
Trichoderma reesei
Eukaryot. Cell
8
1837-1844
2009
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-
-
-
-
-
-
-
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1
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-
-
-
-
-
-
-
-
-
1
1
-
-
-
695737
Fonseca
Use of in vivo 13C nuclear mag ...
Candida arabinofermentans, Candida arabinofermentans PYCC 5603T, Meyerozyma guilliermondii, Meyerozyma guilliermondii PYCC 3012
Appl. Environ. Microbiol.
74
1845-1855
2008
-
-
-
-
-
-
-
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-
-
-
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-
5
-
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-
-
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4
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2
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2
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-
-
4
-
-
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-
-
-
-
-
-
-
-
-
-
-
-
684627
Sullivan
Cloning, characterization, and ...
Neurospora crassa
Appl. Microbiol. Biotechnol.
77
845-852
2007
-
1
1
-
-
-
-
4
-
1
3
-
-
3
-
-
1
-
-
-
-
2
4
1
1
-
2
4
1
1
-
4
-
-
-
-
1
1
4
-
-
-
-
-
-
4
-
1
3
-
-
-
-
1
-
-
-
2
4
1
1
-
2
4
1
1
-
-
-
-
-
-
-
-
686661
Fonseca
L-Arabinose transport and cata ...
Candida arabinofermentans, Candida arabinofermentans PYCC, Meyerozyma guilliermondii, Meyerozyma guilliermondii PYCC 3012
FEBS J.
274
3589-3600
2007
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2
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5
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2
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4
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668063
de Groot
Metabolic control analysis of ...
Aspergillus niger
Biotechnol. Prog.
21
1610-1616
2005
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-
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4
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1
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2
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1
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2
2
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2
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2
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4
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1
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1
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2
2
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-
669541
Suzuki
Cloning and expression of NAD+ ...
Aspergillus oryzae
J. Biosci. Bioeng.
100
472-474
2005
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1
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4
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3
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1
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1
1
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3
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655480
Pail
The metabolic role and evoluti ...
Trichoderma reesei
Eur. J. Biochem.
271
1864-1872
2004
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-
1
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14
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6
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1
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14
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1
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14
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1
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14
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655390
Seiboth
D-xylose metabolism in Hypocre ...
Trichoderma reesei
Eukaryot. Cell
2
867-875
2003
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