EzCatDB: T00210

DB codeT00210
CATH domainDomain 13.40.50.970
Domain 23.40.50.920Catalytic domain
Domain 33.40.50.970
E.C.1.2.4.4
CSA1dtw
MACiEM0280

CATH domainRelated DB codes (homologues)
3.40.50.970T00237,T00230

Enzyme Name
Swiss-protKEGG

P12694P21953
Protein name2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial2-oxoisovalerate dehydrogenase subunit beta, mitochondrial3-methyl-2-oxobutanoate dehydrogenase(2-methylpropanoyl-transferring)
2-oxoisocaproate dehydrogenase
2-oxoisovalerate (lipoate) dehydrogenase
3-methyl-2-oxobutanoate dehydrogenase (lipoamide)
3-methyl-2-oxobutanoate:lipoamide oxidoreductase (decarboxylatingand acceptor-2-methylpropanoylating)
alpha-keto-alpha-methylvalerate dehydrogenase
alpha-ketoisocaproate dehydrogenase
alpha-ketoisocaproic dehydrogenase
alpha-ketoisocaproic-alpha-keto-alpha-methylvaleric dehydrogenase
alpha-ketoisovalerate dehydrogenase
alpha-oxoisocaproate dehydrogenase
BCKDH
BCOAD
branched chain keto acid dehydrogenase
branched-chain (-2-oxoacid) dehydrogenase (BCD)
branched-chain 2-keto acid dehydrogenase
branched-chain 2-oxo acid dehydrogenase
branched-chain alpha-keto acid dehydrogenase
branched-chain alpha-oxo acid dehydrogenase
branched-chain keto acid dehydrogenase
branched-chain ketoacid dehydrogenase
dehydrogenase, 2-oxoisovalerate (lipoate)
dehydrogenase, branched chain alpha-keto acid
SynonymsEC 1.2.4.4
Branched-chain alpha-keto acid dehydrogenase E1 component alpha chain
BCKDH E1-alpha
BCKDE1A
EC 1.2.4.4
Branched-chain alpha-keto acid dehydrogenase E1 component beta chain
BCKDH E1-beta

KEGG pathways
MAP codePathways
MAP00280Valine, leucine and isoleucine degradation

Swiss-prot:Accession NumberP12694P21953
Entry nameODBA_HUMANODBB_HUMAN
Activity3-methyl-2-oxobutanoate + [dihydrolipoyllysine-residue (2-methylpropanoyl)transferase] lipoyllysine = [dihydrolipoyllysine-residue (2- methylpropanoyl)transferase] S-(2- methylpropanoyl)dihydrolipoyllysine + CO(2).3-methyl-2-oxobutanoate + [dihydrolipoyllysine-residue (2-methylpropanoyl)transferase] lipoyllysine = [dihydrolipoyllysine-residue (2- methylpropanoyl)transferase] S-(2- methylpropanoyl)dihydrolipoyllysine + CO(2).
SubunitHeterotetramer of alpha and beta chains.Heterodimer of an alpha and a beta chain.
Subcellular locationMitochondrion matrix.Mitochondrion matrix.
CofactorThiamine pyrophosphate.


CofactorsSubstratesProducts
KEGG-idC00068C00141L00015C15977C00011
CompoundThiamine diphosphate3-Methyl-2-oxobutanoate[dihydrolipoyllysine-residue (2-methylpropanoyl)transferase] lipoyllysine[dihydrolipoyllysine-residue (2-methylpropanoyl)transferase] S-(2-methylpropanoyl)dihydrolipoyllysineCO2
Typeamine group,aromatic ring (with nitrogen atoms),phosphate group/phosphate ioncarbohydrate,carboxyl groupamide group,disulfide bond,lipid,peptide/proteinamide group,carbohydrate,lipid,peptide/protein,sulfhydryl group,sulfide groupothers
1dtwABound:TDPUnboundUnboundUnboundUnbound
1olsABound:TDPUnboundUnboundUnboundUnbound
1oluABound:TDPUnboundUnboundUnboundUnbound
1olxABound:TDPUnboundUnboundUnboundUnbound
1u5bABound:TDPUnboundUnboundUnboundUnbound
1v11ABound:TDPUnboundUnboundUnboundUnbound
1v16ABound:TDPUnboundUnboundUnboundUnbound
1v1mABound:TDPUnboundUnboundUnboundUnbound
1v1rAUnboundUnboundUnboundUnboundUnbound
1x7wABound:TDPUnboundUnboundUnboundUnbound
1x7xABound:TDPUnboundUnboundUnboundUnbound
1x7yABound:TDPUnboundUnboundUnboundUnbound
1x7zABound:TDPUnboundUnboundUnboundUnbound
1x80ABound:TDPUnboundUnboundUnboundUnbound
1dtwB01UnboundUnboundUnboundUnboundUnbound
1olsB01UnboundUnboundUnboundUnboundUnbound
1oluB01UnboundUnboundUnboundUnboundUnbound
1olxB01UnboundUnboundUnboundUnboundUnbound
1u5bB01UnboundUnboundUnboundUnboundUnbound
1v11B01UnboundUnboundUnboundUnboundUnbound
1v16B01UnboundUnboundUnboundUnboundUnbound
1v1mB01UnboundUnboundUnboundUnboundUnbound
1v1rB01UnboundUnboundUnboundUnboundUnbound
1x7wB01UnboundUnboundUnboundUnboundUnbound
1x7xB01UnboundUnboundUnboundUnboundUnbound
1x7yB01UnboundUnboundUnboundUnboundUnbound
1x7zB01UnboundUnboundUnboundUnboundUnbound
1x80B01UnboundUnboundUnboundUnboundUnbound
1dtwB02UnboundUnboundUnboundUnboundUnbound
1olsB02UnboundUnboundUnboundUnboundUnbound
1oluB02UnboundUnboundUnboundUnboundUnbound
1olxB02UnboundUnboundUnboundUnboundUnbound
1u5bB02UnboundUnboundUnboundUnboundUnbound
1v11B02UnboundUnboundUnboundUnboundUnbound
1v16B02UnboundUnboundUnboundUnboundUnbound
1v1mB02UnboundUnboundUnboundUnboundUnbound
1v1rB02UnboundUnboundUnboundUnboundUnbound
1x7wB02UnboundUnboundUnboundUnboundUnbound
1x7xB02UnboundUnboundUnboundUnboundUnbound
1x7yB02UnboundUnboundUnboundUnboundUnbound
1x7zB02UnboundUnboundUnboundUnboundUnbound
1x80B02UnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
literature [23], [27]
pdbCatalytic residuesCofactor-binding residuesModified residuescomment
1dtwAHIS 291
       ;SER 161;PRO 163;THR 166;GLN 167(Potassium-1);GLU 193;ASN 222;TYR 224(Magnesium)
SER 292;       (Phospholylated)
invisible 302-313
1olsAHIS 291
GLN 112;SER 161;PRO 163;THR 166;GLN 167(Potassium-1);GLU 193;ASN 222;TYR 224(Magnesium)
SER 292;       (Phospholylated)
invisible 293-294, 299, 302-307
1oluA       
GLN 112;SER 161;PRO 163;THR 166;GLN 167(Potassium-1);GLU 193;ASN 222;TYR 224(Magnesium)
       ;       (Phospholylated)
mutant H291A, invisible 288-312
1olxAHIS 291
GLN 112;SER 161;PRO 163;THR 166;GLN 167(Potassium-1);GLU 193;ASN 222;TYR 224(Magnesium)
SER 292;       (Phospholylated)
invisible 302-306
1u5bAHIS 291
       ;SER 161;PRO 163;THR 166;GLN 167(Potassium-1);GLU 193;ASN 222;TYR 224(Magnesium)
SER 292;       (Phospholylated)
invisible 302-305
1v11A       
GLN 112;SER 161;PRO 163;THR 166;GLN 167(Potassium-1);GLU 193;ASN 222;TYR 224(Magnesium)
       ;       (Phospholylated)
mutant R287A, invisible 289-312
1v16A       
GLN 112;SER 161;PRO 163;THR 166;GLN 167(Potassium-1);GLU 193;ASN 222;TYR 224(Magnesium)
       ;       (Phospholylated)
mutant Y300F, invisible 289-312
1v1mA       
GLN 112;SER 161;PRO 163;THR 166;GLN 167(Potassium-1);GLU 193;ASN 222;TYR 224(Magnesium)
       ;       (Phospholylated)
invisible 290-312
1v1rA       
GLN 112;SER 161;PRO 163;THR 166;GLN 167(Potassium-1);GLU 193;ASN 222;       (Magnesium)
       ;       (Phospholylated)
invisible 223-230, 287-313
1x7wA       
GLN 112;SER 161;PRO 163;THR 166;GLN 167(Potassium-1);GLU 193;ASN 222;TYR 224(Magnesium)
       ;       (Phospholylated)
mutant S292Q, invisible 288-312
1x7xA       
GLN 112;SER 161;PRO 163;THR 166;GLN 167(Potassium-1);GLU 193;ASN 222;TYR 224(Magnesium)
       ;       (Phospholylated)
mutant S292E, invisible 288-312
1x7yA       
GLN 112;SER 161;PRO 163;THR 166;GLN 167(Potassium-1);GLU 193;ASN 222;TYR 224(Magnesium)
       ;       (Phospholylated)
mutant S292N, invisible 288-312
1x7zAHIS 291
GLN 112;SER 161;PRO 163;THR 166;GLN 167(Potassium-1);GLU 193;ASN 222;TYR 224(Magnesium)
       ;       (Phospholylated)
mutant S292D, invisible 302-305
1x80A       
GLN 112;SER 161;PRO 163;THR 166;GLN 167(Potassium-1);GLU 193;ASN 222;TYR 224(Magnesium)
       ;       (Phospholylated)
invisible 288-312
1dtwB01               



1olsB01               



1oluB01               



1olxB01               



1u5bB01               



1v11B01               



1v16B01               



1v1mB01               



1v1rB01               



1x7wB01               



1x7xB01               



1x7yB01               



1x7zB01               



1x80B01               



1dtwB02GLU  76;HIS 146
GLY 128;LEU 130;THR 131;CYS 178;ASP 181;ASN 183(Potassium-2)


1olsB02GLU  76;HIS 146
GLY 128;LEU 130;THR 131;CYS 178;ASP 181;ASN 183(Potassium-2)


1oluB02GLU  76;HIS 146
GLY 128;LEU 130;THR 131;CYS 178;ASP 181;ASN 183(Potassium-2)


1olxB02GLU  76;       
GLY 128;LEU 130;THR 131;CYS 178;ASP 181;ASN 183(Potassium-2)

mutant H146A
1u5bB02GLU  76;HIS 146
GLY 128;LEU 130;THR 131;CYS 178;ASP 181;ASN 183(Potassium-2)


1v11B02GLU  76;HIS 146
GLY 128;LEU 130;THR 131;CYS 178;ASP 181;ASN 183(Potassium-2)


1v16B02GLU  76;HIS 146
GLY 128;LEU 130;THR 131;CYS 178;ASP 181;ASN 183(Potassium-2)


1v1mB02GLU  76;HIS 146
GLY 128;LEU 130;THR 131;CYS 178;ASP 181;ASN 183(Potassium-2)


1v1rB02GLU  76;HIS 146
GLY 128;LEU 130;THR 131;CYS 178;ASP 181;ASN 183(Potassium-2)


1x7wB02GLU  76;HIS 146
GLY 128;LEU 130;THR 131;CYS 178;ASP 181;ASN 183(Potassium-2)


1x7xB02GLU  76;HIS 146
GLY 128;LEU 130;THR 131;CYS 178;ASP 181;ASN 183(Potassium-2)


1x7yB02GLU  76;HIS 146
GLY 128;LEU 130;THR 131;CYS 178;ASP 181;ASN 183(Potassium-2)


1x7zB02GLU  76;HIS 146
GLY 128;LEU 130;THR 131;CYS 178;ASP 181;ASN 183(Potassium-2)


1x80B02GLU  76;HIS 146
GLY 128;LEU 130;THR 131;CYS 178;ASP 181;ASN 183(Potassium-2)



References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]Fig.1
[4]Fig.1, Scheme I, p.8508-8510
[8]

[12]Fig.1
[13]Fig.1, p.181-185
[15]p.787-789
[21]Fig.2
[23]p.4170-4171
[24]p.50
[26]Fig.4, p.6999-7001
[27]Fig.7, p.43407-43409
[29]Fig.8, p.1028-1029

references
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JournalEur J Biochem
Year1984
Volume145
Pages587-91
AuthorsCook KG, Bradford AP, Yeaman SJ, Aitken A, Fearnley IM, Walker JE
TitleRegulation of bovine kidney branched-chain 2-oxoacid dehydrogenase complex by reversible phosphorylation.
[2]
PubMed ID2699393
JournalAnn N Y Acad Sci
Year1989
Volume573
Pages1-20
AuthorsPerham RN, Packman LC
Title2-Oxo acid dehydrogenase multienzyme complexes: domains, dynamics, and design.
[3]
CommentsVARIANT MSUD ASN-438
Medline ID89198104
PubMed ID2703538
JournalJ Clin Invest
Year1989
Volume83
Pages1425-9
AuthorsZhang B, Edenberg HJ, Crabb DW, Harris RA
TitleEvidence for both a regulatory mutation and a structural mutation in a family with maple syrup urine disease.
Related Swiss-protP12694
[4]
PubMed ID1888719
JournalBiochemistry
Year1991
Volume30
Pages8501-12
AuthorsPerham RN
TitleDomains, motifs, and linkers in 2-oxo acid dehydrogenase multienzyme complexes: a paradigm in the design of a multifunctional protein.
[5]
CommentsVARIANT MSUD ARG-206
Medline ID94060128
PubMed ID8161368
JournalBiochim Biophys Acta
Year1993
Volume1225
Pages64-70
AuthorsNobukuni Y, Mitsubuchi H, Hayashida Y, Ohta K, Indo Y, Ichiba Y, Endo F, Matsuda I
TitleHeterogeneity of mutations in maple syrup urine disease (MSUD): screening and identification of affected E1 alpha and E1 beta subunits of the branched-chain alpha-keto-acid dehydrogenase multienzyme complex.
Related Swiss-protP21953
[6]
PubMed ID8262228
JournalFEBS Lett
Year1993
Volume336
Pages197-200
AuthorsBunik V, Follmann H
TitleThioredoxin reduction dependent on alpha-ketoacid oxidation by alpha-ketoacid dehydrogenase complexes.
[7]
CommentsVARIANT MSUD CYS-413
Medline ID94311310
PubMed ID8037208
JournalAm J Hum Genet
Year1994
Volume55
Pages297-304
AuthorsChuang JL, Fisher CR, Cox RP, Chuang DT
TitleMolecular basis of maple syrup urine disease: novel mutations at the E1 alpha locus that impair E1(alpha 2 beta 2) assembly or decrease steady-state E1 alpha mRNA levels of branched-chain alpha-keto acid dehydrogenase complex.
Related Swiss-protP12694
[8]
PubMed ID8537366
JournalJ Biol Chem
Year1995
Volume270
Pages31071-6
AuthorsHawes JW, Schnepf RJ, Jenkins AE, Shimomura Y, Popov KM, Harris RA
TitleRoles of amino acid residues surrounding phosphorylation site 1 of branched-chain alpha-ketoacid dehydrogenase (BCKDH) in catalysis and phosphorylation site recognition by BCKDH kinase.
[9]
CommentsVARIANTS MSUD ARG-290 AND CYS-409
Medline ID95190052
PubMed ID7883996
JournalJ Clin Invest
Year1995
Volume95
Pages954-63
AuthorsChuang JL, Davie JR, Chinsky JM, Wynn RM, Cox RP, Chuang DT
TitleMolecular and biochemical basis of intermediate maple syrup urine disease. Occurrence of homozygous G245R and F364C mutations at the E1 alpha locus of Hispanic-Mexican patients.
Related Swiss-protP12694
[10]
PubMed ID7651225
JournalMethods Enzymol
Year1995
Volume251
Pages436-48
AuthorsPerham RN
TitleStructure and posttranslational modification of lipoyl domain of 2-oxo-acid dehydrogenase multienzyme complexes.
[11]
PubMed ID9381974
JournalAdv Enzyme Regul
Year1997
Volume37
Pages271-93
AuthorsHarris RA, Hawes JW, Popov KM, Zhao Y, Shimomura Y, Sato J, Jaskiewicz J, Hurley TD
TitleStudies on the regulation of the mitochondrial alpha-ketoacid dehydrogenase complexes and their kinases.
[12]
PubMed ID9278141
JournalBiol Chem
Year1997
Volume378
Pages617-34
AuthorsBerg A, de Kok A
Title2-Oxo acid dehydrogenase multienzyme complexes. The central role of the lipoyl domain.
[13]
PubMed ID9655906
JournalBiochim Biophys Acta
Year1998
Volume1385
Pages177-86
AuthorsSchellenberger A
TitleSixty years of thiamin diphosphate biochemistry.
[14]
PubMed ID10187830
JournalJ Biol Chem
Year1999
Volume274
Pages10405-12
AuthorsHuang YS, Chuang DT
TitleMechanisms for GroEL/GroES-mediated folding of a large 86-kDa fusion polypeptide in vitro.
[15]
PubMed ID10426958
JournalNat Struct Biol
Year1999
Volume6
Pages785-92
AuthorsAevarsson A, Seger K, Turley S, Sokatch JR, Hol WG
TitleCrystal structure of 2-oxoisovalerate and dehydrogenase and the architecture of 2-oxo acid dehydrogenase multienzyme complexes.
Related PDB1qs0
[16]
PubMed ID10644743
JournalJ Biol Chem
Year2000
Volume275
Pages2786-94
AuthorsWynn RM, Song JL, Chuang DT
TitleGroEL/GroES promote dissociation/reassociation cycles of a heterodimeric intermediate during alpha(2)beta(2) protein assembly. Iterative annealing at the quaternary structure level.
[17]
CommentsX-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 46-445 IN COMPLEX WITH THIAMINE PYROPHOSPHATE AND POTASSIUM IONS, AND SUBUNIT STRUCTURE.
PubMed ID10745006
JournalStructure Fold Des
Year2000
Volume8
Pages277-91
AuthorsAevarsson A, Chuang JL, Wynn RM, Turley S, Chuang DT, Hol WG
TitleCrystal structure of human branched-chain alpha-ketoacid dehydrogenase and the molecular basis of multienzyme complex deficiency in maple syrup urine disease.
Related PDB1dtw
Related Swiss-protP12694
[18]
PubMed ID11509994
JournalAm J Hum Genet
Year2001
Volume69
Pages863-8
AuthorsEdelmann L, Wasserstein MP, Kornreich R, Sansaricq C, Snyderman SE, Diaz GA
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Year2001
Volume70
Pages149-80
AuthorsHuang X, Holden HM, Raushel FM
TitleChanneling of substrates and intermediates in enzyme-catalyzed reactions.
[20]
PubMed ID11168412
JournalEur J Biochem
Year2001
Volume268
Pages727-36
AuthorsOno K, Hakozaki M, Suzuki T, Mori T, Hata H, Kochi H
TitlecDNA cloning of the chicken branched-chain alpha-keto acid dehydrogenase complex. Chicken-specific residues of the acyltransferase affect the overall activity and the interaction with the dehydrogenase.
[21]
PubMed ID11477096
JournalJ Biol Chem
Year2001
Volume276
Pages38329-36
AuthorsReed LJ
TitleA trail of research from lipoic acid to alpha-keto acid dehydrogenase complexes.
[22]
PubMed ID11507102
JournalJ Biol Chem
Year2001
Volume276
Pages40241-6
AuthorsSong JL, Chuang DT
TitleNatural osmolyte trimethylamine N-oxide corrects assembly defects of mutant branched-chain alpha-ketoacid decarboxylase in maple syrup urine disease.
[23]
PubMed ID11069910
JournalJ Biol Chem
Year2001
Volume276
Pages4168-74
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TitleRoles of active site and novel K+ ion-binding site residues in human mitochondrial branched-chain alpha-ketoacid decarboxylase/dehydrogenase.
[24]
PubMed ID12023822
JournalBiochem Soc Trans
Year2002
Volume30
Pages47-51
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TitleSubstrate channelling in 2-oxo acid dehydrogenase multienzyme complexes.
[25]
PubMed ID12383259
JournalEur J Biochem
Year2002
Volume269
Pages5004-15
AuthorsBunik VI, Sievers C
TitleInactivation of the 2-oxo acid dehydrogenase complexes upon generation of intrinsic radical species.
[26]
PubMed ID12795594
JournalBiochemistry
Year2003
Volume42
Pages6996-7002
AuthorsFries M, Jung HI, Perham RN
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[27]
CommentsX-ray crystallography
PubMed ID12902323
JournalJ Biol Chem
Year2003
Volume278
Pages43402-10
AuthorsWynn RM, Machius M, Chuang JL, Li J, Tomchick DR, Chuang DT
TitleRoles of His291-alpha and His146-beta' in the reductive acylation reaction catalyzed by human branched-chain alpha-ketoacid dehydrogenase: refined phosphorylation loop structure in the active site.
Related PDB1ols,1olu,1olx
[28]
CommentsX-ray crystallography
PubMed ID15166214
JournalJ Biol Chem
Year2004
Volume279
Pages32968-78
AuthorsLi J, Wynn RM, Machius M, Chuang JL, Karthikeyan S, Tomchick DR, Chuang DT
TitleCross-talk between thiamin diphosphate binding and phosphorylation loop conformation in human branched-chain alpha-keto acid decarboxylase/dehydrogenase.
Related PDB1v11,1v16,1v1m,1v1r
[29]
PubMed ID15033367
JournalJ Mol Biol
Year2004
Volume337
Pages1011-33
AuthorsNakai T, Nakagawa N, Maoka N, Masui R, Kuramitsu S, Kamiya N
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[30]
CommentsX-ray crystallography
PubMed ID15576032
JournalStructure (Camb)
Year2004
Volume12
Pages2185-96
AuthorsWynn RM, Kato M, Machius M, Chuang JL, Li J, Tomchick DR, Chuang DT
TitleMolecular mechanism for regulation of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase complex by phosphorylation.
Related PDB1u5b,1x7w,1x7x,1x7y,1x7z,1x80

comments
Although this enzyme complex binds magnesium and potassium ions, they are not involved in catalysis.
One of the substrates for this enzyme seems to be a modified lysine residue, lipoyllysine, of dihydrolipoyllysine-residue (2-methylpropanoyl)transferase, or E2 component (E.C. 2.3.1.168; ODB2_HUMAN;P11182).
This enzyme is called branched-chain alpha-keto acid dehydrogenase E1 component.
The following enzymes form multienzyme complex:
pyruvate decarboxylase (E1p, EC 1.2.4.1)
2-oxoglutarate decarboxylase (E1o, EC 1.2.4.2)
dihydrolipoyl acetyltransferase (E2p, EC 2.3.1.12)
dihydrolipoyl succinyltransferase (E2o, EC 2.3.1.61)
dihydrolipoamide dehydrogenase (E3, EC 1.6.4.3)
dihydrolipoyl dehydrogenase (E3, EC 1.8.1.4)
According to the literature [25], [26] and [28], this enzyme catalyzes the following reactions:
(A) Addition of thiazole ring of thiamine diphosphate (ThDP) to carbonyl carbon of the substrate, 3-Methyl-2-oxobutanoate, forming tetrahedral intermediate:
(B) Elimination of CO2, leading to alpha-carbanion/enamine intermediate:
(C) Transfer of sulfur atom from the other sulfur atom of disulfide bond of lipoyllysine to the carbanion, forming the second tetrahedral intermediate:
(D) Elimination of product, S-(2-methylpropanoyl)dihydrolipoyllysine, from ThDP:

createdupdated
2004-03-252009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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