EzCatDB: T00234
Related links:    PDB-formatted query search system Fasta-formatted query search system Fasta-formatted query search system

DB codeT00234
CATH domainDomain 13.20.20.350 : TIM BarrelCatalytic domain
Domain 23.40.50.10150 : Rossmann fold
Domain 31.-.-.-
E.C.4.2.1.28
CSA1dio


Enzyme Name
UniProtKBKEGG

Q59470Q59471Q59472
Protein name


propanediol dehydratase
meso-2,3-butanediol dehydrase
diol dehydratase
DL-1,2-propanediol hydro-lyase
diol dehydrase
adenosylcobalamin-dependent diol dehydratase
propanediol dehydrase
coenzyme B12-dependent diol dehydrase
1,2-propanediol dehydratase
dioldehydratase
propane-1,2-diol hydro-lyase
SynonymsDiol dehydrase alpha subunit
EC 4.2.1.28
Diol dehydrase beta subunit
EC 4.2.1.28
Diol dehydrase gamma subunit
EC 4.2.1.28
RefSeqYP_005016275.1 (Protein)
NC_016612.1 (DNA/RNA sequence)
YP_005016276.1 (Protein)
NC_016612.1 (DNA/RNA sequence)
YP_005016277.1 (Protein)
NC_016612.1 (DNA/RNA sequence)
PfamPF02286 (Dehydratase_LU)
[Graphical view]
PF02288 (Dehydratase_MU)
[Graphical view]
PF02287 (Dehydratase_SU)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00561Glycerolipid metabolism

UniProtKB:Accession NumberQ59470Q59471Q59472
Entry nameQ59470_KLEOXQ59471_KLEOXQ59472_KLEOX
Activity


Subunit


Subcellular location


Cofactor



Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00194C00238C00583C00479C00001
CompoundCobamide coenzymePotassiumPropane-1,2-diolPropanalH2O
Typeamide group,amine group,aromatic ring (with nitrogen atoms),carbohydrate,heavy metal,nucleoside,nucleotideunivalent metal (Na+, K+)carbohydratecarbohydrateH2O
ChEBI
29103
16997
17153
15377
PubChem
813
1030
527
962
22247451
             
1dioAAnalogue:B12Bound:__KBound:PGOUnbound 
1dioLAnalogue:B12Bound:__KBound:PGOUnbound 
1eexAAnalogue:COYBound:__K 603Bound:PGOUnbound 
1eexLAnalogue:COYBound:__K 603Bound:PGOUnbound 
1egmAAnalogue:CNCBound:__KBound:PGOUnbound 
1egmLAnalogue:CNCBound:__KBound:PGOUnbound 
1egvAAnalogue:COYBound:__K 603Bound:PGOUnbound 
1egvLAnalogue:COYBound:__K 603Bound:PGOUnbound 
1iwbAAnalogue:B12Bound:__K 2602UnboundUnbound 
1iwbLAnalogue:B12Bound:__K 3602UnboundUnbound 
1uc4AAnalogue:CNCBound:__KBound:PGOUnbound 
1uc4LAnalogue:CNCBound:__KBound:PGOUnbound 
1uc5AAnalogue:CNCBound:__KBound:PGRUnbound 
1uc5LAnalogue:CNCBound:__KBound:PGRUnbound 
1dioBUnboundUnboundUnboundUnbound 
1dioEUnboundUnboundUnboundUnbound 
1eexBUnboundUnboundUnboundUnbound 
1eexEUnboundUnboundUnboundUnbound 
1egmBUnboundUnboundUnboundUnbound 
1egmEUnboundUnboundUnboundUnbound 
1egvBUnboundUnboundUnboundUnbound 
1egvEUnboundUnboundUnboundUnbound 
1iwbBUnboundUnboundUnboundUnbound 
1iwbEUnboundUnboundUnboundUnbound 
1uc4BUnboundUnboundUnboundUnbound 
1uc4EUnboundUnboundUnboundUnbound 
1uc5BUnboundUnboundUnboundUnbound 
1uc5EUnboundUnboundUnboundUnbound 
1dioGUnboundUnboundUnboundUnbound 
1dioMUnboundUnboundUnboundUnbound 
1eexGUnboundUnboundUnboundUnbound 
1eexMUnboundUnboundUnboundUnbound 
1egmGUnboundUnboundUnboundUnbound 
1egmMUnboundUnboundUnboundUnbound 
1egvGUnboundUnboundUnboundUnbound 
1egvMUnboundUnboundUnboundUnbound 
1iwbGUnboundUnboundUnboundUnbound 
1iwbMUnboundUnboundUnboundUnbound 
1uc4GUnboundUnboundUnboundUnbound 
1uc4MUnboundUnboundUnboundUnbound 
1uc5GUnboundUnboundUnboundUnbound 
1uc5MUnboundUnboundUnboundUnbound 

Active-site residues
resource
PDB;1dio & literature [21]
pdbCatalytic residuesCofactor-binding residues
          
1dioAHIS 143;GLU 170;GLN 296;ASP 335
GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1dioLHIS 143;GLU 170;GLN 296;ASP 335
GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1eexAHIS 143;GLU 170;GLN 296;ASP 335
GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1eexLHIS 143;GLU 170;GLN 296;ASP 335
GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1egmAHIS 143;GLU 170;GLN 296;ASP 335
GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1egmLHIS 143;GLU 170;GLN 296;ASP 335
GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1egvAHIS 143;GLU 170;GLN 296;ASP 335
GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1egvLHIS 143;GLU 170;GLN 296;ASP 335
GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1iwbAHIS 143;GLU 170;GLN 296;ASP 335
GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1iwbLHIS 143;GLU 170;GLN 296;ASP 335
GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1uc4AHIS 143;GLU 170;GLN 296;ASP 335
GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1uc4LHIS 143;GLU 170;GLN 296;ASP 335
GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1uc5AHIS 143;GLU 170;GLN 296;ASP 335
GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1uc5LHIS 143;GLU 170;GLN 296;ASP 335
GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1dioB 
 
1dioE 
 
1eexB 
 
1eexE 
 
1egmB 
 
1egmE 
 
1egvB 
 
1egvE 
 
1iwbB 
 
1iwbE 
 
1uc4B 
 
1uc4E 
 
1uc5B 
 
1uc5E 
 
1dioG 
 
1dioM 
 
1eexG 
 
1eexM 
 
1egmG 
 
1egmM 
 
1egvG 
 
1egvM 
 
1iwbG 
 
1iwbM 
 
1uc4G 
 
1uc4M 
 
1uc5G 
 
1uc5M 
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]Scheme 2, equation (7), p.535-5384
[3]Scheme I
[9]Fig.4, p.652-6545
[10]Fig.9p.1005-1006
[11]Scheme 3, Scheme 4, p.6255-6256
[12]Fig.8, p.108-1176
[13]Fig.8, p.782-7856
[14]Fig.11, p.138-140
[15]

[18]Fig.7, p.12613-12616
[19]Fig.8, Fig.9, p.359-3636
[20]p.2098, p.2105-2111, p.2114-2117, Fig.12, Fig.156
[21]p.22724-22725, Fig.7

references
[1]
PubMed ID2869515
JournalPhilos Trans R Soc Lond B Biol Sci
Year1985
Volume311
Pages531-44
AuthorsDixon RM, Golding BT, Mwesigye-Kibende S, Ramakrishna Rao DN
TitleConcerning the intermediacy of organic radicals in vitamin B12-dependent enzymic reactions.
[2]
PubMed ID2936306
JournalArch Biochem Biophys
Year1986
Volume245
Pages144-52
AuthorsHartmanis MG, Stadtman TC
TitleDiol metabolism and diol dehydratase in Clostridium glycolicum.
[3]
PubMed ID3298236
JournalJ Biol Chem
Year1987
Volume262
Pages8544-50
AuthorsToraya T, Watanabe N, Ichikawa M, Matsumoto T, Ushio K, Fukui S
TitleActivation and cleavage of the carbon-cobalt bond of adeninylethylcobalamin by diol dehydrase.
[4]
PubMed ID9003432
JournalBiochim Biophys Acta
Year1997
Volume1337
Pages11-6
AuthorsToraya T, Yamanishi M, Muguruma H, Ushio K, Yamauchi J, Kawamura T
TitleAn electron paramagnetic resonance study on the mechanism-based inactivation of adenosylcobalamin-dependent diol dehydrase by glycerol and other substrates.
[5]
PubMed ID9151970
JournalEur J Biochem
Year1997
Volume245
Pages398-401
AuthorsPoppe L, Retey J
TitleKinetic investigations with inhibitors that mimic the posthomolysis intermediate in the reactions of coenzyme-B12-dependent glycerol dehydratase and diol dehydratase.
[6]
PubMed ID9428677
JournalEur J Biochem
Year1997
Volume250
Pages303-7
AuthorsPoppe L, Stupperich E, Hull WE, Buckel T, Retey J
TitleA base-off analogue of coenzyme-B12 with a modified nucleotide loop--1H-NMR structure analysis and kinetic studies with (R)-methylmalonyl-CoA mutase, glycerol dehydratase, and diol dehydratase.
[7]
PubMed ID9537996
JournalBiochemistry
Year1998
Volume37
Pages4799-803
AuthorsYamanishi M, Yamada S, Muguruma H, Murakami Y, Tobimatsu T, Ishida A, Yamauchi J, Toraya T
TitleEvidence for axial coordination of 5,6-dimethylbenzimidazole to the cobalt atom of adenosylcobalamin bound to diol dehydratase.
[8]
PubMed ID9722671
JournalJ Biochem (Tokyo)
Year1998
Volume124
Pages598-601
AuthorsYamanishi M, Yamada S, Ishida A, Yamauchi J, Toraya T
TitleEPR spectroscopic evidence for the mechanism-based inactivation of adenosylcobalamin-dependent diol dehydratase by coenzyme analogs.
[9]
PubMed ID10502670
JournalJ Biochem (Tokyo)
Year1999
Volume126
Pages650-4
AuthorsToraya T, Yoshizawa K, Eda M, Yamabe T
TitleDirect participation of potassium ion in the catalysis of coenzyme B(12)-dependent diol dehydratase.
[10]
CommentsX-ray crystallography
PubMed ID10467140
JournalStructure Fold Des
Year1999
Volume7
Pages997-1008
AuthorsShibata N, Masuda J, Tobimatsu T, Toraya T, Suto K, Morimoto Y, Yasuoka N
TitleA new mode of B12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase.
Related PDB1dio
[11]
PubMed ID10821701
JournalBiochemistry
Year2000
Volume39
Pages6250-7
AuthorsAbend A, Bandarian V, Reed GH, Frey PA
TitleIdentification of cis-ethanesemidione as the organic radical derived from glycolaldehyde in the suicide inactivation of dioldehydrase and of ethanolamine ammonia-lyase.
[12]
PubMed ID10949584
JournalCell Mol Life Sci
Year2000
Volume57
Pages106-27
AuthorsToraya T
TitleRadical catalysis of B12 enzymes: structure, mechanism, inactivation, and reactivation of diol and glycerol dehydratases.
[13]
CommentsX-ray crystallography
PubMed ID10903944
JournalStructure Fold Des
Year2000
Volume8
Pages775-88
AuthorsMasuda J, Shibata N, Morimoto Y, Toraya T, Yasuoka N
TitleHow a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex.
Related PDB1eex,1egm,1egv
[14]
PubMed ID11395404
JournalAnnu Rev Biochem
Year2001
Volume70
Pages121-48
AuthorsFrey PA
TitleRadical mechanisms of enzymatic catalysis.
[15]
PubMed ID11456766
JournalJ Am Chem Soc
Year2001
Volume123
Pages1664-75
AuthorsSmith DM, Golding BT, Radom L
TitleUnderstanding the mechanism of B(12)-dependent diol dehydratase: a synergistic retro-push--pull proposal.
[16]
PubMed ID11679769
JournalJ Synchrotron Radiat
Year2001
Volume8
Pages1182-5
AuthorsMasuda J, Shibata N, Morimoto Y, Toraya T, Yasuoka N
TitleRadical production simulated by photoirradiation of the diol dehydratase-adeninylpentylcobalamin complex.
[17]
PubMed ID11814365
JournalBiochemistry
Year2002
Volume41
Pages1695-702
AuthorsMagnusson OT, Frey PA
TitleInteractions of diol dehydrase and 3',4'-anhydroadenosylcobalamin: suicide inactivation by electron transfer.
[18]
PubMed ID12379103
JournalBiochemistry
Year2002
Volume41
Pages12607-17
AuthorsShibata N, Masuda J, Morimoto Y, Yasuoka N, Toraya T
TitleSubstrate-induced conformational change of a coenzyme B12-dependent enzyme: crystal structure of the substrate-free form of diol dehydratase.
Related PDB1iwb
[19]
PubMed ID12369058
JournalChem Rec
Year2002
Volume2
Pages352-66
AuthorsToraya T
TitleEnzymatic radical catalysis: coenzyme B12-dependent diol dehydratase.
[20]
PubMed ID12797825
JournalChem Rev
Year2003
Volume103
Pages2095-127
AuthorsToraya T
TitleRadical catalysis in coenzyme B12-dependent isomerization (eliminating) reactions.
[21]
PubMed ID12684496
JournalJ Biol Chem
Year2003
Volume278
Pages22717-25
AuthorsShibata N, Nakanishi Y, Fukuoka M, Yamanishi M, Yasuoka N, Toraya T
TitleStructural rationalization for the lack of stereospecificity in coenzyme B12-dependent diol dehydratase.
Related PDB1uc4,1uc5

comments
This enzyme is composed of three distinct subunits, alpha, beta, and gamma.
Although this enzyme is classified into lyase enzymes, it catalyzes radical reactions (see literature [11], [12], [13], [14], [18], [19], [20] & [21]).

createdupdated
2004-04-122009-03-10


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 2008)
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)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
© Biotechnology Research Institute for Drug Discovery, AIST, 2015-2016 All Rights Reserved.
© Computational Biology Research Center, AIST, 2004-2016 All Rights Reserved.