DB code: T00234

CATH domain 3.20.20.350 : TIM Barrel Catalytic domain
3.40.50.10150 : Rossmann fold
1.-.-.- :
E.C. 4.2.1.28
CSA 1dio
M-CSA 1dio
MACiE

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
Q59470
Diol dehydrase alpha subunit
EC 4.2.1.28
YP_005016275.1 (Protein)
NC_016612.1 (DNA/RNA sequence)
PF02286 (Dehydratase_LU)
[Graphical View]
Q59471
Diol dehydrase beta subunit
EC 4.2.1.28
YP_005016276.1 (Protein)
NC_016612.1 (DNA/RNA sequence)
PF02288 (Dehydratase_MU)
[Graphical View]
Q59472
Diol dehydrase gamma subunit
EC 4.2.1.28
YP_005016277.1 (Protein)
NC_016612.1 (DNA/RNA sequence)
PF02287 (Dehydratase_SU)
[Graphical View]

KEGG enzyme 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

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q59470 Q59470_KLEOX
Q59471 Q59471_KLEOX
Q59472 Q59472_KLEOX

KEGG Pathways
Map code Pathways E.C.
MAP00561 Glycerolipid metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00194 C00238 C00583 C00479 C00001
E.C.
Compound Cobamide coenzyme Potassium Propane-1,2-diol Propanal H2O
Type amide group,amine group,aromatic ring (with nitrogen atoms),carbohydrate,heavy metal,nucleoside,nucleotide univalent metal (Na+, K+) carbohydrate carbohydrate H2O
ChEBI 29103
16997
17153
15377
PubChem 813
1030
527
22247451
962
1dioA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:B12 Bound:__K Bound:PGO Unbound
1dioL Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:B12 Bound:__K Bound:PGO Unbound
1eexA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:COY Bound:__K_603 Bound:PGO Unbound
1eexL Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:COY Bound:__K_603 Bound:PGO Unbound
1egmA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:CNC Bound:__K Bound:PGO Unbound
1egmL Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:CNC Bound:__K Bound:PGO Unbound
1egvA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:COY Bound:__K_603 Bound:PGO Unbound
1egvL Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:COY Bound:__K_603 Bound:PGO Unbound
1iwbA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:B12 Bound:__K_2602 Unbound Unbound
1iwbL Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:B12 Bound:__K_3602 Unbound Unbound
1uc4A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:CNC Bound:__K Bound:PGO Unbound
1uc4L Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:CNC Bound:__K Bound:PGO Unbound
1uc5A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:CNC Bound:__K Bound:PGR Unbound
1uc5L Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:CNC Bound:__K Bound:PGR Unbound
1dioB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1dioE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1eexB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1eexE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1egmB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1egmE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1egvB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1egvE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1iwbB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1iwbE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1uc4B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1uc4E Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1uc5B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1uc5E Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1dioG Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1dioM Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1eexG Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1eexM Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1egmG Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1egmM Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1egvG Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1egvM Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1iwbG Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1iwbM Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1uc4G Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1uc4M Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1uc5G Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1uc5M Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
PDB;1dio & literature [21]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1dioA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 143;GLU 170;GLN 296;ASP 335 GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1dioL Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 143;GLU 170;GLN 296;ASP 335 GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1eexA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 143;GLU 170;GLN 296;ASP 335 GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1eexL Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 143;GLU 170;GLN 296;ASP 335 GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1egmA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 143;GLU 170;GLN 296;ASP 335 GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1egmL Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 143;GLU 170;GLN 296;ASP 335 GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1egvA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 143;GLU 170;GLN 296;ASP 335 GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1egvL Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 143;GLU 170;GLN 296;ASP 335 GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1iwbA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 143;GLU 170;GLN 296;ASP 335 GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1iwbL Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 143;GLU 170;GLN 296;ASP 335 GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1uc4A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 143;GLU 170;GLN 296;ASP 335 GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1uc4L Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 143;GLU 170;GLN 296;ASP 335 GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1uc5A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 143;GLU 170;GLN 296;ASP 335 GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1uc5L Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 143;GLU 170;GLN 296;ASP 335 GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding)
1dioB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dioE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1eexB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1eexE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1egmB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1egmE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1egvB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1egvE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1iwbB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1iwbE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1uc4B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1uc4E Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1uc5B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1uc5E Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dioG Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dioM Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1eexG Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1eexM Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1egmG Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1egmM Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1egvG Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1egvM Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1iwbG Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1iwbM Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1uc4G Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1uc4M Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1uc5G Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1uc5M Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
Scheme 2, equation (7), p.535-538 4
[3]
Scheme I
[9]
Fig.4, p.652-654 5
[10]
Fig.9 p.1005-1006
[11]
Scheme 3, Scheme 4, p.6255-6256
[12]
Fig.8, p.108-117 6
[13]
Fig.8, p.782-785 6
[14]
Fig.11, p.138-140
[15]
[18]
Fig.7, p.12613-12616
[19]
Fig.8, Fig.9, p.359-363 6
[20]
p.2098, p.2105-2111, p.2114-2117, Fig.12, Fig.15 6
[21]
p.22724-22725, Fig.7

References
[1]
Resource
Comments
Medline ID
PubMed ID 2869515
Journal Philos Trans R Soc Lond B Biol Sci
Year 1985
Volume 311
Pages 531-44
Authors Dixon RM, Golding BT, Mwesigye-Kibende S, Ramakrishna Rao DN
Title Concerning the intermediacy of organic radicals in vitamin B12-dependent enzymic reactions.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 2936306
Journal Arch Biochem Biophys
Year 1986
Volume 245
Pages 144-52
Authors Hartmanis MG, Stadtman TC
Title Diol metabolism and diol dehydratase in Clostridium glycolicum.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 3298236
Journal J Biol Chem
Year 1987
Volume 262
Pages 8544-50
Authors Toraya T, Watanabe N, Ichikawa M, Matsumoto T, Ushio K, Fukui S
Title Activation and cleavage of the carbon-cobalt bond of adeninylethylcobalamin by diol dehydrase.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 9003432
Journal Biochim Biophys Acta
Year 1997
Volume 1337
Pages 11-6
Authors Toraya T, Yamanishi M, Muguruma H, Ushio K, Yamauchi J, Kawamura T
Title An electron paramagnetic resonance study on the mechanism-based inactivation of adenosylcobalamin-dependent diol dehydrase by glycerol and other substrates.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 9151970
Journal Eur J Biochem
Year 1997
Volume 245
Pages 398-401
Authors Poppe L, Retey J
Title Kinetic investigations with inhibitors that mimic the posthomolysis intermediate in the reactions of coenzyme-B12-dependent glycerol dehydratase and diol dehydratase.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 9428677
Journal Eur J Biochem
Year 1997
Volume 250
Pages 303-7
Authors Poppe L, Stupperich E, Hull WE, Buckel T, Retey J
Title A 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.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 9537996
Journal Biochemistry
Year 1998
Volume 37
Pages 4799-803
Authors Yamanishi M, Yamada S, Muguruma H, Murakami Y, Tobimatsu T, Ishida A, Yamauchi J, Toraya T
Title Evidence for axial coordination of 5,6-dimethylbenzimidazole to the cobalt atom of adenosylcobalamin bound to diol dehydratase.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 9722671
Journal J Biochem (Tokyo)
Year 1998
Volume 124
Pages 598-601
Authors Yamanishi M, Yamada S, Ishida A, Yamauchi J, Toraya T
Title EPR spectroscopic evidence for the mechanism-based inactivation of adenosylcobalamin-dependent diol dehydratase by coenzyme analogs.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 10502670
Journal J Biochem (Tokyo)
Year 1999
Volume 126
Pages 650-4
Authors Toraya T, Yoshizawa K, Eda M, Yamabe T
Title Direct participation of potassium ion in the catalysis of coenzyme B(12)-dependent diol dehydratase.
Related PDB
Related UniProtKB
[10]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10467140
Journal Structure Fold Des
Year 1999
Volume 7
Pages 997-1008
Authors Shibata N, Masuda J, Tobimatsu T, Toraya T, Suto K, Morimoto Y, Yasuoka N
Title A new mode of B12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase.
Related PDB 1dio
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 10821701
Journal Biochemistry
Year 2000
Volume 39
Pages 6250-7
Authors Abend A, Bandarian V, Reed GH, Frey PA
Title Identification of cis-ethanesemidione as the organic radical derived from glycolaldehyde in the suicide inactivation of dioldehydrase and of ethanolamine ammonia-lyase.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 10949584
Journal Cell Mol Life Sci
Year 2000
Volume 57
Pages 106-27
Authors Toraya T
Title Radical catalysis of B12 enzymes: structure, mechanism, inactivation, and reactivation of diol and glycerol dehydratases.
Related PDB
Related UniProtKB
[13]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10903944
Journal Structure Fold Des
Year 2000
Volume 8
Pages 775-88
Authors Masuda J, Shibata N, Morimoto Y, Toraya T, Yasuoka N
Title How a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex.
Related PDB 1eex 1egm 1egv
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 11395404
Journal Annu Rev Biochem
Year 2001
Volume 70
Pages 121-48
Authors Frey PA
Title Radical mechanisms of enzymatic catalysis.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 11456766
Journal J Am Chem Soc
Year 2001
Volume 123
Pages 1664-75
Authors Smith DM, Golding BT, Radom L
Title Understanding the mechanism of B(12)-dependent diol dehydratase: a synergistic retro-push--pull proposal.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 11679769
Journal J Synchrotron Radiat
Year 2001
Volume 8
Pages 1182-5
Authors Masuda J, Shibata N, Morimoto Y, Toraya T, Yasuoka N
Title Radical production simulated by photoirradiation of the diol dehydratase-adeninylpentylcobalamin complex.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 11814365
Journal Biochemistry
Year 2002
Volume 41
Pages 1695-702
Authors Magnusson OT, Frey PA
Title Interactions of diol dehydrase and 3',4'-anhydroadenosylcobalamin: suicide inactivation by electron transfer.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 12379103
Journal Biochemistry
Year 2002
Volume 41
Pages 12607-17
Authors Shibata N, Masuda J, Morimoto Y, Yasuoka N, Toraya T
Title Substrate-induced conformational change of a coenzyme B12-dependent enzyme: crystal structure of the substrate-free form of diol dehydratase.
Related PDB 1iwb
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 12369058
Journal Chem Rec
Year 2002
Volume 2
Pages 352-66
Authors Toraya T
Title Enzymatic radical catalysis: coenzyme B12-dependent diol dehydratase.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 12797825
Journal Chem Rev
Year 2003
Volume 103
Pages 2095-127
Authors Toraya T
Title Radical catalysis in coenzyme B12-dependent isomerization (eliminating) reactions.
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 12684496
Journal J Biol Chem
Year 2003
Volume 278
Pages 22717-25
Authors Shibata N, Nakanishi Y, Fukuoka M, Yamanishi M, Yasuoka N, Toraya T
Title Structural rationalization for the lack of stereospecificity in coenzyme B12-dependent diol dehydratase.
Related PDB 1uc4 1uc5
Related UniProtKB

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]).

Created Updated
2004-04-12 2009-03-10