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 |
|---|---|---|---|---|
| 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] |
| 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] |
| 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 29103 |
16997 16997 |
17153 17153 |
15377 15377 |
|||||||
| PubChem |
813 813 |
1030 1030 |
527 527 |
22247451 962 22247451 962 |
|||||||
| 1dioA |
|
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Analogue:B12 | Bound:__K | Bound:PGO | Unbound | ||
| 1dioL |
|
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|
|
|
Analogue:B12 | Bound:__K | Bound:PGO | Unbound | ||
| 1eexA |
|
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|
|
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Analogue:COY | Bound:__K_603 | Bound:PGO | Unbound | ||
| 1eexL |
|
|
|
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|
Analogue:COY | Bound:__K_603 | Bound:PGO | Unbound | ||
| 1egmA |
|
|
|
|
|
Analogue:CNC | Bound:__K | Bound:PGO | Unbound | ||
| 1egmL |
|
|
|
|
|
Analogue:CNC | Bound:__K | Bound:PGO | Unbound | ||
| 1egvA |
|
|
|
|
|
Analogue:COY | Bound:__K_603 | Bound:PGO | Unbound | ||
| 1egvL |
|
|
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|
|
Analogue:COY | Bound:__K_603 | Bound:PGO | Unbound | ||
| 1iwbA |
|
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|
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Analogue:B12 | Bound:__K_2602 | Unbound | Unbound | ||
| 1iwbL |
|
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|
|
Analogue:B12 | Bound:__K_3602 | Unbound | Unbound | ||
| 1uc4A |
|
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|
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|
Analogue:CNC | Bound:__K | Bound:PGO | Unbound | ||
| 1uc4L |
|
|
|
|
|
Analogue:CNC | Bound:__K | Bound:PGO | Unbound | ||
| 1uc5A |
|
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|
|
Analogue:CNC | Bound:__K | Bound:PGR | Unbound | ||
| 1uc5L |
|
|
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|
Analogue:CNC | Bound:__K | Bound:PGR | Unbound | ||
| 1dioB |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | ||
| 1dioE |
|
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|
|
Unbound | Unbound | Unbound | Unbound | ||
| 1eexB |
|
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|
|
Unbound | Unbound | Unbound | Unbound | ||
| 1eexE |
|
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Unbound | Unbound | Unbound | Unbound | ||
| 1egmB |
|
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Unbound | Unbound | Unbound | Unbound | ||
| 1egmE |
|
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Unbound | Unbound | Unbound | Unbound | ||
| 1egvB |
|
|
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|
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Unbound | Unbound | Unbound | Unbound | ||
| 1egvE |
|
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|
|
Unbound | Unbound | Unbound | Unbound | ||
| 1iwbB |
|
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Unbound | Unbound | Unbound | Unbound | ||
| 1iwbE |
|
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Unbound | Unbound | Unbound | Unbound | ||
| 1uc4B |
|
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Unbound | Unbound | Unbound | Unbound | ||
| 1uc4E |
|
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Unbound | Unbound | Unbound | Unbound | ||
| 1uc5B |
|
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Unbound | Unbound | Unbound | Unbound | ||
| 1uc5E |
|
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|
Unbound | Unbound | Unbound | Unbound | ||
| 1dioG |
|
|
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|
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Unbound | Unbound | Unbound | Unbound | ||
| 1dioM |
|
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Unbound | Unbound | Unbound | Unbound | ||
| 1eexG |
|
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|
|
Unbound | Unbound | Unbound | Unbound | ||
| 1eexM |
|
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Unbound | Unbound | Unbound | Unbound | ||
| 1egmG |
|
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|
Unbound | Unbound | Unbound | Unbound | ||
| 1egmM |
|
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Unbound | Unbound | Unbound | Unbound | ||
| 1egvG |
|
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|
|
|
Unbound | Unbound | Unbound | Unbound | ||
| 1egvM |
|
|
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|
|
Unbound | Unbound | Unbound | Unbound | ||
| 1iwbG |
|
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|
Unbound | Unbound | Unbound | Unbound | ||
| 1iwbM |
|
|
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|
|
Unbound | Unbound | Unbound | Unbound | ||
| 1uc4G |
|
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Unbound | Unbound | Unbound | Unbound | ||
| 1uc4M |
|
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Unbound | Unbound | Unbound | Unbound | ||
| 1uc5G |
|
|
|
|
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Unbound | Unbound | Unbound | Unbound | ||
| 1uc5M |
|
|
|
|
|
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 |
|
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|
HIS 143;GLU 170;GLN 296;ASP 335 | GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding) | |||
| 1dioL |
|
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HIS 143;GLU 170;GLN 296;ASP 335 | GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding) | |||
| 1eexA |
|
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HIS 143;GLU 170;GLN 296;ASP 335 | GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding) | |||
| 1eexL |
|
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|
HIS 143;GLU 170;GLN 296;ASP 335 | GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding) | |||
| 1egmA |
|
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HIS 143;GLU 170;GLN 296;ASP 335 | GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding) | |||
| 1egmL |
|
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|
HIS 143;GLU 170;GLN 296;ASP 335 | GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding) | |||
| 1egvA |
|
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|
HIS 143;GLU 170;GLN 296;ASP 335 | GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding) | |||
| 1egvL |
|
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|
|
|
HIS 143;GLU 170;GLN 296;ASP 335 | GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding) | |||
| 1iwbA |
|
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|
|
|
HIS 143;GLU 170;GLN 296;ASP 335 | GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding) | |||
| 1iwbL |
|
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|
HIS 143;GLU 170;GLN 296;ASP 335 | GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding) | |||
| 1uc4A |
|
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|
HIS 143;GLU 170;GLN 296;ASP 335 | GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding) | |||
| 1uc4L |
|
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|
HIS 143;GLU 170;GLN 296;ASP 335 | GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding) | |||
| 1uc5A |
|
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HIS 143;GLU 170;GLN 296;ASP 335 | GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding) | |||
| 1uc5L |
|
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HIS 143;GLU 170;GLN 296;ASP 335 | GLN 141;GLU 170;GLU 221;GLN 296;SER 362(Potassium binding) | |||
| 1dioB |
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| 1dioE |
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| 1eexB |
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| 1eexE |
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| 1egmB |
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| 1egmE |
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| 1egvB |
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| 1egvE |
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| 1iwbB |
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| 1iwbE |
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| 1uc4B |
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| 1uc4E |
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| 1uc5B |
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| 1uc5E |
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| 1dioG |
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| 1dioM |
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| 1eexG |
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| 1eexM |
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| 1egmG |
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| 1egmM |
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| 1egvG |
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| 1egvM |
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| 1iwbG |
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| 1iwbM |
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| 1uc4G |
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| 1uc4M |
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| 1uc5G |
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| 1uc5M |
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| 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, |
| 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, |
| 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, Although this enzyme is classified into lyase enzymes, |
| Created | Updated |
|---|---|
| 2004-04-12 | 2009-03-10 |