EzCatDB: D00016

DB codeD00016
CATH domainDomain 12.140.10.10Catalytic domain
Domain 24.10.160.10
E.C.1.1.2.7
CSA1g72
MACiEM0099


Enzyme Name
Swiss-protKEGG

P38539P16027P12293P38540P14775P29898
Protein nameMethanol dehydrogenase subunit 1Methanol dehydrogenase subunit 1Methanol dehydrogenase subunit 1Methanol dehydrogenase subunit 2Methanol dehydrogenase subunit 2Methanol dehydrogenase subunit 2methanol dehydrogenase (cytochrome c)
methanol dehydrogenase
MDH
SynonymsEC 1.1.99.8
MDH large alpha subunit
MEDH
EC 1.1.99.8
MDH large alpha subunit
MEDH
EC 1.1.99.8
MDH large alpha subunit
MEDH
EC 1.1.99.8
MDH small subunit beta
MDH-associated peptide
MEDH
EC 1.1.99.8
MDH small subunit beta
MDH-associated peptide
MEDH
EC 1.1.99.8
MDH small subunit beta
MDH-associated peptide
MEDH

KEGG pathways
MAP codePathways
MAP00010Glycolysis / Gluconeogenesis
MAP00625Chloroalkane and chloroalkene degradation
MAP00680Methane metabolism
MAP00910Nitrogen metabolism

Swiss-prot:Accession NumberP38539P16027P12293P38540P14775P29898
Entry nameDHM1_METMEDHM1_METEXDHM1_PARDEDHM2_METMEDHM2_METEXDHM2_PARDE
ActivityA primary alcohol + 2 cytochrome c(L) = an aldehyde + 2 reduced cytochrome c(L).A primary alcohol + 2 cytochrome c(L) = an aldehyde + 2 reduced cytochrome c(L).A primary alcohol + 2 cytochrome c(L) = an aldehyde + 2 reduced cytochrome c(L).A primary alcohol + 2 cytochrome c(L) = an aldehyde + 2 reduced cytochrome c(L).A primary alcohol + 2 cytochrome c(L) = an aldehyde + 2 reduced cytochrome c(L).A primary alcohol + 2 cytochrome c(L) = an aldehyde + 2 reduced cytochrome c(L).
SubunitHeterotetramer of 2 alpha and 2 beta subunits.Heterotetramer composed of 2 alpha and 2 beta subunits.Heterotetramer composed of 2 alpha and 2 beta subunits.Heterotetramer composed of 2 alpha and 2 beta subunits.Heterotetramer composed of 2 alpha and 2 beta subunits.Heterotetramer composed of 2 alpha and 2 beta subunits.
Subcellular locationCell inner membrane, Peripheral membrane protein, Periplasmic side. Note=Periplasmic, but associated with inner membrane.Cell inner membrane, Peripheral membrane protein, Periplasmic side. Note=Periplasmic, but associated with inner membrane.Periplasm.Cell inner membrane, Peripheral membrane protein, Periplasmic side. Note=Periplasmic, but associated with inner membrane.Periplasm.Periplasm.
CofactorBinds 1 calcium ion per subunit.,Binds 1 PQQ per subunit. PQQ is inserted between disulfide Cys-105-Cys-106 and the indole ring of Trp-239.Binds 1 PQQ group per subunit. PQQ is inserted between disulfide Cys-130-Cys-131 and the indole ring of Trp-270.,Binds 1 calcium ion per subunit.Binds 1 PQQ group per subunit. PQQ is inserted between disulfide Cys-135-Cys-136 and the indole ring of Trp-275.,Binds 1 calcium ion per subunit.




CofactorsSubstratesProducts
KEGG-idC00113C00076C00226C18233C00071C18234
CompoundPQQCalciumPrimary alcoholCytochrome cLAldehydeReduced cytochrome cL
Typearomatic ring (with nitrogen atoms),carbohydrate,carboxyl groupdivalent metal (Ca2+, Mg2+)carbohydrateamide group,amine group,aromatic ring (with nitrogen atoms),carboxyl group,heavy metal,peptide/protein,sulfide groupcarbohydrateamide group,amine group,aromatic ring (with nitrogen atoms),carboxyl group,heavy metal,peptide/protein,sulfide group
1b2nABound:PQQBound:_CABound:MOHUnboundUnboundUnbound
1b2nCBound:PQQBound:_CABound:MOHUnboundUnboundUnbound
1g72ABound:PQQBound:_CAUnboundUnboundUnboundUnbound
1g72CBound:PQQBound:_CAUnboundUnboundUnboundUnbound
3aahABound:PQQBound:_CAUnboundUnboundUnboundUnbound
3aahCBound:PQQBound:_CAUnboundUnboundUnboundUnbound
4aahABound:PQQBound:_CAUnboundUnboundUnboundUnbound
4aahCBound:PQQBound:_CAUnboundUnboundUnboundUnbound
1h4iABound:PQQBound:_CAUnboundUnboundUnboundUnbound
1h4iCBound:PQQBound:_CAUnboundUnboundUnboundUnbound
1h4jABound:PQQBound:_CAUnboundUnboundUnboundUnbound
1h4jCBound:PQQBound:_CAUnboundUnboundUnboundUnbound
1h4jEBound:PQQBound:_CAUnboundUnboundUnboundUnbound
1h4jGBound:PQQBound:_CAUnboundUnboundUnboundUnbound
1w6sABound:PQQBound:_CAUnboundUnboundUnboundUnbound
1w6sCBound:PQQBound:_CAUnboundUnboundUnboundUnbound
1lrwABound:PQQBound:_CAUnboundUnboundUnboundUnbound
1lrwCBound:PQQBound:_CAUnboundUnboundUnboundUnbound
1b2nBUnboundUnboundUnboundUnboundUnboundUnbound
1b2nDUnboundUnboundUnboundUnboundUnboundUnbound
1g72BUnboundUnboundUnboundUnboundUnboundUnbound
1g72DUnboundUnboundUnboundUnboundUnboundUnbound
3aahBUnboundUnboundUnboundUnboundUnboundUnbound
3aahDUnboundUnboundUnboundUnboundUnboundUnbound
4aahBUnboundUnboundUnboundUnboundUnboundUnbound
4aahDUnboundUnboundUnboundUnboundUnboundUnbound
1h4iBUnboundUnboundUnboundUnboundUnboundUnbound
1h4iDUnboundUnboundUnboundUnboundUnboundUnbound
1h4jBUnboundUnboundUnboundUnboundUnboundUnbound
1h4jDUnboundUnboundUnboundUnboundUnboundUnbound
1h4jFUnboundUnboundUnboundUnboundUnboundUnbound
1h4jHUnboundUnboundUnboundUnboundUnboundUnbound
1w6sBUnboundUnboundUnboundUnboundUnboundUnbound
1w6sDUnboundUnboundUnboundUnboundUnboundUnbound
1lrwBUnboundUnboundUnboundUnboundUnboundUnbound
1lrwDUnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P38539
pdbCatalytic residuesCofactor-binding residues
1b2nACYS  103;CYS  104;ASP  105;ASP  297
GLU  171;ASN  255(Calcium binding)
1b2nCCYS  103;CYS  104;ASP  105;ASP  297
GLU  171;ASN  255(Calcium binding)
1g72ACYS  103;CYS  104;ASP  105;ASP  297
GLU  171;ASN  255(Calcium binding)
1g72CCYS  103;CYS  104;ASP  105;ASP  297
GLU  171;ASN  255(Calcium binding)
3aahACYS  103;CYS  104;ASP  105;ASP  297
GLU  171;ASN  255(Calcium binding)
3aahCCYS  103;CYS  104;ASP  105;ASP  297
GLU  171;ASN  255(Calcium binding)
4aahACYS  103;CYS  104;ASP  105;ASP  297
GLU  171;ASN  255(Calcium binding)
4aahCCYS  103;CYS  104;ASP  105;ASP  297
GLU  171;ASN  255(Calcium binding)
1h4iACYS  103;CYS  104;ASP  105;ASP  303
GLU  177;ASN  261(Calcium binding)
1h4iCCYS  103;CYS  104;ASP  105;ASP  303
GLU  177;ASN  261(Calcium binding)
1h4jACYS  103;CYS  104;ASP  105;GLU  303
GLU  177;ASN  261(Calcium binding)
1h4jCCYS  103;CYS  104;ASP  105;GLU  303
GLU  177;ASN  261(Calcium binding)
1h4jECYS  103;CYS  104;ASP  105;GLU  303
GLU  177;ASN  261(Calcium binding)
1h4jGCYS  103;CYS  104;ASP  105;GLU  303
GLU  177;ASN  261(Calcium binding)
1w6sACYS  103;CYS  104;ASP  105;ASP  303
GLU  177;ASN  261(Calcium binding)
1w6sCCYS 2103;CYS 2104;ASP 2105;ASP 2303
GLU 2177;ASN 2261(Calcium binding)
1lrwACYS  103;CYS  104;ASP  105;ASP  303
GLU  177;ASN  261(Calcium binding)
1lrwCCYS  103;CYS  104;ASP  105;ASP  303
GLU  177;ASN  261(Calcium binding)
1b2nB

1b2nD

1g72B

1g72D

3aahB

3aahD

4aahB

4aahD

1h4iB

1h4iD

1h4jB

1h4jD

1h4jF

1h4jH

1w6sB

1w6sD

1lrwB

1lrwD


References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]Fig.7, Fig.8
[4]Scheme 1, Scheme 2, p.31-33
[9]p.12957-12958
[10]Fig.7, Fig.8, p.670-671
[13]

[14]p.104-105
[15]p.378
[17]p.182-184
[18]p.492-498
[19]Scheme 1, Scheme 3, Scheme 4, p.11884-11886
[20]Scheme 2, Scheme 3, p.6565-6570
[21]Fig.7, p.1218-1220
[23]Fig.1, Fig.2, p.759-764
[24]Fig.2, p.9807-9808
[25]Fig.1, p.432-433
[26]p.850-853
[27]Fig. 3, p.3-6
[28]p.17-19

references
[1]
PubMed ID3098983
JournalJ Mol Biol
Year1986
Volume191
Pages141-2
AuthorsLim LW, Xia Z, Mathews FS, Davidson VL
TitlePreliminary X-ray crystallographic study of methanol dehydrogenase from Methylophilus methylotrophus.
[2]
PubMed ID3030752
JournalEur J Biochem
Year1987
Volume164
Pages223-7
AuthorsParker MW, Cornish A, Gossain V, Best DJ
TitlePurification, crystallisation and preliminary X-ray diffraction characterisation of methanol dehydrogenase from Methylosinus trichosporium OB3b.
[3]
PubMed ID3289922
JournalEur J Biochem
Year1988
Volume174
Pages331-8
AuthorsFrank J Jr, Dijkstra M, Duine JA, Balny C
TitleKinetic and spectral studies on the redox forms of methanol dehydrogenase from Hyphomicrobium X.
[4]
PubMed ID2673028
JournalAntonie Van Leeuwenhoek
Year1989
Volume56
Pages25-34
AuthorsFrank J, Dijkstra M, Balny C, Verwiel PE, Duine JA
TitleMethanol dehydrogenase: mechanism of action.
[5]
PubMed ID2687021
JournalFEBS Lett
Year1989
Volume258
Pages175-6
AuthorsXia ZX, Hao ZP, Mathews FS, Davidson VL
TitleCrystallization and preliminary X-ray crystallographic study of the quinoprotein methanol dehydrogenase from bacterium W3A1.
[7]
CommentsX-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS)
Medline ID93054513
PubMed ID1331050
JournalJ Biol Chem
Year1992
Volume267
Pages22289-97
AuthorsXia ZX, Dai WW, Xiong JP, Hao ZP, Davidson VL, White S, Mathews FS
TitleThe three-dimensional structures of methanol dehydrogenase from two methylotrophic bacteria at 2.6-A resolution.
Related Swiss-protP38539,P38540
[8]
PubMed ID1447790
JournalJ Mol Biol
Year1992
Volume228
Pages302-5
AuthorsGhosh M, Harlos K, Blake CC, Richardson I, Anthony C
TitleCrystallization and preliminary crystallographic investigation of methanol dehydrogenase from Methylobacterium extorquens AM1.
[9]
CommentsX-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS)
Medline ID94059969
PubMed ID8241148
JournalBiochemistry
Year1993
Volume32
Pages12955-8
AuthorsWhite S, Boyd G, Mathews FS, Xia ZX, Dai WW, Zhang YF, Davidson VL
TitleThe active site structure of the calcium-containing quinoprotein methanol dehydrogenase.
Related Swiss-protP38539,P38540
[10]
PubMed ID7818466
JournalBiochem J
Year1994
Volume304
Pages665-74
AuthorsAnthony C, Ghosh M, Blake CC
TitleThe structure and function of methanol dehydrogenase and related quinoproteins containing pyrrolo-quinoline quinone.
[11]
PubMed ID7945232
JournalBiochem J
Year1994
Volume303
Pages141-5
AuthorsHarris TK, Davidson VL
TitleThermal stability of methanol dehydrogenase is altered by the replacement of enzyme-bound Ca2+ with Sr2+.
[12]
PubMed ID7918485
JournalBiochemistry
Year1994
Volume33
Pages12600-8
AuthorsHarris TK, Davidson VL, Chen L, Mathews FS, Xia ZX
TitleIonic strength dependence of the reaction between methanol dehydrogenase and cytochrome c-551i: evidence of conformationally coupled electron transfer.
[13]
PubMed ID8032156
JournalEXS
Year1994
Volume71
Pages251-60
AuthorsGhosh M, Avezoux A, Anthony C, Harlos K, Blake CC
TitleX-ray structure of PQQ-dependent methanol dehydrogenase.
[14]
PubMed ID7656012
JournalNat Struct Biol
Year1994
Volume1
Pages102-5
AuthorsBlake CC, Ghosh M, Harlos K, Avezoux A, Anthony C
TitleThe active site of methanol dehydrogenase contains a disulphide bridge between adjacent cysteine residues.
[15]
PubMed ID7772016
JournalBiochem J
Year1995
Volume308
Pages375-9
AuthorsCozier GE, Giles IG, Anthony C
TitleThe structure of the quinoprotein alcohol dehydrogenase of Acetobacter aceti modelled on that of methanol dehydrogenase from Methylobacterium extorquens.
[16]
PubMed ID8524150
JournalMethods Enzymol
Year1995
Volume258
Pages191-216
AuthorsMathews FS
TitleX-ray studies of quinoproteins.
[17]
PubMed ID7735834
JournalStructure
Year1995
Volume3
Pages177-87
AuthorsGhosh M, Anthony C, Harlos K, Goodwin MG, Blake C
TitleThe refined structure of the quinoprotein methanol dehydrogenase from Methylobacterium extorquens at 1.94 A.
Related PDB1h4i
[18]
CommentsX-ray crystallography
PubMed ID8676383
JournalJ Mol Biol
Year1996
Volume259
Pages480-501
AuthorsXia Z, Dai W, Zhang Y, White SA, Boyd GD, Mathews FS
TitleDetermination of the gene sequence and the three-dimensional structure at 2.4 angstroms resolution of methanol dehydrogenase from Methylophilus W3A1.
Related PDB3aah,4aah
[19]
PubMed ID9342331
JournalProc Natl Acad Sci U S A
Year1997
Volume94
Pages11881-6
AuthorsZheng YJ, Bruice TC
TitleConformation of coenzyme pyrroloquinoline quinone and role of Ca2+ in the catalytic mechanism of quinoprotein methanol dehydrogenase.
[20]
PubMed ID9572874
JournalBiochemistry
Year1998
Volume37
Pages6562-71
AuthorsItoh S, Kawakami H, Fukuzumi S
TitleModel studies on calcium-containing quinoprotein alcohol dehydrogenases. Catalytic role of Ca2+ for the oxidation of alcohols by coenzyme PQQ (4,5-dihydro-4,5-dioxo-1H-pyrrolo[2,3-f]quinoline-2, 7,9-tricarboxylic acid).
[21]
PubMed ID9930981
JournalBiochemistry
Year1999
Volume38
Pages1214-20
AuthorsXia ZX, He YN, Dai WW, White SA, Boyd GD, Mathews FS
TitleDetailed active site configuration of a new crystal form of methanol dehydrogenase from Methylophilus W3A1 at 1.9 A resolution.
[22]
PubMed ID11195971
JournalJ Protein Chem
Year2000
Volume19
Pages469-73
AuthorsZhao Y, Wang G, Cao Z, Wang Y, Cheng H, Zhou HM
TitleEffects of Ca2+ on the activity and stability of methanol dehydrogenase.
[23]
PubMed ID11761326
JournalAntioxid Redox Signal
Year2001
Volume3
Pages757-74
AuthorsAnthony C
TitlePyrroloquinoline quinone (PQQ) and quinoprotein enzymes.
[24]
PubMed ID11502173
JournalBiochemistry
Year2001
Volume40
Pages9799-809
AuthorsAfolabi PR, Mohammed F, Amaratunga K, Majekodunmi O, Dales SL, Gill R, Thompson D, Cooper JB, Wood SP, Goodwin PM, Anthony C
TitleSite-directed mutagenesis and X-ray crystallography of the PQQ-containing quinoprotein methanol dehydrogenase and its electron acceptor, cytochrome c(L).
Related PDB1h4j
[25]
CommentsX-ray crystallography
PubMed ID11149955
JournalProc Natl Acad Sci U S A
Year2001
Volume98
Pages432-4
AuthorsZheng YJ, Xia Zx, Chen Zw, Mathews FS, Bruice TC
TitleCatalytic mechanism of quinoprotein methanol dehydrogenase: A theoretical and x-ray crystallographic investigation.
Related PDB1g72,1b2n
[26]
PubMed ID14505072
JournalJ Biol Inorg Chem
Year2003
Volume8
Pages843-54
AuthorsXia ZX, Dai WW, He YN, White SA, Mathews FS, Davidson VL
TitleX-ray structure of methanol dehydrogenase from Paracoccus denitrificans and molecular modeling of its interactions with cytochrome c-551i.
Related PDB1lrw
[27]
PubMed ID15234264
JournalArch Biochem Biophys
Year2004
Volume428
Pages2-9
AuthorsAnthony C
TitleThe quinoprotein dehydrogenases for methanol and glucose.
[28]
PubMed ID15234265
JournalArch Biochem Biophys
Year2004
Volume428
Pages10-21
AuthorsToyama H, Mathews FS, Adachi O, Matsushita K
TitleQuinohemoprotein alcohol dehydrogenases: structure, function, and physiology.
[29]
PubMed ID15520392
JournalProc Natl Acad Sci U S A
Year2004
Volume101
Pages15887-92
AuthorsReddy SY, Bruice TC
TitleMechanisms of ammonia activation and ammonium ion inhibition of quinoprotein methanol dehydrogenase: a computational approach.
[30]
PubMed ID15608378
JournalActa Crystallogr D Biol Crystallogr
Year2005
Volume61
Pages75-9
AuthorsWilliams PA, Coates L, Mohammed F, Gill R, Erskine PT, Coker A, Wood SP, Anthony C, Cooper JB
TitleThe atomic resolution structure of methanol dehydrogenase from Methylobacterium extorquens.
Related PDB1w6s

comments
Cytochrome c proteins, such as cytochrome cL (PDB; 1umm) and cytochrome c-551i (PDB; 1fi3), which are electron transfer proteins, play a role as a substrate, which accepts two electrons from this enzyme.
Thus, this enzyme catalyzes the following reactions:
(A) Hydride transfer from a primary alcohole to PQQ, giving an aldehyde and PQQH2.
(B) Single electron transfer from PQQH2 to the electron transfer, cytochrome c. (This reaction occurs twice.)
Asp105 and disulfide bond between Cys103-Cys104 might be involved in the electron transfer (see [27]).
***
The related enzymes are as follows:
ALDH (acceptor) (E.C.1.1.99.8) corresponds to this entry (D00016),
ALDH1 and 2 (E.C. 1.2.1.3) correspond to D00019 (in EzCatDB),
NADP-dependent ALDH (E.C. 1.2.1.4) corresponds to D00475,
ALDH3 (E.C. 1.2.1.5) corresponds to D00020,
NADP-dependent GAPDH (E.C. 1.2.1.9) corresponds to D00022,
NAD(P)-dependent GAPDH (phosphorylating) (E.C. 1.2.1.59) corresponds to D00476,
GAPDH (phosphorylating) (E.C. 1.2.1.12) corresponds to D00024,
NADP-dependent GAPDH (phosphorylating) (E.C. 1.2.1.13) has no entry currently.

createdupdated
2005-01-182012-10-03


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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