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Protein

Quinohemoprotein alcohol dehydrogenase ADH IIB

Gene

qbdA

Organism
Pseudomonas putida (Arthrobacter siderocapsulatus)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the dye-linked oxidation of primary alcohols to the corresponding aldehydes and the (subsequent) oxidation of the aldehydes to carboxylic acids. Exhibits activity with longer mono-alcohols (C-4 to C-7) but not with methanol or glycerol. Reacts with 1,2-propanediol and 1,3-propanediol but not with sugar alcohols such as D-sorbitol.3 Publications

Catalytic activityi

A primary alcohol + azurin = an aldehyde + reduced azurin.3 Publications

Cofactori

Protein has several cofactor binding sites:
  • pyrroloquinoline quinone2 PublicationsNote: Binds 1 PQQ group per subunit. PQQ is inserted between disulfide Cys-127-Cys-128 and the plane of Trp-254.2 Publications
  • Ca2+1 PublicationNote: Binds 1 Ca2+ ion per subunit.1 Publication
  • heme2 PublicationsNote: Binds 1 heme group per subunit.2 Publications

Enzyme regulationi

Inhibited by 10 mM 1-butanol.1 Publication

Redox potential

E0 is +185 mV for heme c at pH 7.0, +188 mV for heme c at pH 8.0, +172 mV for heme c at pH 8.0 and 0.3 M KCl and +189 mV for ADH IIB-Azurin complex.3 Publications

Kineticsi

  1. KM=5.61 mM for ethanol3 Publications
  2. KM=0.105 mM for butane-1-ol3 Publications
  3. KM=10.2 mM for propane-1,2-diol3 Publications
  4. KM=3.71 mM for (S+)propane-1,2-diol3 Publications
  5. KM=4.58 mM for (R-)propane-1,2-diol3 Publications
  6. KM=0.015 mM for butane-1-ol3 Publications
  7. KM=100 µM for azurin (from P.putida in the presence of 30 mM Tris-HCl pH 8.0)3 Publications
  8. KM=51 µM for azurin (from P.putida in the presence of 30 mM Tris-HCl pH 8.0 and 0.1 M KCl)3 Publications
  9. KM=25 µM for azurin (from P.putida in the presence of 30 mM Tris-HCl pH 8.0 and 0.5 M KCl)3 Publications
  10. KM=202 µM for azurin (from P.aerugionosa in the presence of 30 mM Tris-HCl pH 8.0)3 Publications
  11. KM=95 µM for potassium ferricyanide (in the presence of 30 mM Tris-HCl pH 8.0 and 0.1 M KCl)3 Publications
  1. Vmax=15.4 µmol/min/mg enzyme with ethanol as substrate3 Publications
  2. Vmax=17.1 µmol/min/mg enzyme with butane-1-ol as substrate3 Publications
  3. Vmax=4.27 µmol/min/mg enzyme with propane-1,2-diol as substrate3 Publications
  4. Vmax=2.61 µmol/min/mg enzyme with (S+)propane-1,2-diol as substrate3 Publications
  5. Vmax=7.10 µmol/min/mg enzyme with (R-)propane-1,2-diol as substrate3 Publications
  6. Vmax=31 µmol/min/mg enzyme with butane-1-ol as substrate3 Publications
  7. Vmax=62.5 µmol/min/mg enzyme toward azurin (from P.putida in the presence of 30 mM Tris-HCl pH 8.0)3 Publications
  8. Vmax=52.6 µmol/min/mg enzyme toward azurin (from P.putida in the presence of 30 mM Tris-HCl pH 8.0 and 0.1 M KCl)3 Publications
  9. Vmax=41.7 µmol/min/mg enzyme toward azurin (from P.putida in the presence of 30 mM Tris-HCl pH 8.0 and 0.1 M KCl)3 Publications
  10. Vmax=22.3 µmol/min/mg enzyme toward azurin (from P.aeruginosa in the presence of 30 mM Tris-HCl pH 8.0)3 Publications
  11. Vmax=45.5 µmol/min/mg enzyme toward potassium ferricyanide (in the presence of 30 mM Tris-HCl pH 8.0)3 Publications

pH dependencei

Optimum pH is 8.0.3 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei81 – 811PQQ
Binding sitei133 – 1331PQQ
Binding sitei177 – 1771PQQ
Metal bindingi195 – 1951Calcium1 Publication
Metal bindingi272 – 2721Calcium1 Publication
Binding sitei272 – 2721PQQ
Active sitei317 – 3171Proton acceptorSequence analysisBy similarity
Metal bindingi317 – 3171Calcium1 Publication
Binding sitei317 – 3171Substrate1 Publication
Binding sitei344 – 3441PQQ
Binding sitei399 – 3991Substrate; via carbonyl oxygen1 Publication
Binding sitei613 – 6131Heme (covalent)PROSITE-ProRule annotation1 Publication
Binding sitei616 – 6161Heme (covalent)PROSITE-ProRule annotation1 Publication
Metal bindingi617 – 6171Iron (heme axial ligand); via tele nitrogenPROSITE-ProRule annotation1 Publication
Metal bindingi655 – 6551Iron (heme axial ligand)PROSITE-ProRule annotation1 Publication

GO - Molecular functioni

  • calcium ion binding Source: UniProtKB
  • electron carrier activity Source: UniProtKB
  • heme binding Source: UniProtKB
  • metal ion binding Source: UniProtKB
  • oxidoreductase activity Source: UniProtKB
  • oxidoreductase activity, acting on CH-OH group of donors Source: InterPro
  • pyrroloquinoline quinone binding Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

Calcium, Heme, Iron, Metal-binding, PQQ

Enzyme and pathway databases

BRENDAi1.1.9.1. 5092.
1.2.99.3. 5092.

Names & Taxonomyi

Protein namesi
Recommended name:
Quinohemoprotein alcohol dehydrogenase ADH IIBImported (EC:1.1.9.11 Publication)
Short name:
ADH IIB1 Publication
Alternative name(s):
Alcohol dehydrogenase (azurin)By similarity
Gene namesi
Name:qbdAImported
OrganismiPseudomonas putida (Arthrobacter siderocapsulatus)
Taxonomic identifieri303 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas

Subcellular locationi

  • Periplasm By similarityCurated

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 22222 PublicationsAdd
BLAST
Chaini23 – 690668Quinohemoprotein alcohol dehydrogenase ADH IIB1 PublicationPRO_0000419525Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi127 ↔ 1281 Publication

Keywords - PTMi

Disulfide bond

Expressioni

Inductioni

By 1-butanol. Primary and secondary C3,C4 alcohols as well as butyraldehyde.3 Publications

Interactioni

Subunit structurei

Monomer.3 Publications

Structurei

Secondary structure

1
690
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi27 – 326Combined sources
Turni33 – 353Combined sources
Turni60 – 623Combined sources
Helixi63 – 653Combined sources
Beta strandi66 – 738Combined sources
Beta strandi85 – 873Combined sources
Beta strandi90 – 956Combined sources
Helixi96 – 983Combined sources
Beta strandi99 – 1046Combined sources
Turni105 – 1073Combined sources
Beta strandi110 – 1145Combined sources
Helixi120 – 1256Combined sources
Beta strandi136 – 1394Combined sources
Beta strandi141 – 1455Combined sources
Beta strandi149 – 1557Combined sources
Turni156 – 1583Combined sources
Beta strandi161 – 1666Combined sources
Beta strandi181 – 1833Combined sources
Beta strandi186 – 1894Combined sources
Turni194 – 1963Combined sources
Beta strandi201 – 2066Combined sources
Turni207 – 2093Combined sources
Beta strandi212 – 2198Combined sources
Helixi230 – 2367Combined sources
Helixi244 – 2474Combined sources
Beta strandi257 – 2604Combined sources
Turni261 – 2644Combined sources
Beta strandi265 – 2695Combined sources
Beta strandi273 – 2764Combined sources
Helixi278 – 2814Combined sources
Turni289 – 2924Combined sources
Beta strandi293 – 2975Combined sources
Turni299 – 3013Combined sources
Beta strandi304 – 3118Combined sources
Beta strandi324 – 3318Combined sources
Beta strandi334 – 3418Combined sources
Beta strandi346 – 3527Combined sources
Turni353 – 3553Combined sources
Beta strandi358 – 3658Combined sources
Beta strandi369 – 3735Combined sources
Turni375 – 3773Combined sources
Beta strandi380 – 3823Combined sources
Turni384 – 3874Combined sources
Beta strandi389 – 3913Combined sources
Beta strandi393 – 3975Combined sources
Beta strandi409 – 4113Combined sources
Turni412 – 4154Combined sources
Beta strandi416 – 4238Combined sources
Beta strandi426 – 4283Combined sources
Helixi432 – 4343Combined sources
Helixi447 – 4493Combined sources
Helixi455 – 4573Combined sources
Beta strandi459 – 4668Combined sources
Turni467 – 4704Combined sources
Beta strandi471 – 48111Combined sources
Beta strandi486 – 4894Combined sources
Turni490 – 4923Combined sources
Beta strandi493 – 4975Combined sources
Beta strandi501 – 5077Combined sources
Turni508 – 5103Combined sources
Beta strandi513 – 5186Combined sources
Beta strandi528 – 5325Combined sources
Beta strandi535 – 5428Combined sources
Helixi547 – 5515Combined sources
Helixi554 – 5574Combined sources
Beta strandi566 – 5727Combined sources
Helixi599 – 61214Combined sources
Helixi614 – 6174Combined sources
Helixi619 – 6213Combined sources
Beta strandi625 – 6273Combined sources
Helixi630 – 6323Combined sources
Helixi635 – 6395Combined sources
Helixi641 – 6477Combined sources
Helixi651 – 6533Combined sources
Turni659 – 6613Combined sources
Helixi664 – 68421Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1KV9X-ray1.90A23-690[»]
ProteinModelPortaliQ8GR64.
SMRiQ8GR64. Positions 23-686.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8GR64.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini600 – 67879Cytochrome cPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni193 – 1953PQQ binding
Regioni252 – 2543PQQ binding
Regioni404 – 4052PQQ binding

Sequence similaritiesi

Belongs to the bacterial PQQ dehydrogenase family.Sequence analysis
Contains 1 cytochrome c domain.PROSITE-ProRule annotation

Keywords - Domaini

Signal

Family and domain databases

Gene3Di1.10.760.10. 1 hit.
2.140.10.10. 1 hit.
InterProiIPR009056. Cyt_c-like_dom.
IPR018391. PQQ_beta_propeller_repeat.
IPR017512. PQQ_MeOH/EtOH_DH.
IPR002372. PQQ_repeat.
IPR027295. Quinoprotein_ADH-like_fam.
IPR011047. Quinoprotein_ADH-like_supfam.
IPR001479. Quinoprotein_DH_CS.
[Graphical view]
PfamiPF13442. Cytochrome_CBB3. 1 hit.
PF13360. PQQ_2. 2 hits.
[Graphical view]
SMARTiSM00564. PQQ. 5 hits.
[Graphical view]
SUPFAMiSSF46626. SSF46626. 1 hit.
SSF50998. SSF50998. 1 hit.
TIGRFAMsiTIGR03075. PQQ_enz_alc_DH. 1 hit.
PROSITEiPS00364. BACTERIAL_PQQ_2. 1 hit.
PS51007. CYTC. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q8GR64-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKPLRTSLL MLCLATPLAA LAAGVDEAAI RATEQAGGEW LSHGRTYAEQ
60 70 80 90 100
RFSPLKQIDA SNVRSLGLAW YMDLDNTRGL EATPLFHDGV IYTSMSWSRV
110 120 130 140 150
IAVDAASGKE LWRYDPEVAK VKARTSCCDA VNRGVALWGD KVYVGTLDGR
160 170 180 190 200
LIALDAKTGK AIWSQQTTDP AKPYSITGAP RVVKGKVIIG NGGAEYGVRG
210 220 230 240 250
FVSAYDADTG KLAWRFYTVP GDPALPYEHP ELREAAKTWQ GDQYWKLGGG
260 270 280 290 300
GTVWDSMAYD PELDLLYVGT GNGSPWNREV RSPGGGDNLY LSSILAIRPD
310 320 330 340 350
TGKLAWHYQV TPGDSWDFTA TQQITLAELN IDGKPRKVLM QAPKNGFFYV
360 370 380 390 400
LDRTNGKLIS AEKFGKVTWA EKVDLATGRP VEAPGVRYEK EPIVMWPSPF
410 420 430 440 450
GAHNWHSMSF NPGTGLVYIP YQEVPGVYRN EGKDFVTRKA FNTAAGFADA
460 470 480 490 500
TDVPAAVVSG ALLAWDPVKQ KAAWKVPYPT HWNGGTLSTA GNLVFQGTAA
510 520 530 540 550
GQMHAYSADK GEALWQFEAQ SGIVAAPMTF ELAGRQYVAI MAGWGGVATL
560 570 580 590 600
TGGESMNLPG MKNRSRLLVF ALDGKAQLPP PAPAPAKVER VPQPVTAAPE
610 620 630 640 650
QVQAGKQLYG QFCSVCHGMG TISGGLIPDL RQSSDATREH FQQIVLQGAL
660 670 680 690
KPLGMPSFDD SLKPEEVEQI KLYVMSREYE DYMARHKAAP
Length:690
Mass (Da):74,969
Last modified:March 1, 2003 - v1
Checksum:iF5198701D0937613
GO

Mass spectrometryi

Molecular mass is 73262 Da from positions 23 - 690. Determined by MALDI. The measured mass is that of QbdA with a single heme bound.1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB091400 Genomic DNA. Translation: BAC15559.1.
RefSeqiWP_058541185.1. NZ_LKGZ01000023.1.

Genome annotation databases

KEGGiag:BAC15559.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB091400 Genomic DNA. Translation: BAC15559.1.
RefSeqiWP_058541185.1. NZ_LKGZ01000023.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1KV9X-ray1.90A23-690[»]
ProteinModelPortaliQ8GR64.
SMRiQ8GR64. Positions 23-686.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

KEGGiag:BAC15559.

Enzyme and pathway databases

BRENDAi1.1.9.1. 5092.
1.2.99.3. 5092.

Miscellaneous databases

EvolutionaryTraceiQ8GR64.

Family and domain databases

Gene3Di1.10.760.10. 1 hit.
2.140.10.10. 1 hit.
InterProiIPR009056. Cyt_c-like_dom.
IPR018391. PQQ_beta_propeller_repeat.
IPR017512. PQQ_MeOH/EtOH_DH.
IPR002372. PQQ_repeat.
IPR027295. Quinoprotein_ADH-like_fam.
IPR011047. Quinoprotein_ADH-like_supfam.
IPR001479. Quinoprotein_DH_CS.
[Graphical view]
PfamiPF13442. Cytochrome_CBB3. 1 hit.
PF13360. PQQ_2. 2 hits.
[Graphical view]
SMARTiSM00564. PQQ. 5 hits.
[Graphical view]
SUPFAMiSSF46626. SSF46626. 1 hit.
SSF50998. SSF50998. 1 hit.
TIGRFAMsiTIGR03075. PQQ_enz_alc_DH. 1 hit.
PROSITEiPS00364. BACTERIAL_PQQ_2. 1 hit.
PS51007. CYTC. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Molecular cloning of quinohemoprotein alcohol dehydrogenase, ADH IIB, from Pseudomonas putida HK5."
    Toyama H., Fujii T., Aoki N., Matsushita K., Adachi O.
    Biosci. Biotechnol. Biochem. 67:1397-1400(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 23-36; 247-262 AND 388-396, MASS SPECTROMETRY.
    Strain: HK51 Publication.
  2. "Three distinct quinoprotein alcohol dehydrogenases are expressed when Pseudomonas putida is grown on different alcohols."
    Toyama H., Fujii A., Matsushita K., Shinagawa E., Ameyama M., Adachi O.
    J. Bacteriol. 177:2442-2450(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, INDUCTION.
    Strain: HK51 Publication.
  3. "Electron transfer from quinohemoprotein alcohol dehydrogenase to blue copper protein azurin in the alcohol oxidase respiratory chain of Pseudomonas putida HK5."
    Matsushita K., Yamashita T., Aoki N., Toyama H., Adachi O.
    Biochemistry 38:6111-6118(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES.
    Strain: HK51 Publication.
  4. "Molecular cloning and structural analysis of quinohemoprotein alcohol dehydrogenase ADH-IIG from Pseudomonas putida HK5."
    Toyama H., Chen Z.W., Fukumoto M., Adachi O., Matsushita K., Mathews F.S.
    J. Mol. Biol. 352:91-104(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: CATALYTIC ACTIVITY, STEREOSPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES.
    Strain: HK51 Publication.
  5. "Disruption of quinoprotein ethanol dehydrogenase gene and adjacent genes in Pseudomonas putida HK5."
    Promden W., Vangnai A.S., Pongsawasdi P., Adachi O., Matsushita K., Toyama H.
    FEMS Microbiol. Lett. 280:203-209(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INDUCTION.
    Strain: HK51 Publication.
  6. "Analysis of the promoter activities of the genes encoding three quinoprotein alcohol dehydrogenases in Pseudomonas putida HK5."
    Promden W., Vangnai A.S., Toyama H., Matsushita K., Pongsawasdi P.
    Microbiology 155:594-603(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
    Strain: HK51 Publication.
  7. "Crystallization and preliminary diffraction studies of two quinoprotein alcohol dehydrogenases (ADHs): a soluble monomeric ADH from Pseudomonas putida HK5 (ADH-IIB) and a heterotrimeric membrane-bound ADH from Gluconobacter suboxydans (ADH-GS)."
    Chen Z., Baruch P., Mathews F.S., Matsushita K., Yamashita T., Toyama H., Adachi O.
    Acta Crystallogr. D 55:1933-1936(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: CRYSTALLIZATION, PRELIMINARY X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS), SUBUNIT.
    Strain: HK51 Publication.
  8. "Structure at 1.9 A resolution of a quinohemoprotein alcohol dehydrogenase from Pseudomonas putida HK5."
    Chen Z.W., Matsushita K., Yamashita T., Fujii T.A., Toyama H., Adachi O., Bellamy H.D., Mathews F.S.
    Structure 10:837-849(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 23-690 IN COMPLEX WITH CALCIUM; HEME, PQQ AND ACETONE, PROTEIN SEQUENCE OF 23-36, COFACTOR.
    Strain: HK51 Publication.

Entry informationi

Entry nameiQHED_PSEPU
AccessioniPrimary (citable) accession number: Q8GR64
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 3, 2012
Last sequence update: March 1, 2003
Last modified: March 16, 2016
This is version 74 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.