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Q59470

- Q59470_KLEOX

UniProt

Q59470 - Q59470_KLEOX

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Protein
Submitted name:

Diol dehydrase alpha subunit

Gene
pddA
Organism
Klebsiella oxytoca
Status
Unreviewed - Annotation score: 3 out of 5 - Experimental evidence at protein leveli

Functioni

Cofactori

Adenosylcobalamin By similarity.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi141 – 1411CalciumImported
Metal bindingi141 – 1411Potassium 1Imported
Sitei143 – 1431Important for catalytic activityImported
Metal bindingi170 – 1701CalciumImported
Metal bindingi170 – 1701Potassium 1Imported
Sitei170 – 1701Important for catalytic activityImported
Metal bindingi203 – 2031Potassium 2; via carbonyl oxygenImported
Metal bindingi205 – 2051Potassium 2Imported
Metal bindingi208 – 2081Potassium 2Imported
Metal bindingi221 – 2211CalciumImported
Metal bindingi221 – 2211Potassium 1Imported
Metal bindingi222 – 2221Potassium 2Imported
Metal bindingi261 – 2611Potassium 3; via carbonyl oxygenImported
Metal bindingi264 – 2641Potassium 3Imported
Metal bindingi265 – 2651Potassium 3Imported
Metal bindingi280 – 2801Potassium 3Imported
Metal bindingi296 – 2961CalciumImported
Metal bindingi296 – 2961Potassium 1Imported
Sitei296 – 2961Important for catalytic activityImported
Sitei335 – 3351Important for catalytic activityImported
Metal bindingi362 – 3621Calcium; via carbonyl oxygenImported
Metal bindingi362 – 3621Potassium 1; via carbonyl oxygenImported
Binding sitei417 – 4171Phosphate 1Imported
Binding sitei417 – 4171Phosphate 2Imported

GO - Molecular functioni

  1. cobalamin binding Source: UniProtKB-KW
  2. metal ion binding Source: UniProtKB-KW
  3. propanediol dehydratase activity Source: UniProtKB-EC
Complete GO annotation...

Keywords - Molecular functioni

LyaseUniRule annotationImported

Keywords - Ligandi

CalciumImported, CobalaminUniRule annotation, Cobalt, Metal-bindingImported, PotassiumImported

Names & Taxonomyi

Protein namesi
Submitted name:
Diol dehydrase alpha subunitImported (EC:4.2.1.28Imported)
Gene namesi
Name:pddAImported
OrganismiKlebsiella oxytocaImported
Taxonomic identifieri571 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeKlebsiella

Interactioni

Protein-protein interaction databases

MINTiMINT-7997099.

Structurei

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DIOX-ray2.20A/L1-554[»]
1EEXX-ray1.70A/L1-554[»]
1EGMX-ray1.85A/L1-554[»]
1EGVX-ray1.75A/L1-554[»]
1IWBX-ray1.85A/L1-554[»]
1UC4X-ray1.80A/L1-554[»]
1UC5X-ray2.30A/L1-554[»]
3AUJX-ray2.10A/L1-554[»]

Miscellaneous databases

EvolutionaryTraceiQ59470.

Family & Domainsi

Sequence similaritiesi

Family and domain databases

Gene3Di3.20.20.350. 1 hit.
InterProiIPR016176. Cbl-dep_enz_cat.
IPR003206. Diol/glycerol_deHydtase_lsu.
[Graphical view]
PfamiPF02286. Dehydratase_LU. 1 hit.
[Graphical view]
PIRSFiPIRSF018507. Prpndl_dhdrts_lg. 1 hit.
ProDomiPD025428. Diol/glycerol_deHydtase_lsu. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF51703. SSF51703. 1 hit.

Sequencei

Sequence statusi: Complete.

Q59470-1 [UniParc]FASTAAdd to Basket

« Hide

MRSKRFEALA KRPVNQDGFV KEWIEEGFIA MESPNDPKPS IKIVNGAVTE    50
LDGKPVSDFD LIDHFIARYG INLNRAEEVM AMDSVKLANM LCDPNVKRSE 100
IVPLTTAMTP AKIVEVVSHM NVVEMMMAMQ KMRARRTPSQ QAHVTNVKDN 150
PVQIAADAAE GAWRGFDEQE TTVAVARYAP FNAIALLVGS QVGRPGVLTQ 200
CSLEEATELK LGMLGHTCYA ETISVYGTEP VFTDGDDTPW SKGFLASSYA 250
SRGLKMRFTS GSGSEVQMGY AEGKSMLYLE ARCIYITKAA GVQGLQNGSV 300
SCIGVPSAVP SGIRAVLAEN LICSSLDLEC ASSNDQTFTH SDMRRTARLL 350
MQFLPGTDFI SSGYSAVPNY DNMFAGSNED AEDFDDYNVI QRDLKVDGGL 400
RPVREEDVIA IRNKAARALQ AVFAGMGLPP ITDEEVEAAT YAHGSKDMPE 450
RNIVEDIKFA QEIINKNRNG LEVVKALAQG GFTDVAQDML NIQKAKLTGD 500
YLHTSAIIVG DGQVLSAVND VNDYAGPATG YRLQGERWEE IKNIPGALDP 550
NEID 554
Length:554
Mass (Da):60,348
Last modified:November 1, 1996 - v1
Checksum:i5AC48A035B65331D
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
JQ478430 Genomic DNA. Translation: AFJ04717.1.
D45071 Genomic DNA. Translation: BAA08099.1.
PIRiA56111.
RefSeqiYP_005016275.1. NC_016612.1.

Genome annotation databases

GeneIDi11660425.
KEGGikox:KOX_01455.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
JQ478430 Genomic DNA. Translation: AFJ04717.1 .
D45071 Genomic DNA. Translation: BAA08099.1 .
PIRi A56111.
RefSeqi YP_005016275.1. NC_016612.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1DIO X-ray 2.20 A/L 1-554 [» ]
1EEX X-ray 1.70 A/L 1-554 [» ]
1EGM X-ray 1.85 A/L 1-554 [» ]
1EGV X-ray 1.75 A/L 1-554 [» ]
1IWB X-ray 1.85 A/L 1-554 [» ]
1UC4 X-ray 1.80 A/L 1-554 [» ]
1UC5 X-ray 2.30 A/L 1-554 [» ]
3AUJ X-ray 2.10 A/L 1-554 [» ]
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

MINTi MINT-7997099.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 11660425.
KEGGi kox:KOX_01455.

Miscellaneous databases

EvolutionaryTracei Q59470.

Family and domain databases

Gene3Di 3.20.20.350. 1 hit.
InterProi IPR016176. Cbl-dep_enz_cat.
IPR003206. Diol/glycerol_deHydtase_lsu.
[Graphical view ]
Pfami PF02286. Dehydratase_LU. 1 hit.
[Graphical view ]
PIRSFi PIRSF018507. Prpndl_dhdrts_lg. 1 hit.
ProDomi PD025428. Diol/glycerol_deHydtase_lsu. 1 hit.
[Graphical view ] [Entries sharing at least one domain ]
SUPFAMi SSF51703. SSF51703. 1 hit.
ProtoNeti Search...

Publicationsi

  1. "Molecular cloning, sequencing, and expression of the genes encoding adenosylcobalamin-dependent diol dehydrase of Klebsiella oxytoca."
    Tobimatsu T., Hara T., Sakaguchi M., Kishimoto Y., Wada Y., Isoda M., Sakai T., Toraya T.
    J. Biol. Chem. 270:7142-7148(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE.
    Strain: ATCC 8724Imported.
  2. "A new mode of B12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase."
    Shibata N., Masuda J., Tobimatsu T., Toraya T., Suto K., Morimoto Y., Yasuoka N.
    Structure 7:997-1008(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) IN COMPLEX WITH POTASSIUM, ACTIVE SITE.
  3. "How a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex."
    Masuda J., Shibata N., Morimoto Y., Toraya T., Yasuoka N.
    Structure 8:775-788(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COMPLEX WITH POTASSIUM.
  4. "Substrate-induced conformational change of a coenzyme B12-dependent enzyme: crystal structure of the substrate-free form of diol dehydratase."
    Shibata N., Masuda J., Morimoto Y., Yasuoka N., Toraya T.
    Biochemistry 41:12607-12617(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) IN COMPLEX WITH POTASSIUM.
  5. "Structural rationalization for the lack of stereospecificity in coenzyme B12-dependent diol dehydratase."
    Shibata N., Nakanishi Y., Fukuoka M., Yamanishi M., Yasuoka N., Toraya T.
    J. Biol. Chem. 278:22717-22725(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH POTASSIUM.
  6. "Redesign of coenzyme B(12) dependent diol dehydratase to be resistant to the mechanism-based inactivation by glycerol and act on longer chain 1,2-diols."
    Yamanishi M., Kinoshita K., Fukuoka M., Saito T., Tanokuchi A., Ikeda Y., Obayashi H., Mori K., Shibata N., Tobimatsu T., Toraya T.
    FEBS J. 279:793-804(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEX WITH CALCIUM AND PHOSPHATE.
  7. Lipinski D., Przystalowska H., Slomski R., Zeyland J.
    Submitted (JAN-2012) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE.
    Strain: ATCC 700324Imported.

Entry informationi

Entry nameiQ59470_KLEOX
AccessioniPrimary (citable) accession number: Q59470
Entry historyi
Integrated into UniProtKB/TrEMBL: November 1, 1996
Last sequence update: November 1, 1996
Last modified: June 11, 2014
This is version 67 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureImported

External Data

Dasty 3

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