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Protein
Submitted name:

Diol dehydrase alpha subunit

Gene

pddA

Organism
Klebsiella oxytoca
Status
Unreviewed-Annotation score: Annotation score: 2 out of 5-Experimental evidence at protein leveli

Functioni

Cofactori

adenosylcob(III)alaminUniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi141 – 1411Calcium
Sitei143 – 1431Important for catalytic activityCombined sources
Metal bindingi170 – 1701Calcium
Sitei170 – 1701Important for catalytic activityCombined sources
Metal bindingi221 – 2211Calcium
Metal bindingi296 – 2961Calcium
Sitei296 – 2961Important for catalytic activityCombined sources
Sitei335 – 3351Important for catalytic activityCombined sources
Metal bindingi362 – 3621Calcium; via carbonyl oxygen

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

CalciumCombined sources, CobalaminUniRule annotation, Cobalt, Metal-bindingCombined sources

Names & Taxonomyi

Protein namesi
Submitted name:
Diol dehydrase alpha subunitImported (EC:4.2.1.28Imported)
Submitted name:
Propanediol dehydrataseImported
Gene namesi
Name:pddAImported
Synonyms:pduCImported
ORF Names:FF19_11660Imported, HR38_27590Imported, MC52_02990Imported
OrganismiKlebsiella oxytocaImported
Taxonomic identifieri571 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeKlebsiella
ProteomesiUP000027606: Genome

Interactioni

Protein-protein interaction databases

MINTiMINT-7997099.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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[»]
ProteinModelPortaliQ59470.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ59470.

Family & Domainsi

Sequence similaritiesi

Belongs to the diol/glycerol dehydratase large subunit family.UniRule annotation

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

        10         20         30         40         50
MRSKRFEALA KRPVNQDGFV KEWIEEGFIA MESPNDPKPS IKIVNGAVTE
60 70 80 90 100
LDGKPVSDFD LIDHFIARYG INLNRAEEVM AMDSVKLANM LCDPNVKRSE
110 120 130 140 150
IVPLTTAMTP AKIVEVVSHM NVVEMMMAMQ KMRARRTPSQ QAHVTNVKDN
160 170 180 190 200
PVQIAADAAE GAWRGFDEQE TTVAVARYAP FNAIALLVGS QVGRPGVLTQ
210 220 230 240 250
CSLEEATELK LGMLGHTCYA ETISVYGTEP VFTDGDDTPW SKGFLASSYA
260 270 280 290 300
SRGLKMRFTS GSGSEVQMGY AEGKSMLYLE ARCIYITKAA GVQGLQNGSV
310 320 330 340 350
SCIGVPSAVP SGIRAVLAEN LICSSLDLEC ASSNDQTFTH SDMRRTARLL
360 370 380 390 400
MQFLPGTDFI SSGYSAVPNY DNMFAGSNED AEDFDDYNVI QRDLKVDGGL
410 420 430 440 450
RPVREEDVIA IRNKAARALQ AVFAGMGLPP ITDEEVEAAT YAHGSKDMPE
460 470 480 490 500
RNIVEDIKFA QEIINKNRNG LEVVKALAQG GFTDVAQDML NIQKAKLTGD
510 520 530 540 550
YLHTSAIIVG DGQVLSAVND VNDYAGPATG YRLQGERWEE IKNIPGALDP

NEID
Length:554
Mass (Da):60,348
Last modified:November 1, 1996 - v1
Checksum:i5AC48A035B65331D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
JQ478430 Genomic DNA. Translation: AFJ04717.1.
CP008841 Genomic DNA. Translation: AIE72070.1.
D45071 Genomic DNA. Translation: BAA08099.1.
JNCH01000030 Genomic DNA. Translation: KFC40966.1.
JTBQ01000003 Genomic DNA. Translation: KGZ19723.1.
PIRiA56111.
RefSeqiYP_005016275.1. NC_016612.1.

Genome annotation databases

EnsemblBacteriaiAIE72070; AIE72070; HR38_27590.
GeneIDi11660425.
KEGGikox:KOX_01455.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
JQ478430 Genomic DNA. Translation: AFJ04717.1.
CP008841 Genomic DNA. Translation: AIE72070.1.
D45071 Genomic DNA. Translation: BAA08099.1.
JNCH01000030 Genomic DNA. Translation: KFC40966.1.
JTBQ01000003 Genomic DNA. Translation: KGZ19723.1.
PIRiA56111.
RefSeqiYP_005016275.1. NC_016612.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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[»]
ProteinModelPortaliQ59470.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

MINTiMINT-7997099.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAIE72070; AIE72070; HR38_27590.
GeneIDi11660425.
KEGGikox:KOX_01455.

Miscellaneous databases

EvolutionaryTraceiQ59470.

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.
ProtoNetiSearch...

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), 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).
  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).
  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).
  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.
  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.
  8. "Genome sequencing of Klebsiella oxytoca r8a."
    Chan K.-G., Goh S.Y.
    Submitted (MAY-2014) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE.
    Strain: R8AImported.
  9. "Whole Genome Sequence of Klebsiella oxytoca M1."
    Shin S.H., Um Y., Cho S., Kim J., Roh H., Yang K.-S.
    Submitted (JUN-2014) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE.
    Strain: M1Imported.
  10. "FDA MicroDB: Microbial Confirmatory Reference Database."
    Sichtig H., Goldberg B., Campos J., Hobson J., DeShong Sadzewicz L., Tallon L., Nagaraj S., McCracken C.L., Daugherty S., Sengamalay N.
    Submitted (NOV-2014) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE.
    Strain: FDA_MicroDB_66Imported.

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: February 4, 2015
This is version 72 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureCombined sources, Complete proteomeImported

External Data

Dasty 3

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 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.