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Protein
Submitted name:

Diol dehydrase beta subunit

Gene

pddB

Organism
Klebsiella oxytoca
Status
Unreviewed-Annotation score: Annotation score: 1 out of 5-Experimental evidence at protein leveli

Functioni

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

LyaseImported

Enzyme and pathway databases

BRENDAi4.2.1.28. 2811.

Names & Taxonomyi

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

Interactioni

Protein-protein interaction databases

MINTiMINT-7997115.
STRINGi1006551.KOX_01460.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DIOX-ray2.20B/E1-224[»]
1EEXX-ray1.70B/E1-224[»]
1EGMX-ray1.85B/E1-224[»]
1EGVX-ray1.75B/E1-224[»]
1IWBX-ray1.85B/E1-224[»]
1UC4X-ray1.80B/E1-224[»]
1UC5X-ray2.30B/E1-224[»]
3AUJX-ray2.10B/E1-224[»]
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Phylogenomic databases

KOiK13919.

Family and domain databases

Gene3Di3.40.50.10150. 1 hit.
InterProiIPR010254. B12-dep_deHydtase_bsu.
IPR003208. Dehydtase/Dehydtase_re.
IPR025541. Ppandiol/glycerol_DHydtase_msu.
[Graphical view]
PfamiPF02288. Dehydratase_MU. 1 hit.
[Graphical view]
PIRSFiPIRSF018506. Prpndl_dhdrts_md. 1 hit.
SUPFAMiSSF52968. SSF52968. 1 hit.

Sequencei

Sequence statusi: Complete.

Q59471-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEINEKLLRQ IIEDVLSEMK GSDKPVSFNA PAASAAPQAT PPAGDGFLTE
60 70 80 90 100
VGEARQGTQQ DEVIIAVGPA FGLAQTVNIV GIPHKSILRE VIAGIEEEGI
110 120 130 140 150
KARVIRCFKS SDVAFVAVEG NRLSGSGISI GIQSKGTTVI HQQGLPPLSN
160 170 180 190 200
LELFPQAPLL TLETYRQIGK NAARYAKRES PQPVPTLNDQ MARPKYQAKS
210 220
AILHIKETKY VVTGKNPQEL RVAL
Length:224
Mass (Da):24,114
Last modified:November 1, 1996 - v1
Checksum:iC0A7C45A55CFAC7D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D45071 Genomic DNA. Translation: BAA08100.1.
PIRiB56111.
RefSeqiYP_005016276.1. NC_016612.1.

Genome annotation databases

EnsemblBacteriaiKGZ19724; KGZ19724; MC52_02995.
KEGGikox:KOX_01460.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D45071 Genomic DNA. Translation: BAA08100.1.
PIRiB56111.
RefSeqiYP_005016276.1. NC_016612.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DIOX-ray2.20B/E1-224[»]
1EEXX-ray1.70B/E1-224[»]
1EGMX-ray1.85B/E1-224[»]
1EGVX-ray1.75B/E1-224[»]
1IWBX-ray1.85B/E1-224[»]
1UC4X-ray1.80B/E1-224[»]
1UC5X-ray2.30B/E1-224[»]
3AUJX-ray2.10B/E1-224[»]
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

MINTiMINT-7997115.
STRINGi1006551.KOX_01460.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiKGZ19724; KGZ19724; MC52_02995.
KEGGikox:KOX_01460.

Phylogenomic databases

KOiK13919.

Enzyme and pathway databases

BRENDAi4.2.1.28. 2811.

Family and domain databases

Gene3Di3.40.50.10150. 1 hit.
InterProiIPR010254. B12-dep_deHydtase_bsu.
IPR003208. Dehydtase/Dehydtase_re.
IPR025541. Ppandiol/glycerol_DHydtase_msu.
[Graphical view]
PfamiPF02288. Dehydratase_MU. 1 hit.
[Graphical view]
PIRSFiPIRSF018506. Prpndl_dhdrts_md. 1 hit.
SUPFAMiSSF52968. SSF52968. 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).
  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).

Entry informationi

Entry nameiQ59471_KLEOX
AccessioniPrimary (citable) accession number: Q59471
Entry historyi
Integrated into UniProtKB/TrEMBL: November 1, 1996
Last sequence update: November 1, 1996
Last modified: June 24, 2015
This is version 70 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureCombined sources

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.