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Q59470 (Q59470_KLEOX) Unreviewed, UniProtKB/TrEMBL

Last modified March 19, 2014. Version 65. Feed History...

Clusters with 100%, 90%, 50% identity | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry infoCustomize order

Names and origin

Protein names
EC=4.2.1.28 EMBL BAA08099.1
Gene names
Name:pddA EMBL BAA08099.1
OrganismKlebsiella oxytoca EMBL BAA08099.1
Taxonomic identifier571 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeKlebsiella

Protein attributes

Sequence length554 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Cofactor

Adenosylcobalamin By similarity. PIRNR PIRNR018507

Sequence similarities

Belongs to the diol/glycerol dehydratase large subunit family. PIRNR PIRNR018507

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Sites

Metal binding1411Calcium PDB 3AUJ
Metal binding1411Potassium 1
Metal binding1701Calcium PDB 3AUJ
Metal binding1701Potassium 1
Metal binding2031Potassium 2; via carbonyl oxygen PDB 1IWB
Metal binding2051Potassium 2 PDB 1IWB
Metal binding2081Potassium 2 PDB 1IWB
Metal binding2211Calcium PDB 3AUJ
Metal binding2211Potassium 1
Metal binding2221Potassium 2 PDB 1IWB
Metal binding2611Potassium 3; via carbonyl oxygen PDB 1EEX PDB 1EGV PDB 1IWB
Metal binding2641Potassium 3 PDB 1EEX PDB 1EGV PDB 1IWB
Metal binding2651Potassium 3 PDB 1EEX PDB 1EGV PDB 1IWB
Metal binding2801Potassium 3 PDB 1EEX PDB 1EGV PDB 1IWB
Metal binding2961Calcium PDB 3AUJ
Metal binding2961Potassium 1
Metal binding3621Calcium; via carbonyl oxygen PDB 3AUJ
Metal binding3621Potassium 1; via carbonyl oxygen
Binding site4171Phosphate 1 PDB 3AUJ
Binding site4171Phosphate 2 PDB 3AUJ
Site1431Important for catalytic activity
Site1701Important for catalytic activity
Site2961Important for catalytic activity
Site3351Important for catalytic activity

Sequences

Sequence LengthMass (Da)Tools
Q59470 [UniParc].

Last modified November 1, 1996. Version 1.
Checksum: 5AC48A035B65331D

FASTA55460,348
        10         20         30         40         50         60 
MRSKRFEALA KRPVNQDGFV KEWIEEGFIA MESPNDPKPS IKIVNGAVTE LDGKPVSDFD 

        70         80         90        100        110        120 
LIDHFIARYG INLNRAEEVM AMDSVKLANM LCDPNVKRSE IVPLTTAMTP AKIVEVVSHM 

       130        140        150        160        170        180 
NVVEMMMAMQ KMRARRTPSQ QAHVTNVKDN PVQIAADAAE GAWRGFDEQE TTVAVARYAP 

       190        200        210        220        230        240 
FNAIALLVGS QVGRPGVLTQ CSLEEATELK LGMLGHTCYA ETISVYGTEP VFTDGDDTPW 

       250        260        270        280        290        300 
SKGFLASSYA SRGLKMRFTS GSGSEVQMGY AEGKSMLYLE ARCIYITKAA GVQGLQNGSV 

       310        320        330        340        350        360 
SCIGVPSAVP SGIRAVLAEN LICSSLDLEC ASSNDQTFTH SDMRRTARLL MQFLPGTDFI 

       370        380        390        400        410        420 
SSGYSAVPNY DNMFAGSNED AEDFDDYNVI QRDLKVDGGL RPVREEDVIA IRNKAARALQ 

       430        440        450        460        470        480 
AVFAGMGLPP ITDEEVEAAT YAHGSKDMPE RNIVEDIKFA QEIINKNRNG LEVVKALAQG 

       490        500        510        520        530        540 
GFTDVAQDML NIQKAKLTGD YLHTSAIIVG DGQVLSAVND VNDYAGPATG YRLQGERWEE 

       550 
IKNIPGALDP NEID 

« Hide

References

[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 8724 EMBL BAA08099.1.
[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.
[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 700324 EMBL AFJ04717.1.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
JQ478430 Genomic DNA. Translation: AFJ04717.1.
D45071 Genomic DNA. Translation: BAA08099.1.
PIRA56111.
RefSeqYP_005016275.1. NC_016612.1.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

MINTMINT-7997099.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID11660425.
KEGGkox:KOX_01455.

Phylogenomic databases

KOK01699.

Family and domain databases

Gene3D3.20.20.350. 1 hit.
InterProIPR016176. Cbl-dep_enz_cat.
IPR003206. Diol/glycerol_deHydtase_lsu.
[Graphical view]
PfamPF02286. Dehydratase_LU. 1 hit.
[Graphical view]
PIRSFPIRSF018507. Prpndl_dhdrts_lg. 1 hit.
ProDomPD025428. Diol/glycerol_deHydtase_lsu. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMSSF51703. SSF51703. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceQ59470.

Entry information

Entry nameQ59470_KLEOX
AccessionPrimary (citable) accession number: Q59470
Entry history
Integrated into UniProtKB/TrEMBL: November 1, 1996
Last sequence update: November 1, 1996
Last modified: March 19, 2014
This is version 65 of the entry and version 1 of the sequence. [Complete history]
Entry statusUnreviewed (UniProtKB/TrEMBL)