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Q88E47 (HGD_PSEPK) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 72. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Homogentisate 1,2-dioxygenase

Short name=HGDO
EC=1.13.11.5
Alternative name(s):
Homogentisate oxygenase
Homogentisic acid oxidase
Homogentisicase
Gene names
Name:hmgA
Ordered Locus Names:PP_4621
OrganismPseudomonas putida (strain KT2440) [Complete proteome] [HAMAP]
Taxonomic identifier160488 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas

Protein attributes

Sequence length433 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Involved in the catabolism of homogentisate (2,5-dihydroxyphenylacetate or 2,5-OH-PhAc), a central intermediate in the degradation of phenylalanine and tyrosine. Catalyzes the oxidative ring cleavage of the ar omatic ring of 2,5-dihydroxyphenylacetate to yield maleylacetoacetate. Ref.2 Ref.3

Catalytic activity

Homogentisate + O2 = 4-maleylacetoacetate. Ref.3

Cofactor

Iron. Ref.3

Pathway

Amino-acid degradation; L-phenylalanine degradation; acetoacetate and fumarate from L-phenylalanine: step 4/6. HAMAP-Rule MF_00334

Subunit structure

Hexamer; dimer of trimers. Ref.3

Induction

Induced by homogentisate and repressed by HmgR. HAMAP-Rule MF_00334

Sequence similarities

Belongs to the homogentisate dioxygenase family.

Biophysicochemical properties

Kinetic parameters:

Kcat is 79.5 sec(-1) for the oxidative ring cleavage of homogentisate.

KM=53.2 µM for homogentisate Ref.2 Ref.3

Vmax=99.4 µmol/min/mg enzyme

Temperature dependence:

Optimum temperature is 37 degrees Celsius.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 433433Homogentisate 1,2-dioxygenase HAMAP-Rule MF_00334
PRO_0000220250

Sites

Active site2881Proton acceptor Ref.3
Metal binding3311Iron
Metal binding3371Iron
Metal binding3671Iron
Binding site3461homogentisate
Binding site3671homogentisate

Experimental info

Mutagenesis2881H → F: Reduces the catalytic efficiency 75-fold. Ref.3
Mutagenesis3461Y → F: Decreases the affinity for homogentisate more than 60-fold and reduces the catalytic efficiency 20-fold. Ref.3

Secondary structure

.............................................................................. 433
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q88E47 [UniParc].

Last modified June 6, 2003. Version 1.
Checksum: 6D5F4C7F91BE4512

FASTA43348,011
        10         20         30         40         50         60 
MNRDTSPDLH YLSGFGNEFA SEALPGALPV GQNSPQKAPY GLYAELLSGT AFTMARSELR 

        70         80         90        100        110        120 
RTWLYRIRPS ALHPRFERLA RQPLGGPLGG INPNRLRWSP QPIPAEPTDF IEGWLPMAAN 

       130        140        150        160        170        180 
AGAEKPAGVS IYIYRANRSM ERVFFNADGE LLLVPEQGRL RIATELGVME VEPLEIAVIP 

       190        200        210        220        230        240 
RGMKFRVELL DGQARGYIAE NHGAPLRLPD LGPIGSNGLA NPRDFLTPVA HYEEAEGPVQ 

       250        260        270        280        290        300 
LVQKFLGEHW ACELQHSPLD VVAWHGSNVP YKYDLRRFNT IGTVSFDHPD PSIFTVLTSP 

       310        320        330        340        350        360 
TSVHGMANMD FVIFPPRWMV AENTFRPPWF HRNLMNEFMG LINGAYDAKA EGFLPGGASL 

       370        380        390        400        410        420 
HGVMSAHGPD AETCEKAIAA DLAPHKIDNT MAFMFETSQV LRPSLQALEC PQLQADYDSC 

       430 
WATLPSTFNP NRR 

« Hide

References

« Hide 'large scale' references
[1]"Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440."
Nelson K.E., Weinel C., Paulsen I.T., Dodson R.J., Hilbert H., Martins dos Santos V.A.P., Fouts D.E., Gill S.R., Pop M., Holmes M., Brinkac L.M., Beanan M.J., DeBoy R.T., Daugherty S.C., Kolonay J.F., Madupu R., Nelson W.C., White O. expand/collapse author list , Peterson J.D., Khouri H.M., Hance I., Chris Lee P., Holtzapple E.K., Scanlan D., Tran K., Moazzez A., Utterback T.R., Rizzo M., Lee K., Kosack D., Moestl D., Wedler H., Lauber J., Stjepandic D., Hoheisel J., Straetz M., Heim S., Kiewitz C., Eisen J.A., Timmis K.N., Duesterhoeft A., Tuemmler B., Fraser C.M.
Environ. Microbiol. 4:799-808(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: KT2440.
[2]"The homogentisate pathway: a central catabolic pathway involved in the degradation of L-phenylalanine, L-tyrosine, and 3-hydroxyphenylacetate in Pseudomonas putida."
Arias-Barrau E., Olivera E.R., Luengo J.M., Fernandez C., Galan B., Garcia J.L., Diaz E., Minambres B.
J. Bacteriol. 186:5062-5077(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES.
Strain: U.
[3]"Visualizing the substrate-, superoxo-, alkylperoxo-, and product-bound states at the nonheme Fe(II) site of homogentisate dioxygenase."
Jeoung J.H., Bommer M., Lin T.Y., Dobbek H.
Proc. Natl. Acad. Sci. U.S.A. 110:12625-12630(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH HOMOGENTISATE AND IRON IONS, FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF HIS-288 AND TYR-346, ACTIVE SITE, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, REACTION MECHANISM, SUBUNIT.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AE015451 Genomic DNA. Translation: AAN70194.1.
RefSeqNP_746730.1. NC_002947.3.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3ZDSX-ray1.70A/B/C/D/E/F/G/H/I/J/K/L1-433[»]
4AQ2X-ray1.95A/B/C/D/E/F/G/H/I/J/K/L1-433[»]
4AQ6X-ray1.98A/B/C/D/E/F/G/H/I/J/K/L1-433[»]
ProteinModelPortalQ88E47.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING160488.PP_4621.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAN70194; AAN70194; PP_4621.
GeneID1041590.
KEGGppu:PP_4621.
PATRIC19947980. VBIPsePut30601_4927.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG3508.
HOGENOMHOG000139824.
KOK00451.
OMARCFYNSD.
OrthoDBEOG6D5FZK.

Enzyme and pathway databases

BioCycPPUT160488:GIXO-4708-MONOMER.
UniPathwayUPA00139; UER00339.

Family and domain databases

Gene3D2.60.120.10. 2 hits.
HAMAPMF_00334. Homogentis_dioxygen.
InterProIPR005708. Homogentis_dOase.
IPR022950. Homogentis_dOase_bac.
IPR014710. RmlC-like_jellyroll.
IPR011051. RmlC_Cupin.
[Graphical view]
PANTHERPTHR11056. PTHR11056. 1 hit.
PfamPF04209. HgmA. 1 hit.
[Graphical view]
SUPFAMSSF51182. SSF51182. 1 hit.
TIGRFAMsTIGR01015. hmgA. 1 hit.
ProtoNetSearch...

Entry information

Entry nameHGD_PSEPK
AccessionPrimary (citable) accession number: Q88E47
Entry history
Integrated into UniProtKB/Swiss-Prot: June 6, 2003
Last sequence update: June 6, 2003
Last modified: June 11, 2014
This is version 72 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways