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Q88E47

- HGD_PSEPK

UniProt

Q88E47 - HGD_PSEPK

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Protein

Homogentisate 1,2-dioxygenase

Gene

hmgA

Organism
Pseudomonas putida (strain KT2440)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

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.2 Publications

Catalytic activityi

Homogentisate + O2 = 4-maleylacetoacetate.1 PublicationUniRule annotation

Cofactori

Iron.1 PublicationUniRule annotation

Kineticsi

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

  1. KM=53.2 µM for homogentisate2 Publications

Vmax=99.4 µmol/min/mg enzyme2 Publications

Temperature dependencei

Optimum temperature is 37 degrees Celsius.2 Publications

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei288 – 2881Proton acceptor1 PublicationUniRule annotation
Metal bindingi331 – 3311Iron
Metal bindingi337 – 3371Iron
Binding sitei346 – 3461homogentisate1 PublicationUniRule annotation
Metal bindingi367 – 3671Iron
Binding sitei367 – 3671homogentisate1 PublicationUniRule annotation

GO - Molecular functioni

  1. homogentisate 1,2-dioxygenase activity Source: UniProtKB
  2. iron ion binding Source: UniProtKB

GO - Biological processi

  1. L-phenylalanine catabolic process Source: UniProtKB
  2. tyrosine catabolic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Dioxygenase, Oxidoreductase

Keywords - Biological processi

Phenylalanine catabolism, Tyrosine catabolism

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciPPUT160488:GIXO-4708-MONOMER.
UniPathwayiUPA00139; UER00339.

Names & Taxonomyi

Protein namesi
Recommended name:
Homogentisate 1,2-dioxygenaseUniRule annotation (EC:1.13.11.5UniRule annotation)
Short name:
HGDOUniRule annotation
Alternative name(s):
Homogentisate oxygenaseUniRule annotation
Homogentisic acid oxidaseUniRule annotation
HomogentisicaseUniRule annotation
Gene namesi
Name:hmgAUniRule annotation
Ordered Locus Names:PP_4621
OrganismiPseudomonas putida (strain KT2440)
Taxonomic identifieri160488 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
ProteomesiUP000000556: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi288 – 2881H → F: Reduces the catalytic efficiency 75-fold. 1 Publication
Mutagenesisi346 – 3461Y → F: Decreases the affinity for homogentisate more than 60-fold and reduces the catalytic efficiency 20-fold. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 433433Homogentisate 1,2-dioxygenasePRO_0000220250Add
BLAST

Expressioni

Inductioni

Induced by homogentisate and repressed by HmgR.

Interactioni

Subunit structurei

Hexamer; dimer of trimers.1 PublicationUniRule annotation

Protein-protein interaction databases

STRINGi160488.PP_4621.

Structurei

Secondary structure

1
433
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi11 – 133
Beta strandi19 – 246
Beta strandi35 – 373
Helixi39 – 413
Beta strandi43 – 486
Helixi56 – 583
Beta strandi61 – 688
Beta strandi96 – 983
Turni110 – 1123
Beta strandi114 – 1218
Beta strandi128 – 13811
Beta strandi141 – 1488
Beta strandi150 – 1589
Beta strandi160 – 1645
Beta strandi167 – 1715
Beta strandi175 – 1795
Beta strandi185 – 1895
Beta strandi194 – 2018
Helixi212 – 2143
Helixi222 – 2243
Beta strandi226 – 2283
Beta strandi236 – 24510
Beta strandi248 – 2569
Beta strandi261 – 2677
Beta strandi271 – 2744
Helixi275 – 2773
Beta strandi281 – 2877
Helixi291 – 2944
Beta strandi295 – 2995
Beta strandi308 – 3147
Beta strandi316 – 3194
Beta strandi330 – 34415
Beta strandi350 – 3523
Beta strandi358 – 3614
Helixi371 – 3799
Beta strandi385 – 3873
Beta strandi391 – 3999
Beta strandi402 – 4043
Helixi405 – 4095
Helixi417 – 4215

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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[»]
ProteinModelPortaliQ88E47.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the homogentisate dioxygenase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG3508.
HOGENOMiHOG000139824.
KOiK00451.
OMAiRCFYNSD.
OrthoDBiEOG6D5FZK.

Family and domain databases

Gene3Di2.60.120.10. 2 hits.
HAMAPiMF_00334. Homogentis_dioxygen.
InterProiIPR005708. Homogentis_dOase.
IPR022950. Homogentis_dOase_bac.
IPR014710. RmlC-like_jellyroll.
IPR011051. RmlC_Cupin.
[Graphical view]
PANTHERiPTHR11056. PTHR11056. 1 hit.
PfamiPF04209. HgmA. 1 hit.
[Graphical view]
SUPFAMiSSF51182. SSF51182. 1 hit.
TIGRFAMsiTIGR01015. hmgA. 1 hit.

Sequencei

Sequence statusi: Complete.

Q88E47-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MNRDTSPDLH YLSGFGNEFA SEALPGALPV GQNSPQKAPY GLYAELLSGT
60 70 80 90 100
AFTMARSELR RTWLYRIRPS ALHPRFERLA RQPLGGPLGG INPNRLRWSP
110 120 130 140 150
QPIPAEPTDF IEGWLPMAAN AGAEKPAGVS IYIYRANRSM ERVFFNADGE
160 170 180 190 200
LLLVPEQGRL RIATELGVME VEPLEIAVIP RGMKFRVELL DGQARGYIAE
210 220 230 240 250
NHGAPLRLPD LGPIGSNGLA NPRDFLTPVA HYEEAEGPVQ LVQKFLGEHW
260 270 280 290 300
ACELQHSPLD VVAWHGSNVP YKYDLRRFNT IGTVSFDHPD PSIFTVLTSP
310 320 330 340 350
TSVHGMANMD FVIFPPRWMV AENTFRPPWF HRNLMNEFMG LINGAYDAKA
360 370 380 390 400
EGFLPGGASL HGVMSAHGPD AETCEKAIAA DLAPHKIDNT MAFMFETSQV
410 420 430
LRPSLQALEC PQLQADYDSC WATLPSTFNP NRR
Length:433
Mass (Da):48,011
Last modified:June 6, 2003 - v1
Checksum:i6D5F4C7F91BE4512
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE015451 Genomic DNA. Translation: AAN70194.1.
RefSeqiNP_746730.1. NC_002947.3.

Genome annotation databases

EnsemblBacteriaiAAN70194; AAN70194; PP_4621.
GeneIDi1041590.
KEGGippu:PP_4621.
PATRICi19947980. VBIPsePut30601_4927.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE015451 Genomic DNA. Translation: AAN70194.1 .
RefSeqi NP_746730.1. NC_002947.3.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3ZDS X-ray 1.70 A/B/C/D/E/F/G/H/I/J/K/L 1-433 [» ]
4AQ2 X-ray 1.95 A/B/C/D/E/F/G/H/I/J/K/L 1-433 [» ]
4AQ6 X-ray 1.98 A/B/C/D/E/F/G/H/I/J/K/L 1-433 [» ]
ProteinModelPortali Q88E47.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 160488.PP_4621.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAN70194 ; AAN70194 ; PP_4621 .
GeneIDi 1041590.
KEGGi ppu:PP_4621.
PATRICi 19947980. VBIPsePut30601_4927.

Phylogenomic databases

eggNOGi COG3508.
HOGENOMi HOG000139824.
KOi K00451.
OMAi RCFYNSD.
OrthoDBi EOG6D5FZK.

Enzyme and pathway databases

UniPathwayi UPA00139 ; UER00339 .
BioCyci PPUT160488:GIXO-4708-MONOMER.

Family and domain databases

Gene3Di 2.60.120.10. 2 hits.
HAMAPi MF_00334. Homogentis_dioxygen.
InterProi IPR005708. Homogentis_dOase.
IPR022950. Homogentis_dOase_bac.
IPR014710. RmlC-like_jellyroll.
IPR011051. RmlC_Cupin.
[Graphical view ]
PANTHERi PTHR11056. PTHR11056. 1 hit.
Pfami PF04209. HgmA. 1 hit.
[Graphical view ]
SUPFAMi SSF51182. SSF51182. 1 hit.
TIGRFAMsi TIGR01015. hmgA. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. 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.

Entry informationi

Entry nameiHGD_PSEPK
AccessioniPrimary (citable) accession number: Q88E47
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 6, 2003
Last sequence update: June 6, 2003
Last modified: October 29, 2014
This is version 75 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3