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Protein

Homogentisate 1,2-dioxygenase

Gene

hmgA

Organism
Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)
Status
Reviewed-Annotation score: 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.UniRule annotation1 Publication

Cofactori

Fe cationUniRule annotation1 Publication

Kineticsi

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

  1. KM=53.2 µM for homogentisate2 Publications
  1. Vmax=99.4 µmol/min/mg enzyme2 Publications

Temperature dependencei

Optimum temperature is 37 degrees Celsius.2 Publications

Pathwayi: L-phenylalanine degradation

This protein is involved in step 4 of the subpathway that synthesizes acetoacetate and fumarate from L-phenylalanine.UniRule annotation
Proteins known to be involved in the 6 steps of the subpathway in this organism are:
  1. no protein annotated in this organism
  2. no protein annotated in this organism
  3. no protein annotated in this organism
  4. Homogentisate 1,2-dioxygenase (hmgA)
  5. no protein annotated in this organism
  6. no protein annotated in this organism
This subpathway is part of the pathway L-phenylalanine degradation, which is itself part of Amino-acid degradation.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes acetoacetate and fumarate from L-phenylalanine, the pathway L-phenylalanine degradation and in Amino-acid degradation.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei288Proton acceptorUniRule annotation1 Publication1
Metal bindingi331Iron1
Metal bindingi337Iron1
Binding sitei346homogentisateUniRule annotation1 Publication1
Metal bindingi367Iron1
Binding sitei367homogentisateUniRule annotation1 Publication1

GO - Molecular functioni

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

GO - Biological processi

  • L-phenylalanine catabolic process Source: UniProtKB
  • 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

BRENDAi1.13.11.5. 5092.
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 ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)
Taxonomic identifieri160488 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
Proteomesi
  • UP000000556 Componenti: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi288H → F: Reduces the catalytic efficiency 75-fold. 1 Publication1
Mutagenesisi346Y → F: Decreases the affinity for homogentisate more than 60-fold and reduces the catalytic efficiency 20-fold. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002202501 – 433Homogentisate 1,2-dioxygenaseAdd BLAST433

Expressioni

Inductioni

Induced by homogentisate and repressed by HmgR.

Interactioni

Subunit structurei

Hexamer; dimer of trimers.UniRule annotation1 Publication

Protein-protein interaction databases

STRINGi160488.PP_4621.

Structurei

Secondary structure

1433
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi11 – 13Combined sources3
Beta strandi19 – 24Combined sources6
Beta strandi35 – 37Combined sources3
Helixi39 – 41Combined sources3
Beta strandi43 – 48Combined sources6
Helixi56 – 58Combined sources3
Beta strandi61 – 68Combined sources8
Beta strandi96 – 98Combined sources3
Turni110 – 112Combined sources3
Beta strandi114 – 121Combined sources8
Beta strandi128 – 138Combined sources11
Beta strandi141 – 148Combined sources8
Beta strandi150 – 158Combined sources9
Beta strandi160 – 164Combined sources5
Beta strandi167 – 171Combined sources5
Beta strandi175 – 179Combined sources5
Beta strandi185 – 189Combined sources5
Beta strandi194 – 201Combined sources8
Helixi212 – 214Combined sources3
Helixi222 – 224Combined sources3
Beta strandi226 – 228Combined sources3
Beta strandi236 – 245Combined sources10
Beta strandi248 – 256Combined sources9
Beta strandi261 – 267Combined sources7
Beta strandi271 – 274Combined sources4
Helixi275 – 277Combined sources3
Beta strandi281 – 287Combined sources7
Helixi291 – 294Combined sources4
Beta strandi295 – 299Combined sources5
Beta strandi308 – 314Combined sources7
Beta strandi316 – 319Combined sources4
Beta strandi330 – 344Combined sources15
Beta strandi350 – 352Combined sources3
Beta strandi358 – 361Combined sources4
Helixi371 – 379Combined sources9
Beta strandi385 – 387Combined sources3
Beta strandi391 – 399Combined sources9
Beta strandi402 – 404Combined sources3
Helixi405 – 409Combined sources5
Helixi417 – 421Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
SMRiQ88E47.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the homogentisate dioxygenase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105F1J. Bacteria.
COG3508. LUCA.
HOGENOMiHOG000139824.
KOiK00451.
OMAiRGYLCEN.

Family and domain databases

Gene3Di2.60.120.10. 2 hits.
HAMAPiMF_00334. Homogentis_dioxygen. 1 hit.
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:
EMBLi
GenBanki
DDBJi
Links Updated
AE015451 Genomic DNA. Translation: AAN70194.1.
RefSeqiNP_746730.1. NC_002947.4.
WP_010955283.1. NC_002947.4.

Genome annotation databases

GeneIDi1041590.
KEGGippu:PP_4621.
PATRICi19947980. VBIPsePut30601_4927.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE015451 Genomic DNA. Translation: AAN70194.1.
RefSeqiNP_746730.1. NC_002947.4.
WP_010955283.1. NC_002947.4.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
SMRiQ88E47.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi160488.PP_4621.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1041590.
KEGGippu:PP_4621.
PATRICi19947980. VBIPsePut30601_4927.

Phylogenomic databases

eggNOGiENOG4105F1J. Bacteria.
COG3508. LUCA.
HOGENOMiHOG000139824.
KOiK00451.
OMAiRGYLCEN.

Enzyme and pathway databases

UniPathwayiUPA00139; UER00339.
BRENDAi1.13.11.5. 5092.

Family and domain databases

Gene3Di2.60.120.10. 2 hits.
HAMAPiMF_00334. Homogentis_dioxygen. 1 hit.
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.
ProtoNetiSearch...

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: November 2, 2016
This is version 85 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

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 one 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.