Haloalkane_dehalogenase-HLD2

Relationship

Family: Haloalkane_dehalogenase-HLD2

Block: X

Parent Family: Epoxide-hydrolase_like

Comment

Haloalkane dehalogenases (HLDs) are enzymes that catalyze the cleavage of carbon halogen bonds by a hydrolytic mechanism. The catalytic triad consists of the key nucleophile (Asp) the general base (His) and a catalytic acid (Asp or Glu). HLD where subdivided in three subfamily (Chovancova et al.) according to their substrate specificity and position of active site residues. Class one HLD1 (HLD-I) has catalytic triad Asp-His-Asp and halide-strabilizing residues Trp-Trp. Class two HLDII (HLD-II) has catalytic triad Asp-His-Glu and halide-stabilizing residues Asn-Trp. Class three HLDIII (HLD-III) has catalytic triad Asp-His-Asp and halide-strabilizing residues Asn-Trp. Although the reaction performed is different the Renilla reniformis luciferase belongs to this family. In ESTHER as in HAMAP database class I and III are merged as they are close. Luciferase from Renilla reniformis (RLuc) catalyzes the degradation of coelenterazine in the presence of molecular oxygen, resulting in the product coelenteramide, carbon dioxide, and the desired photon of light (EC 1.13.12.5). This enzyme belongs to the Haloalkane dehalogenase family II with a different catalytic function (EC 3.8.1.5) (this luciferase is different from fireflies luciferases classified as Luciferin 4-monooxygenase; ATP-dependent AMP-binding enzyme family). Reconstruction of an ancestral enzyme shows it has both hydrolase and monooxygenase activities ( Chaloupkova et al.)

Database

Interpro : IPR023594 Haloalkane dehalogenase, subfamily 2

PIRSF : No PIRSF

Pdoc : No Pdoc

Pfam : PF00561 Abhydrolase_1

Prints : No Print

EC Number : 3.8.1.5

Sequences

Peptide in Fasta
Nucleotide in Fasta
Alignment with Multalin Text only
Seed alignment with MAFFT No colour
Alignment with MAFFT No colour
Dendrogram The dnd file

Structures (131)

Genes Proteins in Haloalkane_dehalogenase-HLD2 family (72)

No fragment of genes

Structures in Haloalkane_dehalogenase-HLD2 family (131)

Substrates in Haloalkane_dehalogenase-HLD2 family (35)

Inhibitors in Haloalkane_dehalogenase-HLD2 family (30)

References (26)

Title : Light-Emitting Dehalogenases: Reconstruction of Multifunctional Biocatalysts - Chaloupkova_2019_ACS.Catal_9_48103
Author(s) : Chaloupkova, R , Liskova V , Tool M , Markova K , Sebestova E , Hernychova L , Marek M , Pinto GP , Pluskal D , Waterman J , Prokop Z , Damborsky J
Ref : ACS Catal , 9 :4810 , 2019
PubMedID:
Gene_locus related to this paper: 9zzzz-AncHLDRLuc2 , 9zzzz-AncHLDRLuc , renre-luc

Title : A Haloalkane Dehalogenase from a Marine Microbial Consortium Possessing Exceptionally Broad Substrate Specificity - Buryska_2018_Appl.Environ.Microbiol_84_
Author(s) : Buryska T , Babkova P , Vavra O , Damborsky J , Prokop Z
Ref : Applied Environmental Microbiology , 84 : , 2018
PubMedID: 29101190
Gene_locus related to this paper: 9cyan-q6dnd9

Title : A puzzling homology: a brittle star using a putative cnidarian-type luciferase for bioluminescence - Delroisse_2017_Open.Biol_7_
Author(s) : Delroisse J , Ullrich-Luter E , Blaue S , Ortega-Martinez O , Eeckhaut I , Flammang P , Mallefet J
Ref : Open Biol , 7 : , 2017
PubMedID: 28381628

Title : Engineering a de novo transport tunnel - Brezovsky_2016_ACS.Catal_6_7597
Author(s) : Brezovsky J , Babkova P , Degtjarik O , Fortova A , Gora A , Iermak I , Rezacova P , Dvorak P , Kuta-Smatanova I , Prokop Z , Chaloupkova R , Damborsky J
Ref : ACS Catal , 6 :7597 , 2016
PubMedID:
Gene_locus related to this paper: sphpi-linb

Title : Balancing the stability-activity trade-off by fine-tuning dehalogenase access tunnels - Liskova_2015_ChemCatChem_7_648
Author(s) : Liskova V , Bednar D , Prudnikova T , Rezacova P , Koudelakova T , Sebestova E , Kuta-Smatanova I , Brezovsky J , Chaloupkova R , Damborsky J
Ref : ChemCatChem , 7 :648 , 2015
PubMedID:
Gene_locus related to this paper: rhoso-halo1

Title : Dynamics and hydration explain failed functional transformation in dehalogenase design - Sykora_2014_Nat.Chem.Biol_10_428
Author(s) : Sykora J , Brezovsky J , Koudelakova T , Lahoda M , Fortova A , Chernovets T , Chaloupkova R , Stepankova V , Prokop Z , Smatanova IK , Hof M , Damborsky J
Ref : Nat Chemical Biology , 10 :428 , 2014
PubMedID: 24727901
Gene_locus related to this paper: rhoso-halo1

Title : Biochemical and structural characterisation of a haloalkane dehalogenase from a marine Rhodobacteraceae - Novak_2014_FEBS.Lett_588_1616
Author(s) : Novak HR , Sayer C , Isupov MN , Gotz D , Spragg AM , Littlechild JA
Ref : FEBS Letters , 588 :1616 , 2014
PubMedID: 24613925
Gene_locus related to this paper: 9rhob-KF032932

Title : Crystal structure of the novel haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58 reveals a special halide-stabilizing pair and enantioselectivity mechanism - Guan_2014_Appl.Microbiol.Biotechnol_98_8573
Author(s) : Guan L , Yabuki H , Okai M , Ohtsuka J , Tanokura M
Ref : Applied Microbiology & Biotechnology , 98 :8573 , 2014
PubMedID: 24770384
Gene_locus related to this paper: agrtu-DHAA

Title : Engineering enzyme stability and resistance to an organic cosolvent by modification of residues in the access tunnel - Koudelakova_2013_Angew.Chem.Int.Ed.Engl_52_1959
Author(s) : Koudelakova T , Chaloupkova R , Brezovsky J , Prokop Z , Sebestova E , Hesseler M , Khabiri M , Plevaka M , Kulik D , Kuta Smatanova I , Rezacova P , Ettrich R , Bornscheuer UT , Damborsky J
Ref : Angew Chem Int Ed Engl , 52 :1959 , 2013
PubMedID: 23303607
Gene_locus related to this paper: rhoso-halo1

Title : Expansion of access tunnels and active-site cavities influence activity of haloalkane dehalogenases in organic cosolvents - Stepankova_2013_Chembiochem_14_890
Author(s) : Stepankova V , Khabiri M , Brezovsky J , Pavelka A , Sykora J , Amaro M , Minofar B , Prokop Z , Hof M , Ettrich R , Chaloupkova R , Damborsky J
Ref : Chembiochem , 14 :890 , 2013
PubMedID: 23564727
Gene_locus related to this paper: rhoso-halo1

Title : Crystal Structure and Site-Directed Mutagenesis Analyses of Haloalkane Dehalogenase LinB from Sphingobium sp. Strain MI1205 - Okai_2013_J.Bacteriol_195_2642
Author(s) : Okai M , Ohtsuka J , Imai LF , Mase T , Moriuchi R , Tsuda M , Nagata K , Nagata Y , Tanokura M
Ref : Journal of Bacteriology , 195 :2642 , 2013
PubMedID: 23564170
Gene_locus related to this paper: sphpi-q6vqx3

Title : Structure and activity of DmmA, a marine haloalkane dehalogenase - Gehret_2012_Protein.Sci_21_239
Author(s) : Gehret JJ , Gu L , Geders TW , Brown WC , Gerwick L , Gerwick WH , Sherman DH , Smith JL
Ref : Protein Science , 21 :239 , 2012
PubMedID: 22124946
Gene_locus related to this paper: 9cyan-q6dnd9

Title : Substrate specificity of haloalkane dehalogenases - Koudelakova_2011_Biochem.J_435_345
Author(s) : Koudelakova T , Chovancova E , Brezovsky J , Monincova M , Fortova A , Jarkovsky J , Damborsky J
Ref : Biochemical Journal , 435 :345 , 2011
PubMedID: 21294712
Gene_locus related to this paper: agrtu-DHAA , brael-e2rv62 , braja-dhaa , myctu-linb , myctu-Rv1833c , rhoba-DHLA , rhoso-halo1 , sphpi-linb , xanau-halo1

Title : Enantioselectivity of haloalkane dehalogenases and its modulation by surface loop engineering -
Author(s) : Prokop Z , Sato Y , Brezovsky J , Mozga T , Chaloupkova R , Koudelakova T , Jerabek P , Stepankova V , Natsume R , van Leeuwen JG , Janssen DB , Florian J , Nagata Y , Senda T , Damborsky J
Ref : Angew Chem Int Ed Engl , 49 :6111 , 2010
PubMedID: 20645368
Gene_locus related to this paper: braja-dhaa

Title : Pathways and mechanisms for product release in the engineered haloalkane dehalogenases explored using classical and random acceleration molecular dynamics simulations - Klvana_2009_J.Mol.Biol_392_1339
Author(s) : Klvana M , Pavlova M , Koudelakova T , Chaloupkova R , Dvorak P , Prokop Z , Stsiapanava A , Kuty M , Kuta-Smatanova I , Dohnalek J , Kulhanek P , Wade RC , Damborsky J
Ref : Journal of Molecular Biology , 392 :1339 , 2009
PubMedID: 19577578
Gene_locus related to this paper: rhoso-halo1

Title : X-ray crystal structure of Mycobacterium tuberculosis haloalkane dehalogenase Rv2579 - Mazumdar_2008_Biochim.Biophys.Acta_1784_351
Author(s) : Mazumdar PA , Hulecki JC , Cherney MM , Garen CR , James MN
Ref : Biochimica & Biophysica Acta , 1784 :351 , 2008
PubMedID: 18062934
Gene_locus related to this paper: myctu-linb

Title : Crystal structures of the luciferase and green fluorescent protein from Renilla reniformis - Loening_2007_J.Mol.Biol_374_1017
Author(s) : Loening AM , Fenn TD , Gambhir SS
Ref : Journal of Molecular Biology , 374 :1017 , 2007
PubMedID: 17980388
Gene_locus related to this paper: renre-luc

Title : Weak activity of haloalkane dehalogenase LinB with 1,2,3-trichloropropane revealed by X-Ray crystallography and microcalorimetry - Monincova_2007_Appl.Environ.Microbiol_73_2005
Author(s) : Monincova M , Prokop Z , Vevodova J , Nagata Y , Damborsky J
Ref : Applied Environmental Microbiology , 73 :2005 , 2007
PubMedID: 17259360
Gene_locus related to this paper: sphpi-linb

Title : Phylogenetic analysis of haloalkane dehalogenases - Chovancova_2007_Proteins_67_305
Author(s) : Chovancova E , Kosinski J , Bujnicki JM , Damborsky J
Ref : Proteins , 67 :305 , 2007
PubMedID: 17295320

Title : Crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 A resolution: dynamics of catalytic residues - Oakley_2004_Biochemistry_43_870
Author(s) : Oakley AJ , Klvana M , Otyepka M , Nagata Y , Wilce MC , Damborsky J
Ref : Biochemistry , 43 :870 , 2004
PubMedID: 14744129
Gene_locus related to this paper: sphpi-linb

Title : Evolving haloalkane dehalogenases - Janssen_2004_Curr.Opin.Chem.Biol_8_150
Author(s) : Janssen DB
Ref : Curr Opin Chemical Biology , 8 :150 , 2004
PubMedID: 15062775

Title : Haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26: X-ray crystallographic studies of dehalogenation of brominated substrates - Streltsov_2003_Biochemistry_42_10104
Author(s) : Streltsov VA , Prokop Z , Damborsky J , Nagata Y , Oakley A , Wilce MC
Ref : Biochemistry , 42 :10104 , 2003
PubMedID: 12939138
Gene_locus related to this paper: sphpi-linb

Title : Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: evidence for product- and water-mediated inhibition - Oakley_2002_Biochemistry_41_4847
Author(s) : Oakley AJ , Prokop Z , Bohac M , Kmunicek J , Jedlicka T , Monincova M , Kuta-Smatanova I , Nagata Y , Damborsky J , Wilce MC
Ref : Biochemistry , 41 :4847 , 2002
PubMedID: 11939779
Gene_locus related to this paper: sphpi-linb

Title : Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26 - Marek_2000_Biochemistry_39_14082
Author(s) : Marek J , Vevodova J , Smatanova IK , Nagata Y , Svensson LA , Newman J , Takagi M , Damborsky J
Ref : Biochemistry , 39 :14082 , 2000
PubMedID: 11087355
Gene_locus related to this paper: sphpi-linb

Title : Haloalkane dehalogenases: structure of a Rhodococcus enzyme - Newman_1999_Biochemistry_38_16105
Author(s) : Newman J , Peat TS , Richard R , Kan L , Swanson PE , Affholter JA , Holmes IH , Schindler JF , Unkefer CJ , Terwilliger TC
Ref : Biochemistry , 38 :16105 , 1999
PubMedID: 10587433
Gene_locus related to this paper: rhoso-halo1

Title : Repositioning the catalytic triad aspartic acid of haloalkane dehalogenase: effects on stability, kinetics, and structure - Krooshof_1997_Biochemistry_36_9571
Author(s) : Krooshof GH , Kwant EM , Damborsky J , Koca J , Janssen DB
Ref : Biochemistry , 36 :9571 , 1997
PubMedID: 9236003