LINA_SPHJU
ID LINA_SPHJU Reviewed; 156 AA.
AC P51697; D4Z258;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 4.
DT 03-AUG-2022, entry version 86.
DE RecName: Full=Gamma-hexachlorocyclohexane dehydrochlorinase {ECO:0000303|PubMed:20813114, ECO:0000303|PubMed:7686793};
DE Short=Gamma-HCH dehydrochlorinase {ECO:0000303|PubMed:7686793};
DE EC=4.5.1.- {ECO:0000269|PubMed:11099497, ECO:0000269|Ref.6};
GN Name=linA {ECO:0000303|PubMed:20813114};
GN OrderedLocusNames=SJA_C1-18560 {ECO:0000312|EMBL:BAI96690.1};
OS Sphingobium japonicum (strain DSM 16413 / CCM 7287 / MTCC 6362 / UT26 /
OS NBRC 101211 / UT26S).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Sphingobium.
OX NCBI_TaxID=452662;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=DSM 16413 / CCM 7287 / MTCC 6362 / UT26 / NBRC 101211 / UT26S;
RX PubMed=1718942; DOI=10.1128/jb.173.21.6811-6819.1991;
RA Imai R., Nagata Y., Fukuda M., Takagi M., Yano K.;
RT "Molecular cloning of a Pseudomonas paucimobilis gene encoding a 17-
RT kilodalton polypeptide that eliminates HCl molecules from gamma-
RT hexachlorocyclohexane.";
RL J. Bacteriol. 173:6811-6819(1991).
RN [2]
RP SEQUENCE REVISION.
RA Imai R., Nagata Y., Fukuda M., Takagi M., Yano K.;
RL Submitted (MAR-1999) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 16413 / CCM 7287 / MTCC 6362 / UT26 / NBRC 101211 / UT26S;
RX PubMed=20817768; DOI=10.1128/jb.00961-10;
RA Nagata Y., Ohtsubo Y., Endo R., Ichikawa N., Ankai A., Oguchi A., Fukui S.,
RA Fujita N., Tsuda M.;
RT "Complete genome sequence of the representative gamma-
RT hexachlorocyclohexane-degrading bacterium Sphingobium japonicum UT26.";
RL J. Bacteriol. 192:5852-5853(2010).
RN [4]
RP PROTEIN SEQUENCE OF 2-10, AND SUBCELLULAR LOCATION.
RX PubMed=10464214; DOI=10.1128/jb.181.17.5409-5413.1999;
RA Nagata Y., Futamura A., Miyauchi K., Takagi M.;
RT "Two different types of dehalogenases, LinA and LinB, involved in gamma-
RT hexachlorocyclohexane degradation in Sphingomonas paucimobilis UT26 are
RT localized in the periplasmic space without molecular processing.";
RL J. Bacteriol. 181:5409-5413(1999).
RN [5]
RP FUNCTION, AND PATHWAY.
RC STRAIN=DSM 16413 / CCM 7287 / MTCC 6362 / UT26 / NBRC 101211 / UT26S;
RX PubMed=7686793; DOI=10.1271/bbb.57.703;
RA Nagata Y., Imai R., Sakai A., Fukuda M., Yano K., Takagi M.;
RT "Isolation and characterization of Tn5-induced mutants of Pseudomonas
RT paucimobilis UT26 defective in gamma-hexachlorocyclohexane
RT dehydrochlorinase (LinA).";
RL Biosci. Biotechnol. Biochem. 57:703-709(1993).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RC STRAIN=DSM 16413 / CCM 7287 / MTCC 6362 / UT26 / NBRC 101211 / UT26S;
RX DOI=10.1271/bbb.57.1582;
RA Nagata Y., Imai R., Sakai A., Fukuda M., Yano K., Takagi M.;
RT "Purification and characterization of gamma-hexachlorocyclohexane (gamma-
RT HCH) dehydrochlorinase (LinA) from Pseudomonas paucimobilis.";
RL Biosci. Biotechnol. Biochem. 57:1582-1583(1993).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, AND REACTION MECHANISM.
RC STRAIN=DSM 16413 / CCM 7287 / MTCC 6362 / UT26 / NBRC 101211 / UT26S;
RX PubMed=11099497; DOI=10.1074/jbc.m007452200;
RA Trantirek L., Hynkova K., Nagata Y., Murzin A.G., Ansorgova A., Sklenar V.,
RA Damborsky J.;
RT "Reaction mechanism and stereochemistry of gamma-hexachlorocyclohexane
RT dehydrochlorinase LinA.";
RL J. Biol. Chem. 276:7734-7740(2001).
RN [8]
RP MUTAGENESIS OF LYS-20; ASP-25; TRP-42; TYR-50; LEU-64; MET-67; HIS-73;
RP LEU-96; PHE-113; ASP-115; ARG-129 AND PHE-144, 3D-STRUCTURE MODELING, AND
RP ACTIVE SITE.
RX PubMed=11746694; DOI=10.1002/prot.10007;
RA Nagata Y., Mori K., Takagi M., Murzin A.G., Damborsky J.;
RT "Identification of protein fold and catalytic residues of gamma-
RT hexachlorocyclohexane dehydrochlorinase LinA.";
RL Proteins 45:471-477(2001).
RN [9] {ECO:0007744|PDB:3A76}
RP X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS), SUBUNIT, AND ACTIVE SITE.
RC STRAIN=DSM 16413 / CCM 7287 / MTCC 6362 / UT26 / NBRC 101211 / UT26S;
RX PubMed=20813114; DOI=10.1016/j.jmb.2010.08.043;
RA Okai M., Kubota K., Fukuda M., Nagata Y., Nagata K., Tanokura M.;
RT "Crystal structure of gamma-hexachlorocyclohexane dehydrochlorinase LinA
RT from Sphingobium japonicum UT26.";
RL J. Mol. Biol. 403:260-269(2010).
CC -!- FUNCTION: Catalyzes the conversion of the important environmental
CC pollutant gamma-hexachlorocyclohexane (gamma-HCH or lindane) to
CC 1,3,4,6-tetrachloro-1,4-cyclohexadiene (1,4-TCDN) via gamma-
CC pentachlorocyclohexene (gamma-PCCH), proceeding by two successive 1,2-
CC anti conformationally dependent dehydrochlorinations (PubMed:11099497).
CC Also shows activity with alpha- and delta-HCH, giving alpha- and delta-
CC PCCH respectively, but not with the beta isomer (Ref.6). Is involved in
CC the degradation pathway that allows S.japonicum UT26 to grow on gamma-
CC HCH as the sole source of carbon and energy (PubMed:7686793).
CC {ECO:0000269|PubMed:11099497, ECO:0000269|PubMed:7686793,
CC ECO:0000269|Ref.6}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=gamma-hexachlorocyclohexane = (3R,4S,5S,6R)-
CC pentachlorocyclohexene + chloride + H(+); Xref=Rhea:RHEA:45480,
CC ChEBI:CHEBI:10576, ChEBI:CHEBI:15378, ChEBI:CHEBI:17996,
CC ChEBI:CHEBI:32888; Evidence={ECO:0000269|PubMed:11099497,
CC ECO:0000269|Ref.6};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(3R,4S,5S,6R)-pentachlorocyclohexene = (3R,6R)-1,3,4,6-
CC tetrachlorocyclohexa-1,4-diene + chloride + H(+);
CC Xref=Rhea:RHEA:12152, ChEBI:CHEBI:10576, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:17996, ChEBI:CHEBI:18904;
CC Evidence={ECO:0000269|PubMed:11099497};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 7.5. {ECO:0000269|Ref.6};
CC -!- PATHWAY: Xenobiotic degradation; gamma-hexachlorocyclohexane
CC degradation. {ECO:0000269|PubMed:7686793}.
CC -!- SUBUNIT: Homotrimer. {ECO:0000269|PubMed:20813114}.
CC -!- SUBCELLULAR LOCATION: Periplasm {ECO:0000269|PubMed:10464214}.
CC -!- INDUCTION: Constitutively expressed.
CC -!- MISCELLANEOUS: Is not N-terminally processed during export, so it may
CC be secreted into the periplasmic space via a hitherto unknown
CC mechanism. {ECO:0000305|PubMed:10464214}.
CC -!- MISCELLANEOUS: Gamma-hexachlorocyclohexane (lindane) is an
CC organochlorine insecticide which has been used worldwide since the
CC 1940s. Because of its toxicity and long persistence in soil, most
CC countries have prohibited the use of gamma-HCH. However, many
CC contaminated sites still remain throughout the world. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the HCH dehydrochlorinase family. {ECO:0000305}.
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DR EMBL; S63514; AAC60443.1; ALT_SEQ; Genomic_DNA.
DR EMBL; D90355; BAA14369.2; -; Genomic_DNA.
DR EMBL; AP010803; BAI96690.1; -; Genomic_DNA.
DR PIR; A41334; A41334.
DR RefSeq; WP_013040172.1; NC_014006.1.
DR PDB; 3A76; X-ray; 2.25 A; A/B/C=1-156.
DR PDBsum; 3A76; -.
DR AlphaFoldDB; P51697; -.
DR SMR; P51697; -.
DR STRING; 452662.SJA_C1-18560; -.
DR EnsemblBacteria; BAI96690; BAI96690; SJA_C1-18560.
DR KEGG; sjp:SJA_C1-18560; -.
DR eggNOG; COG3631; Bacteria.
DR HOGENOM; CLU_106738_7_3_5; -.
DR BioCyc; MetaCyc:LINAPSEPA-MON; -.
DR BRENDA; 4.5.1.B1; 10293.
DR UniPathway; UPA00689; -.
DR EvolutionaryTrace; P51697; -.
DR Proteomes; UP000007753; Chromosome 1.
DR GO; GO:0042597; C:periplasmic space; IEA:UniProtKB-SubCell.
DR GO; GO:0016829; F:lyase activity; IEA:UniProtKB-KW.
DR GO; GO:0009636; P:response to toxic substance; IEA:UniProtKB-KW.
DR InterPro; IPR032710; NTF2-like_dom_sf.
DR InterPro; IPR037401; SnoaL-like.
DR Pfam; PF13577; SnoaL_4; 1.
DR SUPFAM; SSF54427; SSF54427; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Detoxification; Direct protein sequencing; Lyase; Periplasm;
KW Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:10464214"
FT CHAIN 2..156
FT /note="Gamma-hexachlorocyclohexane dehydrochlorinase"
FT /id="PRO_0000084436"
FT ACT_SITE 25
FT /evidence="ECO:0000305|PubMed:11746694,
FT ECO:0000305|PubMed:20813114"
FT ACT_SITE 73
FT /note="Proton acceptor"
FT /evidence="ECO:0000305|PubMed:11746694,
FT ECO:0000305|PubMed:20813114"
FT MUTAGEN 20
FT /note="K->M: 69% of wild-type activity."
FT /evidence="ECO:0000269|PubMed:11746694"
FT MUTAGEN 20
FT /note="K->Q: 3% of wild-type activity."
FT /evidence="ECO:0000269|PubMed:11746694"
FT MUTAGEN 25
FT /note="D->N,L: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11746694"
FT MUTAGEN 42
FT /note="W->L: 5% of wild-type activity."
FT /evidence="ECO:0000269|PubMed:11746694"
FT MUTAGEN 50
FT /note="Y->A: 62% of wild-type activity."
FT /evidence="ECO:0000269|PubMed:11746694"
FT MUTAGEN 64
FT /note="L->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11746694"
FT MUTAGEN 67
FT /note="M->A: No change in activity."
FT /evidence="ECO:0000269|PubMed:11746694"
FT MUTAGEN 73
FT /note="H->Q: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11746694"
FT MUTAGEN 96
FT /note="L->A: 10% of wild-type activity."
FT /evidence="ECO:0000269|PubMed:11746694"
FT MUTAGEN 113
FT /note="F->L: 38% of wild-type activity."
FT /evidence="ECO:0000269|PubMed:11746694"
FT MUTAGEN 113
FT /note="F->Y: 1% of wild-type activity."
FT /evidence="ECO:0000269|PubMed:11746694"
FT MUTAGEN 115
FT /note="D->L: 69% of wild-type activity."
FT /evidence="ECO:0000269|PubMed:11746694"
FT MUTAGEN 115
FT /note="D->N: 73% of wild-type activity."
FT /evidence="ECO:0000269|PubMed:11746694"
FT MUTAGEN 129
FT /note="R->Y,M: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11746694"
FT MUTAGEN 144
FT /note="F->L: No change in activity."
FT /evidence="ECO:0000269|PubMed:11746694"
FT HELIX 2..26
FT /evidence="ECO:0007829|PDB:3A76"
FT HELIX 29..33
FT /evidence="ECO:0007829|PDB:3A76"
FT STRAND 36..44
FT /evidence="ECO:0007829|PDB:3A76"
FT TURN 45..47
FT /evidence="ECO:0007829|PDB:3A76"
FT STRAND 48..51
FT /evidence="ECO:0007829|PDB:3A76"
FT HELIX 52..62
FT /evidence="ECO:0007829|PDB:3A76"
FT HELIX 64..67
FT /evidence="ECO:0007829|PDB:3A76"
FT STRAND 68..100
FT /evidence="ECO:0007829|PDB:3A76"
FT HELIX 102..104
FT /evidence="ECO:0007829|PDB:3A76"
FT STRAND 105..120
FT /evidence="ECO:0007829|PDB:3A76"
FT STRAND 123..138
FT /evidence="ECO:0007829|PDB:3A76"
SQ SEQUENCE 156 AA; 17342 MW; 2D96AF282FE1BCA0 CRC64;
MSDLDRLASR AAIQDLYSDK LIAVDKRQEG RLASIWWDDA EWTIEGIGTY KGPEGALDLA
NNVLWPMFHE CIHYGTNLRL EFVSADKVNG IGDVLLLGNL VEGNQSILIA AVFTDEYERR
DGVWKFSKRN ACTNYFTPLA GIHFAPPGIH FAPSGA
