NYLC_FLASK
ID NYLC_FLASK Reviewed; 355 AA.
AC Q79F77; A0A493R6J6; Q57326;
DT 07-APR-2021, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 1.
DT 03-AUG-2022, entry version 44.
DE RecName: Full=6-aminohexanoate-oligomer endohydrolase {ECO:0000305};
DE EC=3.5.1.117 {ECO:0000269|PubMed:17827307, ECO:0000269|PubMed:8285701};
DE AltName: Full=6-aminohexanoate oligomer hydrolase {ECO:0000303|PubMed:17827307};
DE AltName: Full=Ahx endo-type-oligomer hydrolase {ECO:0000303|PubMed:17827307};
DE AltName: Full=Nylon hydrolase {ECO:0000303|PubMed:22187439};
DE AltName: Full=Nylon oligomer-degrading enzyme EIII {ECO:0000303|PubMed:1459943};
DE AltName: Full=Nylonase {ECO:0000303|PubMed:22187439};
DE Contains:
DE RecName: Full=6-aminohexanoate-oligomer endohydrolase alpha subunit {ECO:0000305};
DE Contains:
DE RecName: Full=6-aminohexanoate-oligomer endohydrolase beta subunit {ECO:0000305};
GN Name=nylC {ECO:0000303|PubMed:1459943};
OS Flavobacterium sp. (strain K172).
OG Plasmid pOAD2.
OC Bacteria; Actinobacteria; Micrococcales; Micrococcaceae; Paenarthrobacter.
OX NCBI_TaxID=37931;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K172; PLASMID=pOAD2;
RX PubMed=1459943; DOI=10.1128/jb.174.24.7948-7953.1992;
RA Kakudo S., Negoro S., Urabe I., Okada H.;
RT "A new nylon oligomer degradation gene (nylC) on plasmid pOAD2 of
RT Flavobacterium sp.";
RL J. Bacteriol. 174:7948-7953(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=KI723T1; PLASMID=pOAD2;
RX PubMed=7582019; DOI=10.1099/13500872-141-10-2585;
RA Kato K., Ohtsuki K., Koda Y., Maekawa T., Yomo T., Negoro S., Urabe I.;
RT "A plasmid encoding enzymes for nylon oligomer degradation: nucleotide
RT sequence and analysis of pOAD2.";
RL Microbiology 141:2585-2590(1995).
RN [3]
RP PROTEIN SEQUENCE OF 1-6 AND 267-271, FUNCTION, CATALYTIC ACTIVITY, PATHWAY,
RP AND PROTEOLYTIC PROCESSING.
RC STRAIN=K172; PLASMID=pOAD2;
RX PubMed=8285701; DOI=10.1128/aem.59.11.3978-3980.1993;
RA Kakudo S., Negoro S., Urabe I., Okada H.;
RT "Nylon oligomer degradation gene, nylC, on plasmid pOAD2 from a
RT Flavobacterium strain encodes endo-type 6-aminohexanoate oligomer
RT hydrolase: purification and characterization of the nylC gene product.";
RL Appl. Environ. Microbiol. 59:3978-3980(1993).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND PATHWAY.
RC PLASMID=pOAD2;
RX PubMed=17827307; DOI=10.1128/aem.00777-07;
RA Yasuhira K., Tanaka Y., Shibata H., Kawashima Y., Ohara A., Kato D.,
RA Takeo M., Negoro S.;
RT "6-Aminohexanoate oligomer hydrolases from the alkalophilic bacteria
RT Agromyces sp. strain KY5R and Kocuria sp. strain KY2.";
RL Appl. Environ. Microbiol. 73:7099-7102(2007).
RN [5]
RP MUTAGENESIS OF GLY-111; ASP-122; HIS-130 AND LEU-137.
RC PLASMID=pOAD2;
RX PubMed=22187439; DOI=10.1074/jbc.m111.321992;
RA Negoro S., Shibata N., Tanaka Y., Yasuhira K., Shibata H., Hashimoto H.,
RA Lee Y.H., Oshima S., Santa R., Oshima S., Mochiji K., Goto Y., Ikegami T.,
RA Nagai K., Kato D., Takeo M., Higuchi Y.;
RT "Three-dimensional structure of nylon hydrolase and mechanism of nylon-6
RT hydrolysis.";
RL J. Biol. Chem. 287:5079-5090(2012).
RN [6]
RP CRYSTALLIZATION.
RC STRAIN=K172; PLASMID=pOAD2;
RX PubMed=24100570; DOI=10.1107/s1744309113024263;
RA Nagai K., Yasuhira K., Tanaka Y., Kato D., Takeo M., Higuchi Y., Negoro S.,
RA Shibata N.;
RT "Crystallization and X-ray diffraction analysis of nylon hydrolase (NylC)
RT from Arthrobacter sp. KI72.";
RL Acta Crystallogr. F 69:1151-1154(2013).
RN [7] {ECO:0007744|PDB:5XYG, ECO:0007744|PDB:5XYO, ECO:0007744|PDB:5XYP, ECO:0007744|PDB:5XYQ, ECO:0007744|PDB:5XYS, ECO:0007744|PDB:5XYT, ECO:0007744|PDB:5Y0L, ECO:0007744|PDB:5Y0M}
RP X-RAY CRYSTALLOGRAPHY (1.03 ANGSTROMS) OF WILD-TYPE AND MUTANTS, SUBUNIT,
RP PROTEOLYTIC PROCESSING, ACTIVE SITE, AND MUTAGENESIS OF ASP-122.
RC PLASMID=pOAD2;
RX PubMed=29950566; DOI=10.1038/s41598-018-27860-w;
RA Negoro S., Shibata N., Lee Y.H., Takehara I., Kinugasa R., Nagai K.,
RA Tanaka Y., Kato D.I., Takeo M., Goto Y., Higuchi Y.;
RT "Structural basis of the correct subunit assembly, aggregation, and
RT intracellular degradation of nylon hydrolase.";
RL Sci. Rep. 8:9725-9725(2018).
CC -!- FUNCTION: Involved in the degradation of nylon-6 oligomers
CC (PubMed:8285701, PubMed:17827307). Degrades cyclic and linear oligomers
CC of 6-aminohexanoate (Ahx) with a degree of polymerization greater than
CC three by an endo-type mode (PubMed:8285701, PubMed:17827307). Cannot
CC use Ahx cyclic dimer or the Ahx linear dimer (PubMed:17827307).
CC {ECO:0000269|PubMed:17827307, ECO:0000269|PubMed:8285701}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=[N-(6-aminohexanoyl)]n + H2O = [N-(6-aminohexanoyl)]n-x + [N-
CC (6-aminohexanoyl)]x.; EC=3.5.1.117;
CC Evidence={ECO:0000269|PubMed:17827307, ECO:0000269|PubMed:8285701};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=3.7 mg/ml for Ahx cyclic-oligomer {ECO:0000269|PubMed:17827307};
CC Note=kcat is 6.5 sec(-1) with Ahx cyclic-oligomer as substrate.
CC {ECO:0000269|PubMed:17827307};
CC pH dependence:
CC Optimum pH is 6.5-7.5. {ECO:0000269|PubMed:17827307};
CC -!- PATHWAY: Xenobiotic degradation; nylon-6 oligomer degradation.
CC {ECO:0000269|PubMed:17827307, ECO:0000269|PubMed:8285701}.
CC -!- SUBUNIT: Heterotetramer composed of 4 alpha/beta heterodimers
CC (PubMed:29950566). Exists at the monomer/dimer/trimer equilibrium in
CC aqueous solution (PubMed:29950566). {ECO:0000269|PubMed:29950566}.
CC -!- PTM: Expressed as an inactive precursor that is cleaved
CC autocatalytically at Asn266/Thr267 to generate an active enzyme
CC composed of an alpha subunit and a beta subunit.
CC {ECO:0000269|PubMed:29950566, ECO:0000269|PubMed:8285701}.
CC -!- SIMILARITY: Belongs to the peptidase S58 family. {ECO:0000305}.
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DR EMBL; D10686; BAA01528.1; -; Genomic_DNA.
DR EMBL; D26094; BAA05088.1; -; Genomic_DNA.
DR PIR; A47039; A47039.
DR RefSeq; WP_012476895.1; NZ_BDMH01000051.1.
DR PDB; 5XYG; X-ray; 1.60 A; A/B=1-355.
DR PDB; 5XYO; X-ray; 2.00 A; A/B=1-355.
DR PDB; 5XYP; X-ray; 1.20 A; A/B=1-355.
DR PDB; 5XYQ; X-ray; 1.10 A; A/B=1-355.
DR PDB; 5XYS; X-ray; 1.05 A; A/B=1-355.
DR PDB; 5XYT; X-ray; 1.90 A; A/B=1-355.
DR PDB; 5Y0L; X-ray; 1.39 A; A/B=1-355.
DR PDB; 5Y0M; X-ray; 1.03 A; A/B=1-355.
DR PDBsum; 5XYG; -.
DR PDBsum; 5XYO; -.
DR PDBsum; 5XYP; -.
DR PDBsum; 5XYQ; -.
DR PDBsum; 5XYS; -.
DR PDBsum; 5XYT; -.
DR PDBsum; 5Y0L; -.
DR PDBsum; 5Y0M; -.
DR AlphaFoldDB; Q79F77; -.
DR SMR; Q79F77; -.
DR MEROPS; P01.102; -.
DR KEGG; ag:BAA05088; -.
DR BRENDA; 3.5.1.117; 2302.
DR UniPathway; UPA00207; -.
DR GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR GO; GO:0019876; P:nylon catabolic process; IDA:UniProtKB.
DR InterPro; IPR016117; ArgJ-like_dom_sf.
DR InterPro; IPR005321; Peptidase_S58_DmpA.
DR PANTHER; PTHR36512; PTHR36512; 1.
DR Pfam; PF03576; Peptidase_S58; 1.
DR SUPFAM; SSF56266; SSF56266; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Hydrolase; Nylon degradation;
KW Plasmid.
FT CHAIN 1..266
FT /note="6-aminohexanoate-oligomer endohydrolase alpha
FT subunit"
FT /evidence="ECO:0000305"
FT /id="PRO_0000452354"
FT CHAIN 267..355
FT /note="6-aminohexanoate-oligomer endohydrolase beta
FT subunit"
FT /evidence="ECO:0000305"
FT /id="PRO_0000452355"
FT ACT_SITE 267
FT /note="Nucleophile"
FT /evidence="ECO:0000305|PubMed:29950566"
FT MUTAGEN 111
FT /note="G->S: Decreases thermostability by about 10 degrees
FT Celsius."
FT /evidence="ECO:0000269|PubMed:22187439"
FT MUTAGEN 122
FT /note="D->G: Increases thermostability by 24 degrees
FT Celsius. Increases thermostability by 29 degrees Celsius;
FT when associated with Y-130."
FT /evidence="ECO:0000269|PubMed:22187439"
FT MUTAGEN 122
FT /note="D->K,R: Increases thermostability by 23 degrees
FT Celsius."
FT /evidence="ECO:0000269|PubMed:29950566"
FT MUTAGEN 122
FT /note="D->L: Increases thermostability by 13 degrees
FT Celsius."
FT /evidence="ECO:0000269|PubMed:29950566"
FT MUTAGEN 122
FT /note="D->N: Increases thermostability by 18 degrees
FT Celsius."
FT /evidence="ECO:0000269|PubMed:29950566"
FT MUTAGEN 122
FT /note="D->Q: Increases thermostability by 19 degrees
FT Celsius."
FT /evidence="ECO:0000269|PubMed:29950566"
FT MUTAGEN 122
FT /note="D->V: Increases thermostability by 30 degrees
FT Celsius."
FT /evidence="ECO:0000269|PubMed:29950566"
FT MUTAGEN 130
FT /note="H->Y: Increases thermostability by 11 degrees
FT Celsius. Increases thermostability by 29 degrees Celsius;
FT when associated with G-122."
FT /evidence="ECO:0000269|PubMed:22187439"
FT MUTAGEN 137
FT /note="L->A: Decreases thermostability by about 10 degrees
FT Celsius."
FT /evidence="ECO:0000269|PubMed:22187439"
FT HELIX 9..11
FT /evidence="ECO:0007829|PDB:5XYG"
FT HELIX 35..37
FT /evidence="ECO:0007829|PDB:5Y0M"
FT STRAND 48..52
FT /evidence="ECO:0007829|PDB:5Y0M"
FT STRAND 59..65
FT /evidence="ECO:0007829|PDB:5Y0M"
FT TURN 66..69
FT /evidence="ECO:0007829|PDB:5Y0M"
FT STRAND 70..87
FT /evidence="ECO:0007829|PDB:5Y0M"
FT STRAND 89..91
FT /evidence="ECO:0007829|PDB:5XYS"
FT STRAND 94..96
FT /evidence="ECO:0007829|PDB:5XYG"
FT STRAND 99..109
FT /evidence="ECO:0007829|PDB:5Y0M"
FT HELIX 110..114
FT /evidence="ECO:0007829|PDB:5Y0M"
FT HELIX 115..127
FT /evidence="ECO:0007829|PDB:5Y0M"
FT TURN 128..130
FT /evidence="ECO:0007829|PDB:5Y0M"
FT HELIX 134..136
FT /evidence="ECO:0007829|PDB:5Y0M"
FT STRAND 140..144
FT /evidence="ECO:0007829|PDB:5Y0M"
FT HELIX 148..150
FT /evidence="ECO:0007829|PDB:5XYS"
FT HELIX 159..167
FT /evidence="ECO:0007829|PDB:5Y0M"
FT STRAND 173..179
FT /evidence="ECO:0007829|PDB:5Y0M"
FT HELIX 180..182
FT /evidence="ECO:0007829|PDB:5Y0M"
FT HELIX 192..194
FT /evidence="ECO:0007829|PDB:5Y0M"
FT STRAND 200..207
FT /evidence="ECO:0007829|PDB:5Y0M"
FT STRAND 210..218
FT /evidence="ECO:0007829|PDB:5Y0M"
FT STRAND 221..225
FT /evidence="ECO:0007829|PDB:5Y0M"
FT STRAND 231..234
FT /evidence="ECO:0007829|PDB:5Y0M"
FT TURN 238..240
FT /evidence="ECO:0007829|PDB:5Y0M"
FT STRAND 241..243
FT /evidence="ECO:0007829|PDB:5XYQ"
FT HELIX 246..257
FT /evidence="ECO:0007829|PDB:5Y0M"
FT STRAND 268..276
FT /evidence="ECO:0007829|PDB:5Y0M"
FT HELIX 280..293
FT /evidence="ECO:0007829|PDB:5Y0M"
FT TURN 294..297
FT /evidence="ECO:0007829|PDB:5Y0M"
FT STRAND 298..300
FT /evidence="ECO:0007829|PDB:5Y0M"
FT STRAND 309..318
FT /evidence="ECO:0007829|PDB:5Y0M"
FT HELIX 335..354
FT /evidence="ECO:0007829|PDB:5Y0M"
SQ SEQUENCE 355 AA; 36903 MW; 5E60E3AACE5274F7 CRC64;
MNTTPVHALT DIDGGIAVDP APRLAGPPVF GGPGNDAFDL APVRSTGREM LRFDFPGVSI
GAAHYEEGPT GATVIHIPAG ARTAVDARGG AVGLSGGYDF NHAICLAGGA GYGLEAGAGV
SDALLERLEH RTGFAELQLV SSAVIYDFSA RSTAVYPDKA LGRAALEFAV PGEFPQGRAG
AGMSASAGKV DWDRTEITGQ GAAFRRLGDV RILAVVVPNP VGVIVDRAGT VVRGNYDAQT
GVRRHPVFDY QEAFAEQVPP VTEAGNTTIS AIVTNVRMSP VELNQFAKQV HSSMHRGIQP
FHTDMDGDTL FAVTTDEIDL PTTPGSSRGR LSVNATALGA IASEVMWDAV LEAGK
