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(-) Description

Title :  STRUCTURE OF 6-AMINOHEXANOATE-DIMER HYDROLASE, D1 MUTANT
 
Authors :  N. Shibata, Y. Higuchi, S. Negoro
Date :  20 Jan 07  (Deposition) - 15 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Alpha-Beta, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kawashima, T. Ohki, N. Shibata, Y. Higuchi, Y. Wakitani, Y. Matsuura, Y. Nakata, M. Takeo, D. Kato, S. Negoro
Molecular Design Of A Nylon-6 Byproduct-Degrading Enzyme From A Carboxylesterase With A B-Lactamase Fold.
Febs J. 2009
PubMed: search  |  Reference-DOI: 10.1111/J.1742-4658.2009.06978.X

(-) Compounds

Molecule 1 - 6-AMINOHEXANOATE-DIMER HYDROLASE
    Chains: A
    EC Number: 3.5.1.46
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKP1500
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NYLB, NYLB'
    Mutation: YES
    Organism Scientific: FLAVOBACTERIUM SP.
    Organism Taxid: 261
    Strain: K172
    Synonym: CHIMERA OF NYLON OLIGOMERS-DEGRADING ENZYME EII AND NYLON OLIGOMERS-DEGRADING ENZYME EII'

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3SO42Ligand/IonSULFATE ION
Biological Unit 2 (3, 18)
No.NameCountTypeFull Name
1GOL10Ligand/IonGLYCEROL
2MES4Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3SO44Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:107 , ARG A:251 , ASP A:252 , HOH A:793BINDING SITE FOR RESIDUE SO4 A 508
2AC2SOFTWAREARG A:293 , HOH A:850BINDING SITE FOR RESIDUE SO4 A 509
3AC3SOFTWARELEU A:70 , PRO A:71 , ASP A:72 , ARG A:76 , HOH A:773 , HOH A:879BINDING SITE FOR RESIDUE MES A 506
4AC4SOFTWARETYR A:13 , PRO A:30 , TRP A:34 , ARG A:99 , GLY A:101 , HIS A:309 , GLU A:310 , HOH A:578 , HOH A:734 , HOH A:762BINDING SITE FOR RESIDUE MES A 507
5AC5SOFTWARETYR A:166 , GLU A:168 , VAL A:177 , TYR A:215 , CYS A:216 , SER A:217 , GOL A:502 , HOH A:934BINDING SITE FOR RESIDUE GOL A 501
6AC6SOFTWAREMET A:111 , SER A:112 , ASP A:181 , HIS A:266 , GLY A:267 , ILE A:345 , GOL A:501 , HOH A:531 , HOH A:863 , HOH A:934BINDING SITE FOR RESIDUE GOL A 502
7AC7SOFTWAREASP A:314 , GLY A:316 , PHE A:317 , TRP A:331 , ASP A:370 , HOH A:566 , HOH A:749 , HOH A:873 , HOH A:874BINDING SITE FOR RESIDUE GOL A 503
8AC8SOFTWAREGLN A:79 , GLY A:211 , GLU A:212 , GLU A:310 , ALA A:311 , TRP A:374 , HOH A:621 , HOH A:846 , HOH A:961BINDING SITE FOR RESIDUE GOL A 504
9AC9SOFTWAREASN A:335 , GLU A:336 , HOH A:537 , HOH A:601 , HOH A:877 , HOH A:895BINDING SITE FOR RESIDUE GOL A 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2E8I)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Glu A:20 -Pro A:21
2Pro A:29 -Pro A:30
3Gly A:64 -Ala A:65

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2E8I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2E8I)

(-) Exons   (0, 0)

(no "Exon" information available for 2E8I)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:384
 aligned with NYLB_FLASK | P07061 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:388
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384        
           NYLB_FLASK     5 STGQHPARYPGAAAGEPTLDSWQEAPHNRWAFARLGELLPTAAVSRRDPATPAEPVVRLDALATRLPDLEQRLEETCTDAFLVLRGSEVLAEYYRAGFAPDDRHLLMSVSKSLCGTVVGALIDEGRIDPAQPVTEYVPELAGSVYDGPSVLQVLDMQISIDYNEDYVDPASEVQTHDRSAGWRTRRDGDPADTYEFLTTLRGDGGTGEFQYCSANTDVLAWIVERVTGLRYVEALSTYLWAKLDADRDATITVDQTGFGFANGGVSCTARDLARVGRMMLDGGVAPGGRVVSQGWVESVLAGGSREAMTDEGFTSAFPEGSYTRQWWCTGNERGNVSGIGIHGQNLWLDPRTDSVIVKLSSWPDPDTRHWHGLQSGILLDVSRALDAV 392
               SCOP domains d2e8ia_ A: 6-aminohexanoate-dimer hydrolase NylC                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................hhhhhhhhhhhhh..........----...eee.........hhhhhhhhh.eeeeeeee..eeeeeee.........ee..hhhhhhhhhhhhhhhhh.......hhhhhhhhhh.......hhhhhhh...............hhhhhhhhhh...........hhhhhhhh............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......ee.............eeehhhhhhhhhhhhhh..ee..ee..hhhhhhhhhhh.hhhhh.hhhhhh.....eee..eee.......eeeee...eeeeeehhh.eeeeeee......hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e8i A   5 STGQHPARYPGAAAGEPTLDSWQEPPHNRWAFAHLGEMVPSAAVSRRP----GHALARLGAIAAQLPDLEQRLEQTYTDAFLVLRGTEVVAEYYRAGFAPDDRHLLMSVSKSLCGTVVGALVDEGRIDPAQPVTEYVPELAGSVYDGPSVLQVLDMQISIDYNEDYVDPASEVQTHDRSAGWRTRRHGDPADTYEFLTTLRGDGSTGEFQYCSANTDVLAWIVERVTGLRYVEALSTYLWAKLDADRDATITVDTTGFGFAHGGVSCTARDLARVGRMMLDGGVAPGGRVVSEDWVRRVLAGGSHEAMTDKGFTNTFPDGSYTRQWWCTGNERGNVSGIGIHGQNLWLDPLTDSVIVKLSSWPDPDTEHWHRLQNGILLDVSRALDAV 392
                                    14        24        34        44       | -  |     64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384        
                                                                          52   57                                                                                                                                                                                                                                                                                                                                               


Chain A from PDB  Type:PROTEIN  Length:384
 aligned with NYLC_FLASK | P07062 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:388
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384        
           NYLC_FLASK     5 TTGSHPARYPSAAAGEPTLDSWQEPPHNRWAFAHLGEMVPSAAVSRRPVNAPGHALARLGAIAAQLPDLEQRLEQTYTDAFLVLRGTEVVAEYYRAGFAPDDRHLLMSVSKSLCGTVVGALVDEGRIDPAQPVTEYVPELAGSVYDGPSVLQVLDMQISIDYNEDYVDPASEVQTHGRSAGWRTRATGDPADTYEFLTTLRGDGSTGEFQYCSANTDVLAWIVERVTGLRYVEALSTYLWAKLDADRDATITVDTTGFGFAHGGVSCTARDLARVGRMMLDGGVAPGGRVVSEDWVRRVLAGGSHEAMTDKGFTNTFPDGSYTRQWWCTGNERGNVSGIGIHGQNLWLDPLTDSVIVKLSSWPDPDTEHWHRLQNGILLDVSRALDAV 392
               SCOP domains d2e8ia_ A: 6-aminohexanoate-dimer hydrolase NylC                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................hhhhhhhhhhhhh..........----...eee.........hhhhhhhhh.eeeeeeee..eeeeeee.........ee..hhhhhhhhhhhhhhhhh.......hhhhhhhhhh.......hhhhhhh...............hhhhhhhhhh...........hhhhhhhh............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......ee.............eeehhhhhhhhhhhhhh..ee..ee..hhhhhhhhhhh.hhhhh.hhhhhh.....eee..eee.......eeeee...eeeeeehhh.eeeeeee......hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e8i A   5 STGQHPARYPGAAAGEPTLDSWQEPPHNRWAFAHLGEMVPSAAVSRRP----GHALARLGAIAAQLPDLEQRLEQTYTDAFLVLRGTEVVAEYYRAGFAPDDRHLLMSVSKSLCGTVVGALVDEGRIDPAQPVTEYVPELAGSVYDGPSVLQVLDMQISIDYNEDYVDPASEVQTHDRSAGWRTRRHGDPADTYEFLTTLRGDGSTGEFQYCSANTDVLAWIVERVTGLRYVEALSTYLWAKLDADRDATITVDTTGFGFAHGGVSCTARDLARVGRMMLDGGVAPGGRVVSEDWVRRVLAGGSHEAMTDKGFTNTFPDGSYTRQWWCTGNERGNVSGIGIHGQNLWLDPLTDSVIVKLSSWPDPDTEHWHRLQNGILLDVSRALDAV 392
                                    14        24        34        44       | -  |     64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384        
                                                                          52   57
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2E8I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2E8I)

(-) Gene Ontology  (3, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (NYLB_FLASK | P07061)
molecular function
    GO:0019875    6-aminohexanoate-dimer hydrolase activity    Catalysis of the reaction: N-(6-aminohexanoyl)-6-aminohexanoate + H2O = 2 6-aminohexanoate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
    GO:0019876    nylon catabolic process    The chemical reactions and pathways resulting in the breakdown of nylon, a polymer where the main polymer chain comprises recurring amide groups; these compounds are generally formed from combinations of diamines, diacids and amino acids.

Chain A   (NYLC_FLASK | P07062)
molecular function
    GO:0019875    6-aminohexanoate-dimer hydrolase activity    Catalysis of the reaction: N-(6-aminohexanoyl)-6-aminohexanoate + H2O = 2 6-aminohexanoate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
    GO:0019876    nylon catabolic process    The chemical reactions and pathways resulting in the breakdown of nylon, a polymer where the main polymer chain comprises recurring amide groups; these compounds are generally formed from combinations of diamines, diacids and amino acids.

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  NYLB_FLASK | P07061
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  NYLC_FLASK | P07062
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  3.5.1.46
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NYLB_FLASK | P07061: 1wyc 2dcf 2zly 2zm0 2zm2 2zm7 2zm8 2zm9 2zma 3a65 3a66 3vwl 3vwm 3vwn 3vwp 3vwq 3vwr
        NYLC_FLASK | P07062: 1wyb 1wyc 2dcf 2zly 2zm0 2zm2 2zm7 2zm8 2zm9 2zma 3a65 3a66 3vwl 3vwm 3vwn 3vwp 3vwq 3vwr

(-) Related Entries Specified in the PDB File

1wyb 1wyc 2dcf