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(-) Description

Title :  STRUCTURE OF 6-AMINOHEXANOATE-DIMER HYDROLASE, A61V/A124V/R187S/F264C/G291R/G338A/D370Y MUTANT (HYB-S4M94)
 
Authors :  T. Ohki, N. Shibata, Y. Higuchi, Y. Kawashima, M. Takeo, D. Kato, S. Nego
Date :  10 Apr 08  (Deposition) - 21 Apr 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (1x)
Keywords :  Alpha-Beta, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Ohki, N. Shibata, Y. Higuchi, Y. Kawashima, M. Takeo, D. Kato, S. Negoro
Two Alternative Modes For Optimizing Nylon-6 Byproduct Hydrolytic Activity From A Carboxylesterase With A Beta-Lactamase Fold: X-Ray Crystallographic Analysis Of Directly Evolved 6-Aminohexanoate-Dimer Hydrolase.
Protein Sci. V. 18 1662 2009
PubMed-ID: 19521995  |  Reference-DOI: 10.1002/PRO.185

(-) 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: 239
    Other Details: CHIMERA OF NYLON OLIGOMERS-DEGRADING ENZYME EII (RESIDUES 1-21) AND NYLON OLIGOMERS-DEGRADING ENZYME EII' (RESIDUES 22-392)
    Strain: K172

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MES4Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3SO45Ligand/IonSULFATE ION
Biological Unit 1 (3, 26)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
2MES8Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3SO410Ligand/IonSULFATE ION
Biological Unit 2 (3, 13)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MES4Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3SO45Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:107 , ARG A:251 , ASP A:252 , HOH A:793 , HOH A:959BINDING SITE FOR RESIDUE SO4 A 509
02AC2SOFTWAREARG A:293 , HOH A:904BINDING SITE FOR RESIDUE SO4 A 510
03AC3SOFTWAREPRO A:173 , GLN A:178 , ARG A:182 , ARG A:190 , HOH A:710 , HOH A:979BINDING SITE FOR RESIDUE SO4 A 511
04AC4SOFTWAREARG A:205BINDING SITE FOR RESIDUE SO4 A 512
05AC5SOFTWAREARG A:274 , ARG A:278 , HOH A:594 , HOH A:815 , HOH A:923BINDING SITE FOR RESIDUE SO4 A 513
06AC6SOFTWARESER A:112 , TYR A:215 , GLY A:316 , PHE A:317 , TRP A:331 , ILE A:343 , GLY A:344 , ILE A:345 , TYR A:370 , HOH A:535 , HOH A:627 , HOH A:824 , HOH A:866 , HOH A:920BINDING SITE FOR RESIDUE MES A 501
07AC7SOFTWARETYR A:13 , PRO A:30 , TRP A:34 , HIS A:38 , ARG A:99 , GLY A:101 , HIS A:309 , HOH A:581 , HOH A:762 , HOH A:839BINDING SITE FOR RESIDUE MES A 502
08AC8SOFTWARELEU A:70 , PRO A:71 , ASP A:72 , ARG A:76 , HOH A:772 , HOH A:871BINDING SITE FOR RESIDUE MES A 503
09AC9SOFTWAREMET A:111 , SER A:112 , LYS A:115 , VAL A:177 , HIS A:180 , GLY A:181 , TRP A:186 , SER A:217 , HIS A:266 , GLY A:267 , ILE A:345 , GOL A:505 , HOH A:535BINDING SITE FOR RESIDUE MES A 504
10BC1SOFTWARETYR A:166 , GLU A:168 , TYR A:215 , CYS A:216 , SER A:217 , MES A:504BINDING SITE FOR RESIDUE GOL A 505
11BC2SOFTWAREPRO A:29 , ASP A:159 , GLN A:161 , GLY A:307 , SER A:308 , THR A:327 , ARG A:328 , HOH A:622 , HOH A:724BINDING SITE FOR RESIDUE GOL A 506
12BC3SOFTWAREASN A:335 , GLU A:336 , ARG A:337 , ARG A:387 , HOH A:599 , HOH A:663 , HOH A:870BINDING SITE FOR RESIDUE GOL A 507
13BC4SOFTWAREGLU A:96 , TYR A:98 , PRO A:104 , ASP A:105 , HOH A:567 , HOH A:598 , HOH A:891BINDING SITE FOR RESIDUE GOL A 508

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZM2)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:20 -Pro A:21
2Pro A:29 -Pro A:30

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZM2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZM2)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZM2)

(-) 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 d2zm2a_ A: 6-aminohexanoate-dimer hydrolase NylC                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------Beta-lactamase-2zm2A01 A:71-382                                                                                                                                                                                                                                                                                         ---------- Pfam domains
         Sec.struct. author .........................hhhhhhhhhhhhh..........----...eee..hhhhhh.hhhhhhhhh.eeeeeeee..eeeeeee.........ee..hhhhhhhhhhhhhhhhh.......hhhhhhhhhh.......hhhhhhh...............hhhhhhhhhh...........hhhhhhhh............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......ee.............eeehhhhhhhhhhhhhh..ee..ee..hhhhhhhhhhh.......hhhhhh.....eee..eee.......eeeee...eeeeeehhh.eeeeeee......hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zm2 A   5 STGQHPARYPGAAAGEPTLDSWQEPPHNRWAFAHLGEMVPSAAVSRRP----GHALVRLGAIAAQLPDLEQRLEQTYTDAFLVLRGTEVVAEYYRAGFAPDDRHLLMSVSKSLCGTVVGVLVDEGRIDPAQPVTEYVPELAGSVYDGPSVLQVLDMQISIDYNEDYVDPASEVQTHGRSAGWSTRRHGDPADTYEFLTTLRGDGSTGEFQYCSANTDVLAWIVERVTGLRYVEALSTYLWAKLDADRDATITVDTTGFGCAHGGVSCTARDLARVGRMMLDGGVAPRGRVVSEDWVRRVLAGGSHEAMTDKGFTNTFPDGSYTRQWWCTGNERANVSGIGIHGQNLWLDPLTDSVIVKLSSWPDPYTEHWHRLQNGILLDVSRALDAV 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 d2zm2a_ A: 6-aminohexanoate-dimer hydrolase NylC                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------Beta-lactamase-2zm2A01 A:71-382                                                                                                                                                                                                                                                                                         ---------- Pfam domains
         Sec.struct. author .........................hhhhhhhhhhhhh..........----...eee..hhhhhh.hhhhhhhhh.eeeeeeee..eeeeeee.........ee..hhhhhhhhhhhhhhhhh.......hhhhhhhhhh.......hhhhhhh...............hhhhhhhhhh...........hhhhhhhh............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......ee.............eeehhhhhhhhhhhhhh..ee..ee..hhhhhhhhhhh.......hhhhhh.....eee..eee.......eeeee...eeeeeehhh.eeeeeee......hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zm2 A   5 STGQHPARYPGAAAGEPTLDSWQEPPHNRWAFAHLGEMVPSAAVSRRP----GHALVRLGAIAAQLPDLEQRLEQTYTDAFLVLRGTEVVAEYYRAGFAPDDRHLLMSVSKSLCGTVVGVLVDEGRIDPAQPVTEYVPELAGSVYDGPSVLQVLDMQISIDYNEDYVDPASEVQTHGRSAGWSTRRHGDPADTYEFLTTLRGDGSTGEFQYCSANTDVLAWIVERVTGLRYVEALSTYLWAKLDADRDATITVDTTGFGCAHGGVSCTARDLARVGRMMLDGGVAPRGRVVSEDWVRRVLAGGSHEAMTDKGFTNTFPDGSYTRQWWCTGNERANVSGIGIHGQNLWLDPLTDSVIVKLSSWPDPYTEHWHRLQNGILLDVSRALDAV 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)
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  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 2ZM2)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Beta-lactamase (210)

(-) 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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  2zm2
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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 2e8i 2zly 2zm0 2zm7 2zm8 2zm9 2zma 3a65 3a66 3vwl 3vwm 3vwn 3vwp 3vwq 3vwr
        NYLC_FLASK | P07062: 1wyb 1wyc 2dcf 2e8i 2zly 2zm0 2zm7 2zm8 2zm9 2zma 3a65 3a66 3vwl 3vwm 3vwn 3vwp 3vwq 3vwr

(-) Related Entries Specified in the PDB File

1ywb 1ywc 2dcf 2zly 2zm0