2ZM7 - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF 6-AMINOHEXANOATE-DIMER HYDROLASE, S112A/G181D MUTANT COMPLEXED WITH 6-AMINOHEXANOATE-DIMER

Authors :   T. Ohki, N. Shibata, Y. Higuchi, Y. Kawashima, M. Takeo, D. Kato, S. Nego

Date :   14 Apr 08 (Deposition) - 07 Apr 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)
Biol. Unit 2: A  (1x)

Keywords :   Alpha-Beta, Hydrolase, Nylon Degradation (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 Beta-Lactamase Fold
Febs J. V. 276 2547 2009
PubMed-ID: 19476493 | Reference-DOI: 10.1111/J.1742-4658.2009.06978.X

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
	Synonym	:	NYLON OLIGOMERS-DEGRADING ENZYME EII, NYLON OLIGOMERS- DEGRADING ENZYME EII'

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 11)

No.	Name	Count	Type	Full Name
1	ACA	2	Ligand/Ion	6-AMINOHEXANOIC ACID
2	GOL	3	Ligand/Ion	GLYCEROL
3	MES	2	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 22)

No.	Name	Count	Type	Full Name
1	ACA	4	Ligand/Ion	6-AMINOHEXANOIC ACID
2	GOL	6	Ligand/Ion	GLYCEROL
3	MES	4	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 2 (4, 11)

No.	Name	Count	Type	Full Name
1	ACA	2	Ligand/Ion	6-AMINOHEXANOIC ACID
2	GOL	3	Ligand/Ion	GLYCEROL
3	MES	2	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (22, 22)

No.	Name	Evidence	Residues	Description
01	AC1	unknown	ASP A:127 , GLU A:128 , LYS A:246 , ARG A:293	BINDING SITE FOR RESIDUE SO4 A 508
02	AC2	unknown	ARG A:205 , HOH A:904 , HOH A:909	BINDING SITE FOR RESIDUE SO4 A 509
03	AC3	unknown	ARG A:107 , ARG A:251 , ASP A:252 , HOH A:780 , HOH A:812	BINDING SITE FOR RESIDUE SO4 A 510
04	AC4	unknown	ARG A:274 , ARG A:278 , HOH A:798 , HOH A:941	BINDING SITE FOR RESIDUE SO4 A 511
05	AC5	unknown	ALA A:112 , TYR A:170 , TYR A:215 , PHE A:317 , TRP A:331 , ILE A:343 , ILE A:345 , HOH A:811 , HOH A:875 , HOH A:894	BINDING SITE FOR RESIDUE ACA A 501
06	AC6	unknown	MET A:111 , ALA A:112 , TYR A:170 , ASP A:181 , TRP A:186 , HIS A:266 , GLY A:344 , ILE A:345 , HOH A:846	BINDING SITE FOR RESIDUE ACA A 502
07	AC7	unknown	TYR A:13 , PRO A:30 , TRP A:34 , HIS A:38 , ARG A:99 , GLY A:101 , HIS A:309 , GLU A:310 , HOH A:576 , HOH A:727 , HOH A:752 , HOH A:886	BINDING SITE FOR RESIDUE MES A 503
08	AC8	unknown	LEU A:70 , PRO A:71 , ASP A:72 , ARG A:76 , HOH A:761	BINDING SITE FOR RESIDUE MES A 504
09	AC9	unknown	PRO A:29 , ASP A:159 , ARG A:302 , THR A:327 , ARG A:328 , HOH A:616 , HOH A:627 , HOH A:730	BINDING SITE FOR RESIDUE GOL A 505
10	AD1	SOFTWARE	ASP A:127 , GLU A:128 , LYS A:246 , ARG A:293 , VAL A:294	BINDING SITE FOR RESIDUE SO4 A 508
11	AD2	SOFTWARE	ARG A:205 , HOH A:904 , HOH A:909	BINDING SITE FOR RESIDUE SO4 A 509
12	AD3	SOFTWARE	ARG A:107 , ARG A:251 , ASP A:252 , HOH A:780 , HOH A:812	BINDING SITE FOR RESIDUE SO4 A 510
13	AD4	SOFTWARE	ARG A:274 , ARG A:278 , HOH A:798 , HOH A:941	BINDING SITE FOR RESIDUE SO4 A 511
14	AD5	SOFTWARE	ALA A:112 , TYR A:170 , TYR A:215 , PHE A:317 , TRP A:331 , ILE A:343 , ILE A:345 , ACA A:502 , HOH A:811 , HOH A:875 , HOH A:894	BINDING SITE FOR RESIDUE ACA A 501
15	AD6	SOFTWARE	MET A:111 , ALA A:112 , TYR A:170 , ASP A:181 , TRP A:186 , HIS A:266 , GLY A:344 , ILE A:345 , ACA A:501 , HOH A:846	BINDING SITE FOR RESIDUE ACA A 502
16	AD7	SOFTWARE	TYR A:13 , PRO A:30 , TRP A:34 , HIS A:38 , ARG A:99 , GLY A:101 , HIS A:309 , GLU A:310 , HOH A:576 , HOH A:727 , HOH A:752 , HOH A:886	BINDING SITE FOR RESIDUE MES A 503
17	AD8	SOFTWARE	LEU A:70 , PRO A:71 , ASP A:72 , ARG A:76 , HOH A:761	BINDING SITE FOR RESIDUE MES A 504
18	AD9	SOFTWARE	PRO A:29 , ASP A:159 , ARG A:302 , THR A:327 , ARG A:328 , HOH A:616 , HOH A:627 , HOH A:730	BINDING SITE FOR RESIDUE GOL A 505
19	AE1	SOFTWARE	GLN A:79 , GLY A:211 , GLU A:310 , ALA A:311 , TRP A:374 , HOH A:545 , HOH A:620 , HOH A:885	BINDING SITE FOR RESIDUE GOL A 506
20	AE2	SOFTWARE	ALA A:37 , ASP A:106 , ARG A:107 , ARG A:251 , HOH A:662 , HOH A:735 , HOH A:767	BINDING SITE FOR RESIDUE GOL A 507
21	BC1	unknown	GLN A:79 , GLY A:211 , GLU A:310 , ALA A:311 , TRP A:374 , HOH A:545 , HOH A:620 , HOH A:885	BINDING SITE FOR RESIDUE GOL A 506
22	BC2	unknown	ALA A:37 , ASP A:106 , ARG A:107 , ARG A:251 , HOH A:662 , HOH A:735 , HOH A:767	BINDING SITE FOR RESIDUE GOL A 507

(no "SS Bond" information available for 2ZM7)

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 2ZM7)

(no "PROSITE Motif" information available for 2ZM7)

(no "Exon" information available for 2ZM7)

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 d2zm7a_ A: 6-aminohexanoate-dimer hydrolase NylC                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------Beta-lactamase-2zm7A01 A:72-378                                                                                                                                                                                                                                                                                    -------------- Pfam domains
         Sec.struct. author .........................hhhhhhhhhhhhh..........----...eeehhhhh....hhhhhhhhh.eeeeeeee..eeeeeee.........ee..hhhhhhhhhhhhhhhhh.......hhhhhhhhhh.......hhhhhhh...............hhhhhhhhhhh..........hhhhhhhh............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......ee.............eeehhhhhhhhhhhhhh..ee..ee..hhhhhhhhhhh.......hhhhhhhh...eee..eee.......eeeee...eeeeeehhh.eeeeeee......hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zm7 A   5 STGQHPARYPGAAAGEPTLDSWQEPPHNRWAFAHLGEMVPSAAVSRRP----GHALARLGAIAAQLPDLEQRLEQTYTDAFLVLRGTEVVAEYYRAGFAPDDRHLLMAVSKSLCGTVVGALVDEGRIDPAQPVTEYVPELAGSVYDGPSVLQVLDMQISIDYNEDYVDPASEVQTHDRSAGWRTRRHGDPADTYEFLTTLRGDGSTGEFQYCSANTDVLAWIVERVTGLRYVEALSTYLWAKLDADRDATITVDTTGFGFAHGGVSCTARDLARVGRMMLDGGVAPGGRVVSEDWVRRVLAGGSHEAMTDKGFTNTFPDGSYTRQWWCTGNERGNVSGIGIHGQNLWLDPLTDSVIVKLSSWPDPDTEHWHRLQNGILLDVSRALDAV 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 d2zm7a_ A: 6-aminohexanoate-dimer hydrolase NylC                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------Beta-lactamase-2zm7A01 A:72-378                                                                                                                                                                                                                                                                                    -------------- Pfam domains
         Sec.struct. author .........................hhhhhhhhhhhhh..........----...eeehhhhh....hhhhhhhhh.eeeeeeee..eeeeeee.........ee..hhhhhhhhhhhhhhhhh.......hhhhhhhhhh.......hhhhhhh...............hhhhhhhhhhh..........hhhhhhhh............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......ee.............eeehhhhhhhhhhhhhh..ee..ee..hhhhhhhhhhh.......hhhhhhhh...eee..eee.......eeeee...eeeeeehhh.eeeeeee......hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zm7 A   5 STGQHPARYPGAAAGEPTLDSWQEPPHNRWAFAHLGEMVPSAAVSRRP----GHALARLGAIAAQLPDLEQRLEQTYTDAFLVLRGTEVVAEYYRAGFAPDDRHLLMAVSKSLCGTVVGALVDEGRIDPAQPVTEYVPELAGSVYDGPSVLQVLDMQISIDYNEDYVDPASEVQTHDRSAGWRTRRHGDPADTYEFLTTLRGDGSTGEFQYCSANTDVLAWIVERVTGLRYVEALSTYLWAKLDADRDATITVDTTGFGFAHGGVSCTARDLARVGRMMLDGGVAPGGRVVSEDWVRRVLAGGSHEAMTDKGFTNTFPDGSYTRQWWCTGNERGNVSGIGIHGQNLWLDPLTDSVIVKLSSWPDPDTEHWHRLQNGILLDVSRALDAV 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

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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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: beta-lactamase/transpeptidase-like (515)

Superfamily: beta-lactamase/transpeptidase-like (515)

Family: beta-Lactamase/D-ala carboxypeptidase (411)

Protein domain: 6-aminohexanoate-dimer hydrolase NylC (11)

Flavobacterium sp. [TaxId: 239] (11)

d2zm7a_

(no "CATH Domain" information available for 2ZM7)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Beta-lactamase (210)

Family: Beta-lactamase (79)

Flavobacterium sp. (strain K172) (8)

Beta-lactamase-2zm7A01

A:72-378

Asymmetric Unit(hide GO term definitions)

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.

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.

Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:20 - Pro A:21	[ RasMol ]
		Pro A:29 - Pro A:30	[ RasMol ]

Biological Units
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	2zm7
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 11)

Sites (22, 22)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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