2ZM9 - JenaLib

Asymmetric Unit (Jmol Viewer)

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, A61V/S112A/A124V/R187S/F264C/G291R/G338A/D370Y MUTANT (HYB-S4M94) WITH SUBSTRATE

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

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

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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 :   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

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, 8)

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

Biological Unit 1 (4, 16)

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

Biological Unit 2 (4, 8)

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

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	unknown	ARG A:205 , HOH A:897 , HOH A:898 , HOH A:926	BINDING SITE FOR RESIDUE SO4 A 506
02	AC2	unknown	ARG A:107 , ARG A:251 , ASP A:252 , HOH A:777 , HOH A:785	BINDING SITE FOR RESIDUE SO4 A 507
03	AC3	unknown	ALA A:112 , TYR A:170 , TYR A:215 , PHE A:317 , TRP A:331 , ILE A:345 , TYR A:370 , HIS A:375 , HOH A:808 , HOH A:934	BINDING SITE FOR RESIDUE ACA A 501
04	AC4	unknown	GLN A:27 , MET A:111 , ALA A:112 , TYR A:170 , TRP A:186 , HIS A:266 , GLY A:344 , ILE A:345	BINDING SITE FOR RESIDUE ACA A 502
05	AC5	unknown	TYR A:13 , PRO A:30 , TRP A:34 , HIS A:38 , ARG A:99 , GLY A:101 , HIS A:309 , HOH A:573 , HOH A:722 , HOH A:748 , HOH A:813 , HOH A:875	BINDING SITE FOR RESIDUE MES A 503
06	AC6	unknown	LEU A:70 , PRO A:71 , ASP A:72 , ARG A:76 , HOH A:757 , HOH A:837	BINDING SITE FOR RESIDUE MES A 504
07	AC7	unknown	ASP A:159 , GLN A:161 , GLY A:306 , GLY A:307 , SER A:308 , THR A:327 , ARG A:328 , HOH A:612 , HOH A:622	BINDING SITE FOR RESIDUE GOL A 505
08	AC8	SOFTWARE	ARG A:205 , HOH A:897 , HOH A:898 , HOH A:926	BINDING SITE FOR RESIDUE SO4 A 506
09	AC9	SOFTWARE	ARG A:107 , ARG A:251 , ASP A:252 , HOH A:777 , HOH A:785	BINDING SITE FOR RESIDUE SO4 A 507
10	AD1	SOFTWARE	ARG A:293	BINDING SITE FOR RESIDUE SO4 A 508
11	AD2	SOFTWARE	ALA A:112 , TYR A:170 , TYR A:215 , PHE A:317 , TRP A:331 , ILE A:345 , TYR A:370 , HIS A:375 , ACA A:502 , HOH A:808 , HOH A:934	BINDING SITE FOR RESIDUE ACA A 501
12	AD3	SOFTWARE	GLN A:27 , MET A:111 , ALA A:112 , TYR A:170 , TRP A:186 , HIS A:266 , GLY A:344 , ILE A:345 , ACA A:501	BINDING SITE FOR RESIDUE ACA A 502
13	AD4	SOFTWARE	TYR A:13 , PRO A:30 , TRP A:34 , HIS A:38 , ARG A:99 , GLY A:101 , HIS A:309 , HOH A:573 , HOH A:722 , HOH A:748 , HOH A:813 , HOH A:875	BINDING SITE FOR RESIDUE MES A 503
14	AD5	SOFTWARE	LEU A:70 , PRO A:71 , ASP A:72 , ARG A:76 , HOH A:757 , HOH A:837	BINDING SITE FOR RESIDUE MES A 504
15	AD6	SOFTWARE	ASP A:159 , GLN A:161 , GLY A:306 , GLY A:307 , SER A:308 , THR A:327 , ARG A:328 , HOH A:612 , HOH A:622	BINDING SITE FOR RESIDUE GOL A 505

(no "SS Bond" information available for 2ZM9)

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 2ZM9)

(no "PROSITE Motif" information available for 2ZM9)

(no "Exon" information available for 2ZM9)

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 d2zm9a_ A: 6-aminohexanoate-dimer hydrolase NylC                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------Beta-lactamase-2zm9A01 A:72-378                                                                                                                                                                                                                                                                                    -------------- Pfam domains
         Sec.struct. author ..........................hhhhhhhhhhhh..........----...eeehhhhh....hhhhhhhhh.eeeeeeee..eeeeeee.........ee..hhhhhhhhhhhhhhhhh.......hhhhhhhhhh.......hhhhhhh...............hhhhhhhhhh...........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
                 2zm9 A   5 STGQHPARYPGAAAGEPTLDSWQEPPHNRWAFAHLGEMVPSAAVSRRP----GHALVRLGAIAAQLPDLEQRLEQTYTDAFLVLRGTEVVAEYYRAGFAPDDRHLLMAVSKSLCGTVVGVLVDEGRIDPAQPVTEYVPELAGSVYDGPSVLQVLDMQISIDYNEDYVDPASEVQTHGRSAGWSTRRHGDPADTYEFLTTLRGDGSTGEFQYCSANTDVLAWIVERVTGLRYVEALSTYLWAKLDADRDATITVDTTGFGCAHGGVSCTARDLARVGRMMLDGGVAPRGRVVSEDWVRRVLAGGSHEAMTDKGFTNTFPDGSYTRQWWCTGNERANVSGIGIHGQNLWLDPLTDSVIVKLSSWPDPYTEHWHRLQNGILLDVSRALDAV 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 d2zm9a_ A: 6-aminohexanoate-dimer hydrolase NylC                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------Beta-lactamase-2zm9A01 A:72-378                                                                                                                                                                                                                                                                                    -------------- Pfam domains
         Sec.struct. author ..........................hhhhhhhhhhhh..........----...eeehhhhh....hhhhhhhhh.eeeeeeee..eeeeeee.........ee..hhhhhhhhhhhhhhhhh.......hhhhhhhhhh.......hhhhhhh...............hhhhhhhhhh...........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
                 2zm9 A   5 STGQHPARYPGAAAGEPTLDSWQEPPHNRWAFAHLGEMVPSAAVSRRP----GHALVRLGAIAAQLPDLEQRLEQTYTDAFLVLRGTEVVAEYYRAGFAPDDRHLLMAVSKSLCGTVVGVLVDEGRIDPAQPVTEYVPELAGSVYDGPSVLQVLDMQISIDYNEDYVDPASEVQTHGRSAGWSTRRHGDPADTYEFLTTLRGDGSTGEFQYCSANTDVLAWIVERVTGLRYVEALSTYLWAKLDADRDATITVDTTGFGCAHGGVSCTARDLARVGRMMLDGGVAPRGRVVSEDWVRRVLAGGSHEAMTDKGFTNTFPDGSYTRQWWCTGNERANVSGIGIHGQNLWLDPLTDSVIVKLSSWPDPYTEHWHRLQNGILLDVSRALDAV 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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	-	→ 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 '\|'

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)

d2zm9a_

(no "CATH Domain" information available for 2ZM9)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Beta-lactamase (210)

Family: Beta-lactamase (79)

Flavobacterium sp. (strain K172) (8)

Beta-lactamase-2zm9A01

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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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Glu A:20 - Pro A:21	[ RasMol ]
		Pro A:29 - Pro A:30	[ RasMol ]

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	2zm9
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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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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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