3A66 - JenaLib

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Title :   CRYSTAL STRUCTURE OF 6-AMINOHEXANOATE-DIMER HYDROLASE S112A/G181D/H266N/D370Y MUTANT WITH SUBSTRATE

Authors :   Y. Kawashima, N. Shibata, Y. Higuchi, M. Takeo, S. Negoro

Date :   21 Aug 09 (Deposition) - 01 Sep 10 (Release) - 01 Sep 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Hydrolase, Nylon Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kawashima, K. Yasuhira, N. Shibata, Y. Matsuura, Y. Tanaka, M. Taniguchi, Y. Miyoshi, M. Takeo, D. Kato, Y. Higuchi, S. Negoro
Enzymatic Synthesis Of Nylon-6 Units In Organic Sol Contained Low-Water: Structural Requirement Of 6-Aminohexanoate-Dimer Hydrolase For Efficient Amid Synthesis
To Be Published
PubMed: search

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 Strain	:	KP3998
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NYLB, NYLB'
	Mutation	:	YES
	Organism Scientific	:	FLAVOBACTERIUM
	Organism Taxid	:	261
	Other Details	:	CHIMERA OF NYLON OLIGOMERS-DEGRADING ENZYME EII (RESIDUES 1-21) AND NYLON OLIGOMERS-DEGRADING ENZYME EII' (RESIDUES 22-392)
	Other Details - Source	:	STRAIN OF THE SOURCE ORGANISM IS DESCRIBED KI72 IN THE FIRST REFERENCE OF THE DATABASE UNIPROTKB/SWISS-PROT P07061 (NYLB_FLASK) AND P07062 (NYLC_FLASK).
	Strain	:	K172
	Synonym	:	NYLON OLIGOMERS-DEGRADING ENZYME EII, NYLON OLIGOMERS- DEGRADING ENZYME EII'

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 12)

No.	Name	Count	Type	Full Name
1	ACA	1	Ligand/Ion	6-AMINOHEXANOIC ACID
2	GOL	7	Ligand/Ion	GLYCEROL
3	MES	2	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4	NA	2	Ligand/Ion	SODIUM ION

Biological Unit 1 (3, 20)

No.	Name	Count	Type	Full Name
1	ACA	2	Ligand/Ion	6-AMINOHEXANOIC ACID
2	GOL	14	Ligand/Ion	GLYCEROL
3	MES	4	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:123 , ASP A:127 , SER A:296 , TRP A:299 , HOH A:593	BINDING SITE FOR RESIDUE NA A 500
02	AC2	SOFTWARE	HOH A:397 , HOH A:549 , GOL A:606	BINDING SITE FOR RESIDUE NA A 501
03	AC3	SOFTWARE	PRO A:29 , ASP A:159 , GLN A:161 , GLY A:307 , SER A:308 , THR A:327 , ARG A:328 , HOH A:451 , GOL A:605 , HOH A:637	BINDING SITE FOR RESIDUE GOL A 602
04	AC4	SOFTWARE	ARG A:107 , ASP A:250 , ARG A:251 , ASP A:252 , HOH A:395 , HOH A:523	BINDING SITE FOR RESIDUE GOL A 603
05	AC5	SOFTWARE	ALA A:37 , ASP A:106 , ARG A:107 , ARG A:251 , HOH A:523 , HOH A:600 , HOH A:696	BINDING SITE FOR RESIDUE GOL A 604
06	AC6	SOFTWARE	PRO A:29 , LEU A:155 , PRO A:367 , ASP A:368 , HOH A:454 , GOL A:602 , HOH A:617 , HOH A:624 , HOH A:665	BINDING SITE FOR RESIDUE GOL A 605
07	AC7	SOFTWARE	ALA A:112 , TYR A:215 , ILE A:343 , GLY A:344 , ILE A:345 , HOH A:399 , NA A:501 , HOH A:505 , ACA A:601 , GOL A:607	BINDING SITE FOR RESIDUE GOL A 606
08	AC8	SOFTWARE	ASP A:314 , GLY A:316 , PHE A:317 , TRP A:331 , TYR A:370 , HIS A:375 , HOH A:397 , HOH A:533 , GOL A:606	BINDING SITE FOR RESIDUE GOL A 607
09	AC9	SOFTWARE	VAL A:177 , PRO A:369 , HOH A:400 , ACA A:601	BINDING SITE FOR RESIDUE GOL A 608
10	BC1	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:435 , HOH A:644 , HOH A:700 , HOH A:742	BINDING SITE FOR RESIDUE MES A 609
11	BC2	SOFTWARE	GLN A:69 , LEU A:70 , PRO A:71 , ASP A:72 , ARG A:76 , HOH A:799	BINDING SITE FOR RESIDUE MES A 610
12	BC3	SOFTWARE	MET A:111 , ALA A:112 , ASP A:181 , TRP A:186 , TYR A:215 , ASN A:266 , GLY A:344 , ILE A:345 , HOH A:400 , HOH A:589 , HOH A:596 , GOL A:606 , GOL A:608	BINDING SITE FOR RESIDUE ACA A 601

(no "SS Bond" information available for 3A66)

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 3A66)

(no "PROSITE Motif" information available for 3A66)

(no "Exon" information available for 3A66)

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:378
 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................hhhhhhhhhhhhh..........----...eee..hhhhhh.hhhhhhhhh.eeeeeeee..eeeeeee.........ee..hhhhhhhhhhhhhhhhh.......hhhhhhhhhh.......hhhhhhh.........------hhhhhhhhhhh..........hhhhhhhh.............hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......ee.............eeehhhhhhhhhhhhhh..ee..ee..hhhhhhhhhhh.......hhhhhh.....eee..eee.......eeeee...eeeeeehhh.eeeeeee......hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a66 A   5 STGQHPARYPGAAAGEPTLDSWQEPPHNRWAFAHLGEMVPSAAVSRRP----GHALARLGAIAAQLPDLEQRLEQTYTDAFLVLRGTEVVAEYYRAGFAPDDRHLLMAVSKSLCGTVVGALVDEGRIDPAQPVTEYVPELAGSVYDGPSVLQVLDMQISIDYNE------SEVQTHDRSAGWRTRRHGDPADTYEFLTTLRGDGSTGEFQYCSANTDVLAWIVERVTGLRYVEALSTYLWAKLDADRDATITVDTTGFGFANGGVSCTARDLARVGRMMLDGGVAPGGRVVSEDWVRRVLAGGSHEAMTDKGFTNTFPDGSYTRQWWCTGNERGNVSGIGIHGQNLWLDPLTDSVIVKLSSWPDPYTEHWHRLQNGILLDVSRALDAV 392
                                    14        24        34        44       | -  |     64        74        84        94       104       114       124       134       144       154       164   |     -|      184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384        
                                                                          52   57                                                                                                            168    175

Chain A from PDB  Type:PROTEIN  Length:378
 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................hhhhhhhhhhhhh..........----...eee..hhhhhh.hhhhhhhhh.eeeeeeee..eeeeeee.........ee..hhhhhhhhhhhhhhhhh.......hhhhhhhhhh.......hhhhhhh.........------hhhhhhhhhhh..........hhhhhhhh.............hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......ee.............eeehhhhhhhhhhhhhh..ee..ee..hhhhhhhhhhh.......hhhhhh.....eee..eee.......eeeee...eeeeeehhh.eeeeeee......hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a66 A   5 STGQHPARYPGAAAGEPTLDSWQEPPHNRWAFAHLGEMVPSAAVSRRP----GHALARLGAIAAQLPDLEQRLEQTYTDAFLVLRGTEVVAEYYRAGFAPDDRHLLMAVSKSLCGTVVGALVDEGRIDPAQPVTEYVPELAGSVYDGPSVLQVLDMQISIDYNE------SEVQTHDRSAGWRTRRHGDPADTYEFLTTLRGDGSTGEFQYCSANTDVLAWIVERVTGLRYVEALSTYLWAKLDADRDATITVDTTGFGFANGGVSCTARDLARVGRMMLDGGVAPGGRVVSEDWVRRVLAGGSHEAMTDKGFTNTFPDGSYTRQWWCTGNERGNVSGIGIHGQNLWLDPLTDSVIVKLSSWPDPYTEHWHRLQNGILLDVSRALDAV 392
                                    14        24        34        44       | -  |     64        74        84        94       104       114       124       134       144       154       164   |     -|      184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384        
                                                                          52   57                                                                                                            168    175

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 '\|'

(no "SCOP Domain" information available for 3A66)

(no "CATH Domain" information available for 3A66)

(no "Pfam Domain" information available for 3A66)

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 Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	3a66
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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, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

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Gene Ontology (3, 6)

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