2DCF - JenaLib

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Biological Unit 2 (Jmol Viewer)

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

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

Date :   06 Jan 06 (Deposition) - 09 Jan 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

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

Reference :   S. Negoro, T. Ohki, N. Shibata, K. Sasa, H. Hayashi, H. Nakano, K. Yasuhira, D. Kato, M. Takeo, Y. Higuchi
Nylon-Oligomer Degrading Enzyme/Substrate Complex: Catalyti Mechanism Of 6-Aminohexanoate-Dimer Hydrolase
J. Mol. Biol. V. 370 142 2007
PubMed-ID: 17512009 | Reference-DOI: 10.1016/J.JMB.2007.04.043

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
	Mutation	:	YES
	Organism Scientific	:	FLAVOBACTERIUM SP.
	Organism Taxid	:	239

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 9)

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

Biological Unit 1 (4, 9)

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

Biological Unit 2 (4, 18)

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

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:124 , ASP A:127 , GLU A:128 , LYS A:246 , ARG A:293 , VAL A:294	BINDING SITE FOR RESIDUE SO4 A 509
2	AC2	SOFTWARE	TRP A:34 , HIS A:38 , ARG A:99 , HOH A:666 , HOH A:729 , HOH A:826 , HOH A:899	BINDING SITE FOR RESIDUE SO4 A 510
3	AC3	SOFTWARE	ALA A:112 , TYR A:170 , TYR A:215 , ILE A:345 , ACA A:502	BINDING SITE FOR RESIDUE ACA A 501
4	AC4	SOFTWARE	MET A:111 , ALA A:112 , TYR A:170 , VAL A:177 , ASP A:181 , TRP A:186 , SER A:217 , PHE A:264 , ASN A:266 , GLY A:344 , ILE A:345 , ACA A:501 , HOH A:845 , HOH A:907	BINDING SITE FOR RESIDUE ACA A 502
5	AC5	SOFTWARE	LEU A:70 , PRO A:71 , ASP A:72 , ARG A:76 , HOH A:764 , HOH A:853	BINDING SITE FOR RESIDUE MES A 504
6	AC6	SOFTWARE	GLY A:316 , PHE A:317 , HIS A:375 , ASN A:379 , HOH A:542 , HOH A:908	BINDING SITE FOR RESIDUE GOL A 503
7	AC7	SOFTWARE	ASP A:159 , ARG A:302 , THR A:327 , ARG A:328 , HOH A:626 , HOH A:732	BINDING SITE FOR RESIDUE GOL A 505
8	AC8	SOFTWARE	GLN A:79 , GLY A:211 , GLU A:310 , ALA A:311 , TRP A:374 , HOH A:619 , HOH A:898 , HOH A:969	BINDING SITE FOR RESIDUE GOL A 507
9	AC9	SOFTWARE	ALA A:37 , ASP A:106 , ARG A:107 , ARG A:251 , HOH A:706 , HOH A:737 , HOH A:770	BINDING SITE FOR RESIDUE GOL A 508

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

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 2DCF)

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

(no "Exon" information available for 2DCF)

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 d2dcfa1 A:5-392 6-aminohexanoate-dimer hydrolase     NylC                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................hhhhhhhhhhhh..........----...eee..hhhhhh.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
                 2dcf A   5 STGQHPARYPGAAAGEPTLDSWQEPPHNRWAFAHLGEMVPSAAVSRRP----GHALARLGAIAAQLPDLEQRLEQTYTDAFLVLRGTEVVAEYYRAGFAPDDRHLLMAVSKSLCGTVVGALVDEGRIDPAQPVTEYVPELAGSVYDGPSVLQVLDMQISIDYNEDYVDPASEVQTHDRSAGWRTRRHGDPADTYEFLTTLRGDGSTGEFQYCSANTDVLAWIVERVTGLRYVEALSTYLWAKLDADRDATITVDTTGFGFANGGVSCTARDLARVGRMMLDGGVAPGGRVVSEDWVRRVLAGGSHEAMTDKGFTNTFPDGSYTRQWWCTGNERGNVSGIGIHGQNLWLDPLTDSVIVKLSSWPDPDTEHWHRLQNGILLDVSRALDAV 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 d2dcfa1 A:5-392 6-aminohexanoate-dimer hydrolase     NylC                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................hhhhhhhhhhhh..........----...eee..hhhhhh.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
                 2dcf A   5 STGQHPARYPGAAAGEPTLDSWQEPPHNRWAFAHLGEMVPSAAVSRRP----GHALARLGAIAAQLPDLEQRLEQTYTDAFLVLRGTEVVAEYYRAGFAPDDRHLLMAVSKSLCGTVVGALVDEGRIDPAQPVTEYVPELAGSVYDGPSVLQVLDMQISIDYNEDYVDPASEVQTHDRSAGWRTRRHGDPADTYEFLTTLRGDGSTGEFQYCSANTDVLAWIVERVTGLRYVEALSTYLWAKLDADRDATITVDTTGFGFANGGVSCTARDLARVGRMMLDGGVAPGGRVVSEDWVRRVLAGGSHEAMTDKGFTNTFPDGSYTRQWWCTGNERGNVSGIGIHGQNLWLDPLTDSVIVKLSSWPDPDTEHWHRLQNGILLDVSRALDAV 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 Q59710_9FLAO | Q59710 from UniProtKB/TrEMBL  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        
         Q59710_9FLAO     5 TTGSHPARYPDAAAGEPTLDSWQEPPHNRWAFAHLGEMVPSAAVSRRPVNAPGHALARLGAIAAQLPDLEQRLEQTYTDAFLVLRGTEVVAEYYRAGFAPDDRHLLMSVSKSLCGTVVGALVDEGRIDPAQPVTEYVPELAGSVYDGPSVLQVLDMQISIDYNEDYVDPASEVQTHGRSAGWRTRRHGDPADTYEFLTTLRGDGSTGEFQYCSANTDVLAWIVERVTGLRYVEALSTYLWAKLDADRDATITVDTTGFGFAHGGVSCTARDLARVGRMMLDGGVAPGGRVVSEDWVRRVLAGGSHEAMTDKGFTNTFPDGSYTRQWWCTGNERGNVSGIGIHGQNLWLDPLTDSVIVKLSSWPDPDTEHWHRLQNGILLDVSRALDAV 392
               SCOP domains d2dcfa1 A:5-392 6-aminohexanoate-dimer hydrolase     NylC                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................hhhhhhhhhhhh..........----...eee..hhhhhh.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
                 2dcf A   5 STGQHPARYPGAAAGEPTLDSWQEPPHNRWAFAHLGEMVPSAAVSRRP----GHALARLGAIAAQLPDLEQRLEQTYTDAFLVLRGTEVVAEYYRAGFAPDDRHLLMAVSKSLCGTVVGALVDEGRIDPAQPVTEYVPELAGSVYDGPSVLQVLDMQISIDYNEDYVDPASEVQTHDRSAGWRTRRHGDPADTYEFLTTLRGDGSTGEFQYCSANTDVLAWIVERVTGLRYVEALSTYLWAKLDADRDATITVDTTGFGFANGGVSCTARDLARVGRMMLDGGVAPGGRVVSEDWVRRVLAGGSHEAMTDKGFTNTFPDGSYTRQWWCTGNERGNVSGIGIHGQNLWLDPLTDSVIVKLSSWPDPDTEHWHRLQNGILLDVSRALDAV 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 '\|'

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)

d2dcfa1

A:5-392

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

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

Asymmetric Unit(hide GO term definitions)

Chain A (Q59710_9FLAO | Q59710)

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.

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
		ACA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		AC9	[ RasMol ]	+environment [ RasMol ]

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

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	2dcf
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	NYLB_FLASK \| P07061
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	NYLC_FLASK \| P07062
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		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	Q59710_9FLAO \| Q59710
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	3.5.1.46
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		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	Q59710_9FLAO \| Q59710
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (9, 9)

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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SCOP Domains (1, 1)

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Related Entries

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Related Entries Specified in the PDB File