3A2Q - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF 6-AMINOHEXANOATE CYCLIC DIMER HYDROLASE COMPLEXED WITH SUBSTRATE

Authors :   N. Shibata

Date :   26 May 09 (Deposition) - 03 Nov 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

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

Reference :   K. Yasuhira, N. Shibata, G. Mongami, Y. Uedo, Y. Atsumi, Y. Kawashima, A. Hibino, Y. Tanaka, Y. -H. Lee, D. Kato, M. Takeo, Y. Higuchi, S. Negor
X-Ray Crystallographic Analysis Of The 6-Aminohexanoate Cyclic Dimer Hydrolase: Catalytic Mechanism And Evolution O An Enzyme Responsible For Nylon-6 Byproduct Degradation
J. Biol. Chem. V. 285 1239 2010
PubMed-ID: 19889645 | Reference-DOI: 10.1074/JBC.M109.041285

Molecule 1 - 6-AMINOHEXANOATE-CYCLIC-DIMER HYDROLASE
	Chains	:	A
	EC Number	:	3.5.2.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PUC19
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	ARTHROBACTER SP.
	Organism Taxid	:	388925
	Other Details	:	THIS BACTERIUM HAD BEEN CALLED FLAVOBACTERIUM SP. BUT REASSIGNED TO ARTHROBACTER STRAIN
	Strain	:	KI72
	Synonym	:	NYLON OLIGOMERS-DEGRADING ENZYME EI

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	ACA	2	Ligand/Ion	6-AMINOHEXANOIC ACID
2	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	ACA	2	Ligand/Ion	6-AMINOHEXANOIC ACID
2	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	ACA	4	Ligand/Ion	6-AMINOHEXANOIC ACID
2	GOL	2	Ligand/Ion	GLYCEROL

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:124 , ASN A:125 , SER A:150 , ALA A:171 , ALA A:174 , ILE A:320 , ACA A:602	BINDING SITE FOR RESIDUE ACA A 601
2	AC2	SOFTWARE	GLY A:124 , ASN A:125 , SER A:150 , ALA A:171 , ALA A:172 , ALA A:174 , CYS A:316 , ACA A:601	BINDING SITE FOR RESIDUE ACA A 602
3	AC3	SOFTWARE	ASN A:266 , GLY A:269 , PHE A:271 , ALA A:272 , ILE A:440 , HOH A:539 , HOH A:566	BINDING SITE FOR RESIDUE GOL A 603

(no "SS Bond" information available for 3A2Q)

Asymmetric Unit

No.	Residues
1	Gly A:149	-	Ser A:150
2	Gly A:197	-	Pro A:198

(no "SAP(SNP)/Variant" information available for 3A2Q)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AMIDASES	PS00571	Amidases signature.	NYLA_FLASK	148-179	1	A:148-179

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AMIDASES	PS00571	Amidases signature.	NYLA_FLASK	148-179	1	A:148-179

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AMIDASES	PS00571	Amidases signature.	NYLA_FLASK	148-179	2	A:148-179

(no "Exon" information available for 3A2Q)

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:482
 aligned with NYLA_FLASK | P13398 from UniProtKB/Swiss-Prot  Length:493

    Alignment length:482
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483  
           NYLA_FLASK     4 VDLWQDATAQAELVRSGEISRTELLEATIAHVQAVNPEINAVIIPLFEKARRESELASGPFAGVPYLLKDLTVVSQGDINTSSIKGMKESGYRADHDAYFVQRMRAAGFVLLGKTNTPEMGNQVTTEPEAWGATRNPWNLGRSVGGSSGGSGAAVAAALSPVAHGNDAAGSVRIPASVCGVVGLKPTRGRISPGPLVTDSDNVAGAAHEGLFARSVRDIAALLDVVSGHRPGDTFCAPTASRPYAQGISENPGSLRVGVLTHNPVGDFALDPECAAAARGAAAALAALGHDVNDAYPEALGDRSFLKDYSTICDVAIAREIERNGELIGRPLTEDDVEWTSWEMVKRADQVTGRAFAACVDELRYYAGKVERWWEAGWDLLILPTVTRQTPEIGELMLAKGTDLEGRQSAFISGSLQMLAFTVPFNVSGQPAISLPIGMSSDGMPIGVQIVAAYGREDLLLQVAAQLEGALPWVARRPQLLN 485
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhh.......eeeee..............hhhhhhhh......hhhhhhhhhhh.eeeeee..hhhhh.........................hhhhhhhhhh....eeeeee....hhhhhhhhh.eeee............hhhhhhhh..eeeeee.hhhhhhhhhhhhh...............hhhhhh.......eeee...........hhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.......................hhhhhhhhhhhhh..hhhhhhh..eeeeeeee.....eeeeeeee...hhhhhhhhhhhhhhhh......hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------AMIDASES  PDB: A:148-179        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a2q A   4 VDLWQDATAQAELVRSGEISRTELLEATIAHVQAVNPEINAVIIPLFEKARRESELASGPFAGVPYLLKDLTVVSQGDINTSSIKGMKESGYRADHDAYFVQRMRAAGFVLLGKTNTPEMGNQVTTEPEAWGATRNPWNLGRSVGGSSGGSGAAVAAALSPVAHGNDAAGAVRIPASVCGVVGLKPTRGRISPGPLVTDSDNVAGAAHEGLFARSVRDIAALLDVVSGHRPGDTFCAPTASRPYAQGISENPGSLRVGVLTHNPVGDFALDPECAAAARGAAAALAALGHDVNDAYPEALGDRSFLKDYSTICDVAIAREIERNGELIGRPLTEDDVEWTSWEMVKRADQVTGRAFAACVDELRYYAGKVERWWEAGWDLLILPTVTRQTPEIGELMLAKGTDLEGRQSAFISGSLQMLAFTVPFNVSGQPAISLPIGMSSDGMPIGVQIVAAYGREDLLLQVAAQLEGALPWVARRPQLLN 485
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483

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 3A2Q)

(no "CATH Domain" information available for 3A2Q)

(no "Pfam Domain" information available for 3A2Q)

Asymmetric Unit(hide GO term definitions)

Chain A (NYLA_FLASK | P13398)

molecular function
	GO:0019874	6-aminohexanoate-cyclic-dimer hydrolase activity	Catalysis of the reaction: 1,8-diazacyclotetradecane-2,9-dione + H(2)O = N-(6-aminohexanoyl)-6-aminohexanoate.
	GO:0016884	carbon-nitrogen ligase activity, with glutamine as amido-N-donor	Catalysis of the transfer of the amide nitrogen of glutamine to a variety of substrates. GATases catalyze two separate reactions at two active sites, which are located either on a single polypeptide chain or on different subunits. In the glutaminase reaction, glutamine is hydrolyzed to glutamate and ammonia, which is added to an acceptor substrate in the synthase reaction.
	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
		Gly A:149 - Ser A:150	[ RasMol ]
		Gly A:197 - Pro A:198	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	3a2q
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	NYLA_FLASK \| P13398
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	3.5.2.12
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	NYLA_FLASK \| P13398	:	3a2p

3a2p	THE SAME PROTEIN WITHOUT SUBSTRATE

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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