1DJ9 - JenaLib

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Title :   CRYSTAL STRUCTURE OF 8-AMINO-7-OXONANOATE SYNTHASE (OR 7-KETO-8AMINIPELARGONATE OR KAPA SYNTHASE) COMPLEXED WITH PLP AND THE PRODUCT 8(S)-AMINO-7-OXONANONOATE (OR KAPA). THE ENZYME OF BIOTIN BIOSYNTHETIC PATHWAY.

Authors :   S. P. Webster, D. Alexeev, D. J. Campopiano, R. M. Watt, M. Alexeeva, L. S R. L. Baxter

Date :   02 Dec 99 (Deposition) - 06 Dec 00 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   8-Amino-7-Oxononanoate Synthase, Biotin, Pyridoxal-5'-Phosphate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. P. Webster, D. Alexeev, D. J. Campopiano, R. M. Watt, M. Alexeeva, L. Sawyer, R. L. Baxter
Mechanism Of 8-Amino-7-Oxononanoate Synthase: Spectroscopic Kinetic, And Crystallographic Studies.
Biochemistry V. 39 516 2000
PubMed-ID: 10642176 | Reference-DOI: 10.1021/BI991620J
(for further references see the PDB file header)

Molecule 1 - 8-AMINO-7-OXONONANOATE SYNTHASE
	Chains	:	A
	EC Number	:	2.3.1.47
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	7-KAP SYNTHETASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	KAM	1	Ligand/Ion	N-[7-KETO-8-AMINOPELARGONIC ACID]-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	KAM	1	Ligand/Ion	N-[7-KETO-8-AMINOPELARGONIC ACID]-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	KAM	2	Ligand/Ion	N-[7-KETO-8-AMINOPELARGONIC ACID]-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:147 , ARG A:148 , ARG A:149 , HOH A:1203 , HOH A:1245	BINDING SITE FOR RESIDUE SO4 A 401
2	AC2	SOFTWARE	ARG A:22 , ARG A:23 , ARG A:101 , LEU A:256 , HOH A:1238	BINDING SITE FOR RESIDUE SO4 A 402
3	AC3	SOFTWARE	SER A:179 , KAM A:400 , HOH A:1069 , HOH A:1092	BINDING SITE FOR RESIDUE MG A 500
4	AC4	SOFTWARE	ARG A:21 , SER A:76 , SER A:107 , GLY A:108 , PHE A:109 , HIS A:133 , GLU A:175 , SER A:179 , ASP A:204 , ALA A:206 , HIS A:207 , THR A:233 , LYS A:236 , ILE A:263 , TYR A:264 , SER A:265 , THR A:266 , ILE A:348 , THR A:352 , MG A:500 , HOH A:1004 , HOH A:1013 , HOH A:1092 , HOH A:1161 , HOH A:1237	BINDING SITE FOR RESIDUE KAM A 400

(no "SS Bond" information available for 1DJ9)

Asymmetric Unit

No.	Residues
1	Gln A:333	-	Leu A:334
2	Pro A:350	-	Pro A:351

(no "SAP(SNP)/Variant" information available for 1DJ9)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRANSFER_CLASS_2	PS00599	Aminotransferases class-II pyridoxal-phosphate attachment site.	BIOF_ECOLI	233-242	1	A:233-242

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRANSFER_CLASS_2	PS00599	Aminotransferases class-II pyridoxal-phosphate attachment site.	BIOF_ECOLI	233-242	1	A:233-242

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRANSFER_CLASS_2	PS00599	Aminotransferases class-II pyridoxal-phosphate attachment site.	BIOF_ECOLI	233-242	2	A:233-242

(no "Exon" information available for 1DJ9)

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
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Chain A from PDB  Type:PROTEIN  Length:383
 aligned with BIOF_ECOLI | P12998 from UniProtKB/Swiss-Prot  Length:384

    Alignment length:383
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381   
           BIOF_ECOLI     2 SWQEKINAALDARRAADALRRRYPVAQGAGRWLVADDRQYLNFSSNDYLGLSHHPQIIRAWQQGAEQFGIGSGGSGHVSGYSVVHQALEEELAEWLGYSRALLFISGFAANQAVIAAMMAKEDRIAADRLSHASLLEAASLSPSQLRRFAHNDVTHLARLLASPCPGQQMVVTEGVFSMDGDSAPLAEIQQVTQQHNGWLMVDDAHGTGVIGEQGRGSCWLQKVKPELLVVTFGKGFGVSGAAVLCSSTVADYLLQFARHLIYSTSMPPAQAQALRASLAVIRSDEGDARREKLAALITRFRAGVQDLPFTLADSCSAIQPLIVGDNSRALQLAEKLRQQGCWVTAIRPPTVPAGTARLRLTLTAAHEMQDIDRLLEVLHGNG 384
               SCOP domains d1dj9a_ A: PLP-dependent acyl-CoA synthase (8-amino-7-oxonanoate synthase, AONS)                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains -----------------------1dj9A01 A:25-56,A:285-383       1dj9A02 A:57-284 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                1dj9A01 A:25-56,A:285-383 Aspartate Aminotransferase, domain 1                                     - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh...............eeee..eeeee.......hhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhh..eeeee...hhhhhhhhhhh.....eeeeee..........hhhhhhhhhhhh..eeeee........hhhhhhhhhhhh....eeeee.........eeeeehhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........ee..hhhhh...hhhhhhhhhh.ee.................ee.....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFE---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dj9 A   2 SWQEKINAALDARGAADALRRRYPVAQGAGRWLVADDRQYLNFSSNDYLGLSHHPQIIRAWQQGAEQFGIGSGGSGHVSGYSVVHQALEEELAEWLGYSRALLFISGFAANQAVIAAMMAKEDRIAADRLSHASLLEAASLSPSQLRRFAHNDVTHLARLLASPCPGQQMVVTEGVFSMDGDSAPLAEIQQVTQQHNGWLMVDDAHGTGVIGEQGRGSCWLQKVKPELLVVTFGKGFGVSGAAVLCSSTVADYLLQFARHLIYSTSMPPAQAQALRASLAVIRSDEGDARREKLAALITRFRAGVQDLPFTLADSCSAIQPLIVGDNSRALQLAEKLRQQGCWVTGIRPPTVPAGIARLRLTLTAAHEMQDIDRLLEVLHGNG 384
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381

Legend:		→ Mismatch	(orange background)
	-	→ 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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

)

Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: PLP-dependent transferase-like (627)

Superfamily: PLP-dependent transferases (625)

Family: GABA-aminotransferase-like (167)

Protein domain: PLP-dependent acyl-CoA synthase (8-amino-7-oxonanoate synthase, AONS) (3)

Escherichia coli [TaxId: 562] (3)

d1dj9a_

(no "Pfam Domain" information available for 1DJ9)

Asymmetric Unit(hide GO term definitions)

Chain A (BIOF_ECOLI | P12998)

molecular function
	GO:0008710	8-amino-7-oxononanoate synthase activity	Catalysis of the reaction: L-alanine + H(+) + pimelyl-CoA = 8-amino-7-oxononanoate + CO(2) + CoA.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0030170	pyridoxal phosphate binding	Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0009058	biosynthetic process	The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
	GO:0009102	biotin biosynthetic process	The chemical reactions and pathways resulting in the formation of biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

Asymmetric Unit
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	Cis Peptide Bonds
		Gln A:333 - Leu A:334	[ RasMol ]
		Pro A:350 - Pro A:351	[ RasMol ]

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	1dj9
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	2.3.1.47
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	BIOF_ECOLI \| P12998	:	1bs0 1dje 2g6w

1bs0	PLP-FREE APO-FORM OF THE ENZYME

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