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Title :   CRYSTAL STRUCTURE OF 7-KETO-8-AMINOPELARGONIC ACID BOUND 7,8-DIAMINOPELARGONIC ACID SYNTHASE IN BACILLUS SUBTILIS

Authors :   S. Dey, J. C. Sacchettini

Date :   16 Jul 08 (Deposition) - 23 Jun 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A,B

Keywords :   Aminotransferase, Biotin Biosynthesis, Pyridoxal Phosphate, S- Adenosyl-L-Methionine, 7-Keto, 8-Amino Pelargonic Acid, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Dey, J. M. Lane, R. E. Lee, E. J. Rubin, J. C. Sacchettini
Structural Characterization Of The Mycobacterium Tuberculosis Biotin Biosynthesis Enzymes 7, 8-Diaminopelargonic Acid Synthase And Dethiobiotin Synthetase .
Biochemistry V. 49 6746 2010
PubMed-ID: 20565114 | Reference-DOI: 10.1021/BI902097J

Molecule 1 - ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.6.1.62
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BIOA
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Strain	:	168
	Synonym	:	7,8-DIAMINO-PELARGONIC ACID AMINOTRANSFERASE, DAPA AMINOTRANSFERASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	CSX	2	Mod. Amino Acid	S-OXY CYSTEINE
2	KAP	2	Ligand/Ion	7-KETO-8-AMINOPELARGONIC ACID
3	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:112 , GLY A:113 , ALA A:114 , TYR A:146 , HIS A:147 , GLY A:148 , GLU A:217 , ASP A:251 , ALA A:254 , LYS A:280 , HIS B:316 , SER B:317	BINDING SITE FOR RESIDUE PLP A 450
2	AC2	SOFTWARE	TYR A:146 , ASP A:149 , LYS A:280 , ARG A:410 , LEU B:82 , GLY B:315	BINDING SITE FOR RESIDUE KAP A 451
3	AC3	SOFTWARE	HIS A:316 , SER A:317 , SER B:112 , GLY B:113 , ALA B:114 , TYR B:146 , HIS B:147 , GLY B:148 , GLU B:217 , ASP B:251 , ALA B:254 , LYS B:280	BINDING SITE FOR RESIDUE PLP B 450
4	AC4	SOFTWARE	GLY A:315 , PHE B:17 , TYR B:146 , ASP B:149 , LYS B:280 , ARG B:410	BINDING SITE FOR RESIDUE KAP B 451

(no "SS Bond" information available for 3DU4)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:187	-	Asp A:188

(no "SAP(SNP)/Variant" information available for 3DU4)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRANSFER_CLASS_3	PS00600	Aminotransferases class-III pyridoxal-phosphate attachment site.	BIOK_BACSU	248-285	2	A:248-285 B:248-285

(no "Exon" information available for 3DU4)

Asymmetric/Biological 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:448
 aligned with BIOK_BACSU | P53555 from UniProtKB/Swiss-Prot  Length:448

    Alignment length:448
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440        
           BIOK_BACSU     1 MTHDLIEKSKKHLWLPFTQMKDYDENPLIIESGTGIKVKDINGKEYYDGFSSVWLNVHGHRKKELDDAIKKQLGKIAHSTLLGMTNVPATQLAETLIDISPKKLTRVFYSDSGAEAMEIALKMAFQYWKNIGKPEKQKFIAMKNGYHGDTIGAVSVGSIELFHHVYGPLMFESYKAPIPYVYRSESGDPDECRDQCLRELAQLLEEHHEEIAALSIESMVQGASGMIVMPEGYLAGVRELCTTYDVLMIVDEVATGFGRTGKMFACEHENVQPDLMAAGKGITGGYLPIAVTFATEDIYKAFYDDYENLKTFFHGHSYTGNQLGCAVALENLALFESENIVEQVAEKSKKLHFLLQDLHALPHVGDIRQLGFMCGAELVRSKETKEPYPADRRIGYKVSLKMRELGMLTRPLGDVIAFLPPLASTAEELSEMVAIMKQAIHEVTSLED 448
               SCOP domains d3du4a_ A: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase, BioA                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.....hhhhhhhh..eeeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhh..........eehhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhhhh......eeeee.......hhhhhhh.........hhhhh..eeee...........hhhhhhhhhhhhhhhhhhhhh..eeeeeee..ee.....ee...hhhhhhhhhhhhh..eeeee............hhhhhhh....eeeehhhhhh.....eeeeeehhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee..eeeeee..........hhhhhhhhhhhhhhhhh.ee..ee..eeee......hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_3  PDB: A:248-285   ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3du4 A   1 MTHDLIEKSKKHLWLPFTQMKDYDENPLIIESGTGIKVKDINGKEYYDGFSSVWLNVHGHRKKELDDAIKKQLGKIAHSTLLGMTNVPATQLAETLIDISPKKLTRVFYSDSGAEAMEIALKMAFQYWKNIGKPEKQKFIAMKNGYHGDTIGAVSVGSIELFHHVYGPLMFESYKAPIPYVYRSESGDPDECRDQcLRELAQLLEEHHEEIAALSIESMVQGASGMIVMPEGYLAGVRELCTTYDVLMIVDEVATGFGRTGKMFACEHENVQPDLMAAGKGITGGYLPIAVTFATEDIYKAFYDDYENLKTFFHGHSYTGNQLGCAVALENLALFESENIVEQVAEKSKKLHFLLQDLHALPHVGDIRQLGFMCGAELVRSKETKEPYPADRRIGYKVSLKMRELGMLTRPLGDVIAFLPPLASTAEELSEMVAIMKQAIHEVTSLED 448
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190     | 200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440        
                                                                                                                                                                                                                             196-CSX

Chain B from PDB  Type:PROTEIN  Length:448
 aligned with BIOK_BACSU | P53555 from UniProtKB/Swiss-Prot  Length:448

    Alignment length:448
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440        
           BIOK_BACSU     1 MTHDLIEKSKKHLWLPFTQMKDYDENPLIIESGTGIKVKDINGKEYYDGFSSVWLNVHGHRKKELDDAIKKQLGKIAHSTLLGMTNVPATQLAETLIDISPKKLTRVFYSDSGAEAMEIALKMAFQYWKNIGKPEKQKFIAMKNGYHGDTIGAVSVGSIELFHHVYGPLMFESYKAPIPYVYRSESGDPDECRDQCLRELAQLLEEHHEEIAALSIESMVQGASGMIVMPEGYLAGVRELCTTYDVLMIVDEVATGFGRTGKMFACEHENVQPDLMAAGKGITGGYLPIAVTFATEDIYKAFYDDYENLKTFFHGHSYTGNQLGCAVALENLALFESENIVEQVAEKSKKLHFLLQDLHALPHVGDIRQLGFMCGAELVRSKETKEPYPADRRIGYKVSLKMRELGMLTRPLGDVIAFLPPLASTAEELSEMVAIMKQAIHEVTSLED 448
               SCOP domains d3du4b_ B: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase, BioA                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.....hhhhhhhh..eeeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhh..........eehhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhhh......eeeee.......hhhhhh...hhhhhhhhhhhh..eeee...........hhhhhhhhhhhhhhhhhhhhh..eeeeeee..ee.....ee...hhhhhhhhhhhhh..eeeee............hhhhh......eeeehhhhhh.....eeeeehhhhhhh...hhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeee..........hhhhhhhhhhhhhhhhh.ee..ee..eeee......hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_3  PDB: B:248-285   ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3du4 B   1 MTHDLIEKSKKHLWLPFTQMKDYDENPLIIESGTGIKVKDINGKEYYDGFSSVWLNVHGHRKKELDDAIKKQLGKIAHSTLLGMTNVPATQLAETLIDISPKKLTRVFYSDSGAEAMEIALKMAFQYWKNIGKPEKQKFIAMKNGYHGDTIGAVSVGSIELFHHVYGPLMFESYKAPIPYVYRSESGDPDECRDQcLRELAQLLEEHHEEIAALSIESMVQGASGMIVMPEGYLAGVRELCTTYDVLMIVDEVATGFGRTGKMFACEHENVQPDLMAAGKGITGGYLPIAVTFATEDIYKAFYDDYENLKTFFHGHSYTGNQLGCAVALENLALFESENIVEQVAEKSKKLHFLLQDLHALPHVGDIRQLGFMCGAELVRSKETKEPYPADRRIGYKVSLKMRELGMLTRPLGDVIAFLPPLASTAEELSEMVAIMKQAIHEVTSLED 448
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190     | 200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440        
                                                                                                                                                                                                                             196-CSX

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase, BioA (13)

Bacillus subtilis [TaxId: 1423] (2)

1a	d3du4a_	A:
1b	d3du4b_	B:

(no "CATH Domain" information available for 3DU4)

(no "Pfam Domain" information available for 3DU4)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (BIOK_BACSU | P53555)

molecular function
	GO:0004015	adenosylmethionine-8-amino-7-oxononanoate transaminase activity	Catalysis of the reaction: 8-amino-7-oxononanoate + S-adenosyl-L-methionine(1+) = 7,8-diaminononanoate + S-adenosyl-4-methylthio-2-oxobutanoate.
	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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0008483	transaminase activity	Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
	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: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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:187 - Asp A:188	[ RasMol ]

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	3du4
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	BIOK_BACSU \| P53555
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	2.6.1.62
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UniProtKB/Swiss-Prot
	BIOK_BACSU \| P53555	:	3dod 3drd

3dod	PLP-BOUND 7,8-DIAMINOPELARGONIC ACID SYNTHASE
3drd	7,8-DIAMINO PELARGONIC ACID SYNTHASE APOENZYME

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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SCOP Domains (1, 2)

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Gene Ontology (8, 8)

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