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Title :   CRYSTAL STRUCTURE OF MYCOBACTERIUM SMEGMATIS BRANCHED CHAIN AMINOTRANSFERASE IN COMPLEX WITH PYRIDOXAL-5'-PHOSPHATE AT 1.9 ANGSTROM.

Authors :   A. Castell, C. Mille, T. Unge

Date :   23 Sep 09 (Deposition) - 05 May 10 (Release) - 11 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Alpha/Beta, Aminotransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Castell, C. Mille, T. Unge
Structural Analysis Of Mycobacterial Branched-Chain Aminotransferase: Implications For Inhibitor Design.
Acta Crystallogr. , Sect. D V. 66 549 2010
PubMed-ID: 20445230 | Reference-DOI: 10.1107/S0907444910004877

Molecule 1 - BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.6.1.42
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PEXP5-CT/TOPO
	Expression System Strain	:	BL21-AI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ILVE, MSMEG_4276
	Organism Scientific	:	MYCOBACTERIUM SMEGMATIS
	Organism Taxid	:	1772

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:101 , ARG A:194 , LYS A:204 , TYR A:209 , GLU A:240 , GLY A:243 , ASN A:245 , LEU A:268 , GLY A:270 , ILE A:271 , THR A:272 , GLY A:313 , THR A:314 , GOL A:370 , HOH A:382 , HOH A:387 , HOH A:396 , HOH A:450	BINDING SITE FOR RESIDUE PLP A 369
2	AC2	SOFTWARE	ARG B:101 , ARG B:194 , LYS B:204 , TYR B:209 , GLU B:240 , GLY B:243 , ASN B:245 , LEU B:268 , GLY B:270 , ILE B:271 , THR B:272 , GLY B:313 , THR B:314 , GOL B:370 , HOH B:373 , HOH B:380 , HOH B:432	BINDING SITE FOR RESIDUE PLP B 369
3	AC3	SOFTWARE	ARG A:194 , ASN A:208 , TYR A:209 , SER A:212 , TRP A:229 , GLY A:242 , GLY A:243 , PLP A:369	BINDING SITE FOR RESIDUE GOL A 370
4	AC4	SOFTWARE	ARG B:194 , ASN B:208 , SER B:212 , TRP B:229 , GLY B:242 , PLP B:369 , HOH B:382	BINDING SITE FOR RESIDUE GOL B 370

(no "SS Bond" information available for 3JZ6)

(no "Cis Peptide Bond" information available for 3JZ6)

(no "SAP(SNP)/Variant" information available for 3JZ6)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRANSFER_CLASS_4	PS00770	Aminotransferases class-IV signature.	ILVE_MYCS2	240-273	2	A:240-273 B:240-273

(no "Exon" information available for 3JZ6)

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:363
 aligned with ILVE_MYCS2 | A0R066 from UniProtKB/Swiss-Prot  Length:368

    Alignment length:363
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365   
           ILVE_MYCS2     6 LEFTVSANTNPATDAVRESILANPGFGKYYTDHMVSIDYTVDEGWHNAQVIPYGPIQLDPSAIVLHYGQEIFEGLKAYRWADGSIVSFRPEANAARLQSSARRLAIPELPEEVFIESLRQLIAVDEKWVPPAGGEESLYLRPFVIATEPGLGVRPSNEYRYLLIASPAGAYFKGGIKPVSVWLSHEYVRASPGGTGAAKFGGNYAASLLAQAQAAEMGCDQVVWLDAIERRYVEEMGGMNLFFVFGSGGSARLVTPELSGSLLPGITRDSLLQLATDAGFAVEERKIDVDEWQKKAGAGEITEVFACGTAAVITPVSHVKHHDGEFTIADGQPGEITMALRDTLTGIQRGTFADTHGWMARLN 368
               SCOP domains d3jz6a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.......hhhhhhhhhhh.........eeeeeeee...eeeeeeeee...eee....hhhhhh.eee..eeeee.....eeeehhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.......eeeeeeeeee...........eeeeeeeeeee..........eeeee................hhhhhhhhhhhhhhhhhh...eeeee.......eeee..eeeeeee.hhhh.eeee.........hhhhhhhhhhhhhh..eeee...hhhhhhhhhhh..eeeeeeee...eeeeeeeeee..eeee......hhhhhhhhhhhhhhhh.........eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_4  PDB: A:240-27----------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jz6 A   6 LEFTVSANTNPATDAVRESILANPGFGKYYTDHMVSIDYTVDEGWHNAQVIPYGPIQLDPSAIVLHYGQEIFEGLKAYRWADGSIVSFRPEANAARLQSSARRLAIPELPEEVFIESLRQLIAVDEKWVPPAGGEESLYLRPFVIATEPGLGVRPSNEYRYLLIASPAGAYFKGGIKPVSVWLSHEYVRASPGGTGAAKFGGNYAASLLAQAQAAEMGCDQVVWLDAIERRYVEEMGGMNLFFVFGSGGSARLVTPELSGSLLPGITRDSLLQLATDAGFAVEERKIDVDEWQKKAGAGEITEVFACGTAAVITPVSHVKHHDGEFTIADGQPGEITMALRDTLTGIQRGTFADTHGWMARLN 368
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365

Chain B from PDB  Type:PROTEIN  Length:363
 aligned with ILVE_MYCS2 | A0R066 from UniProtKB/Swiss-Prot  Length:368

    Alignment length:363
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365   
           ILVE_MYCS2     6 LEFTVSANTNPATDAVRESILANPGFGKYYTDHMVSIDYTVDEGWHNAQVIPYGPIQLDPSAIVLHYGQEIFEGLKAYRWADGSIVSFRPEANAARLQSSARRLAIPELPEEVFIESLRQLIAVDEKWVPPAGGEESLYLRPFVIATEPGLGVRPSNEYRYLLIASPAGAYFKGGIKPVSVWLSHEYVRASPGGTGAAKFGGNYAASLLAQAQAAEMGCDQVVWLDAIERRYVEEMGGMNLFFVFGSGGSARLVTPELSGSLLPGITRDSLLQLATDAGFAVEERKIDVDEWQKKAGAGEITEVFACGTAAVITPVSHVKHHDGEFTIADGQPGEITMALRDTLTGIQRGTFADTHGWMARLN 368
               SCOP domains d3jz6b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------Aminotran_4-3jz6B01 B:93-349                                                                                                                                                                                                                                     ------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------Aminotran_4-3jz6B02 B:93-349                                                                                                                                                                                                                                     ------------------- Pfam domains (2)
         Sec.struct. author ...ee.......hhhhhhhhhhh.........eeeeeeee...eeeeeeeee...eee....hhhhhh.eee..eeeee.....eeeehhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.......eeeeeeeeee............eeeeeeeeee..........eeeee................hhhhhhhhhhhhhhhhhh...eeeee.......eeee..eeeeeee.hhhh.eeee.........hhhhhhhhhhhhhh..eeee...hhhhhhhhhhh..eeeeeeee...eeeeeeeeee..eeee......hhhhhhhhhhhhhhhh.........eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_4  PDB: B:240-27----------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jz6 B   6 LEFTVSANTNPATDAVRESILANPGFGKYYTDHMVSIDYTVDEGWHNAQVIPYGPIQLDPSAIVLHYGQEIFEGLKAYRWADGSIVSFRPEANAARLQSSARRLAIPELPEEVFIESLRQLIAVDEKWVPPAGGEESLYLRPFVIATEPGLGVRPSNEYRYLLIASPAGAYFKGGIKPVSVWLSHEYVRASPGGTGAAKFGGNYAASLLAQAQAAEMGCDQVVWLDAIERRYVEEMGGMNLFFVFGSGGSARLVTPELSGSLLPGITRDSLLQLATDAGFAVEERKIDVDEWQKKAGAGEITEVFACGTAAVITPVSHVKHHDGEFTIADGQPGEITMALRDTLTGIQRGTFADTHGWMARLN 368
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365

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: Multi-domain proteins (alpha and beta) (2421)

Fold: D-aminoacid aminotransferase-like PLP-dependent enzymes (46)

Superfamily: D-aminoacid aminotransferase-like PLP-dependent enzymes (46)

Family: automated matches (13)

Protein domain: automated matches (13)

Mycobacterium smegmatis [TaxId: 1772] (2)

1a	d3jz6a_	A:
1b	d3jz6b_	B:

(no "CATH Domain" information available for 3JZ6)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Aminotran_4] (8)

Family: Aminotran_4 (8)

Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (1)

1a	Aminotran_4-3jz6B01	B:93-349
1b	Aminotran_4-3jz6B02	B:93-349

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ILVE_MYCS2 | A0R066)

molecular function
	GO:0052656	L-isoleucine transaminase activity	Catalysis of the reaction: 2-oxoglutarate + L-isoleucine = (S)-3-methyl-2-oxopentanoic acid + L-glutamic acid.
	GO:0052654	L-leucine transaminase activity	Catalysis of the reaction: 2-oxoglutarate + L-leucine = 4-methyl-2-oxopentanoate + L-glutamatic acid.
	GO:0052655	L-valine transaminase activity	Catalysis of the reaction: 2-oxoglutarate + L-valine = 3-methyl-2-oxobutanoic acid + L-glutamatic acid.
	GO:0004084	branched-chain-amino-acid transaminase activity	Catalysis of the reaction: a branched-chain amino acid + 2-oxoglutarate = L-glutamate + a 2-oxocarboxylate derived from the branched-chain amino acid.
	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: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:0009082	branched-chain amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
	GO:0009081	branched-chain amino acid metabolic process	The chemical reactions and pathways involving amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0009097	isoleucine biosynthetic process	The chemical reactions and pathways resulting in the formation of isoleucine, (2R,3R)-2-amino-3-methylpentanoic acid.
	GO:0009098	leucine biosynthetic process	The chemical reactions and pathways resulting in the formation of leucine, 2-amino-4-methylpentanoic 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.
	GO:0018272	protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine	The modification of peptidyl-lysine to form N6-pyridoxal phosphate-L-lysine.
	GO:0009099	valine biosynthetic process	The chemical reactions and pathways resulting in the formation of valine, 2-amino-3-methylbutanoic acid.

Asymmetric/Biological Unit
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	3jz6
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	ILVE_MYCS2 \| A0R066	:	3dtf 3dtg

3dtf	APO-FORM OF M. SMEGMATIS BCAT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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