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Title :   COMPLEX STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE AND 4-AMINO-4,5-DIHYDRO-THIOPHENECARBOXYLIC ACID (ADTA)

Authors :   B. W. Lepore, D. Liu, Y. Peng, M. Fu, C. Yasuda, J. M. Manning, R. B. Silver D. Ringe

Date :   10 Feb 10 (Deposition) - 16 Mar 10 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Plp Aminotransferase, Mechanism-Based Inhibitor, Stereo-Specificity, R-Adta, Aminotransferase, Pyridoxal Phosphate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. W. Lepore, D. Liu, Y. Peng, M. Fu, C. Yasuda, J. M. Manning, R. B. Silverman, D. Ringe
Chiral Discrimination Among Aminotransferases: Inactivation By 4-Amino-4, 5-Dihydrothiophenecarboxylic Acid.
Biochemistry V. 49 3138 2010
PubMed-ID: 20192272 | Reference-DOI: 10.1021/BI902052X

Molecule 1 - D-ALANINE AMINOTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.6.1.21
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PEMBL 18
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DAT
	Organism Scientific	:	BACILLUS SP.
	Organism Taxid	:	72579
	Strain	:	YM-1
	Synonym	:	D-ASPARTATE AMINOTRANSFERASE, D-AMINO ACID AMINOTRANSFERASE, D-AMINO ACID TRANSAMINASE, DAAT

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	PSZ	2	Ligand/Ion	4-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]THIOPHENE-2-CARBOXYLIC ACID

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:50 , ARG A:138 , LYS A:145 , GLU A:177 , SER A:180 , SER A:181 , ASN A:182 , LEU A:201 , GLY A:203 , ILE A:204 , THR A:205 , SER A:240 , THR A:241 , THR A:242 , HOH A:293 , HOH A:305 , HOH A:312 , HOH A:372	BINDING SITE FOR RESIDUE PSZ A 595
2	AC2	SOFTWARE	ARG B:50 , ARG B:138 , LYS B:145 , GLU B:177 , SER B:180 , SER B:181 , ASN B:182 , LEU B:201 , GLY B:203 , ILE B:204 , THR B:205 , SER B:240 , THR B:241 , THR B:242 , HOH B:297 , HOH B:304 , HOH B:316 , HOH B:325 , HOH B:349 , ACY B:424	BINDING SITE FOR RESIDUE PSZ B 585
3	AC3	SOFTWARE	ARG A:98 , HIS A:100 , TYR B:31 , VAL B:33 , LYS B:145 , PSZ B:585	BINDING SITE FOR RESIDUE ACY B 424

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

Asymmetric/Biological Unit

No.	Residues
1	Pro A:279	-	Leu A:280

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

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.	DAAA_BACYM	178-207	2	A:177-206 B:177-206

(no "Exon" information available for 3LQS)

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:280
 aligned with DAAA_BACYM | P19938 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:280
                                    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
           DAAA_BACYM     2 GYTLWNDQIVKDEEVKIDKEDRGYQFGDGVYEVVKVYNGEMFTVNEHIDRLYASAEKIRITIPYTKDKFHQLLHELVEKNELNTGHIYFQVTRGTSPRAHQFPENTVKPVIIGYTKENPRPLENLEKGVKATFVEDIRWLRCDIKSLNLLGAVLAKQEAHEKGCYEAILHRNNTVTEGSSSNVFGIKDGILYTHPANNMILKGITRDVVIACANEINMPVKEIPFTTHEALKMDELFVTSTTSEITPVIEIDGKLIRDGKVGEWTRKLQKQFETKIPKPL 281
               SCOP domains d3lqsa_ A: D-aminoacid aminotransferase                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeee.hhh.....hhhhhh..eeeeeeeee..ee.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...eeeeeeee.................eeeeeeee...hhhhhhhheeeeeee.............hhhhhhhhhhhhhh...eeeeee..eeeee...eeeeee..eeee.........hhhhhhhhhhhhhh...ee....hhhhhh...eeeeee...eeeeeeee..ee......hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_4           -------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lqs A   1 GYTLWNDQIVKDEEVKIDKEDRGYQFGDGVYEVVKVYNGEMFTVNEHIDRLYASAEKIRITIPYTKDKFHQLLHELVEKNELNTGHIYFQVTRGTSPRAHQFPENTVKPVIIGYTKENPRPLENLEKGVKATFVEDIRWLRCDIKSLNLLGAVLAKQEAHEKGCYEAILHRNNTVTEGSSSNVFGIKDGILYTHPANNMILKGITRDVVIACANEINMPVKEIPFTTHEALKMDELFVTSTTSEITPVIEIDGKLIRDGKVGEWTRKLQKQFETKIPKPL 280
                                    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

Chain B from PDB  Type:PROTEIN  Length:280
 aligned with DAAA_BACYM | P19938 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:280
                                    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
           DAAA_BACYM     2 GYTLWNDQIVKDEEVKIDKEDRGYQFGDGVYEVVKVYNGEMFTVNEHIDRLYASAEKIRITIPYTKDKFHQLLHELVEKNELNTGHIYFQVTRGTSPRAHQFPENTVKPVIIGYTKENPRPLENLEKGVKATFVEDIRWLRCDIKSLNLLGAVLAKQEAHEKGCYEAILHRNNTVTEGSSSNVFGIKDGILYTHPANNMILKGITRDVVIACANEINMPVKEIPFTTHEALKMDELFVTSTTSEITPVIEIDGKLIRDGKVGEWTRKLQKQFETKIPKPL 281
               SCOP domains d3lqsb_ B: D-aminoacid aminotransferase                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------Aminotran_4-3lqsB01 B:42-272                                                                                                                                                                                                           -------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------Aminotran_4-3lqsB02 B:42-272                                                                                                                                                                                                           -------- Pfam domains (2)
         Sec.struct. author .eeee..eeee.hhh.....hhhhhhh.eeeeeeeee..ee.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh....eeeeeeee.................eeeeeeee...hhhhhhhheeeeeee.............hhhhhhhhhhhhhh...eeeeee..eeeee...eeeeee..eeee.........hhhhhhhhhhhhhh...ee....hhhhhh...eeeeee...eeeeeeee..ee......hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_4           -------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lqs B   1 GYTLWNDQIVKDEEVKIDKEDRGYQFGDGVYEVVKVYNGEMFTVNEHIDRLYASAEKIRITIPYTKDKFHQLLHELVEKNELNTGHIYFQVTRGTSPRAHQFPENTVKPVIIGYTKENPRPLENLEKGVKATFVEDIRWLRCDIKSLNLLGAVLAKQEAHEKGCYEAILHRNNTVTEGSSSNVFGIKDGILYTHPANNMILKGITRDVVIACANEINMPVKEIPFTTHEALKMDELFVTSTTSEITPVIEIDGKLIRDGKVGEWTRKLQKQFETKIPKPL 280
                                    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

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 "CATH Domain" information available for 3LQS)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Aminotran_4 (8)

Bacillus sp. (strain YM-1) (1)

1a	Aminotran_4-3lqsB01	B:42-272
1b	Aminotran_4-3lqsB02	B:42-272

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (DAAA_BACYM | P19938)

molecular function
	GO:0047810	D-alanine:2-oxoglutarate aminotransferase activity	Catalysis of the reaction: D-alanine + 2-oxoglutarate = pyruvate + D-glutamate.
	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:0046437	D-amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of D-amino acids, the D-enantiomers of amino acids.
	GO:0019478	D-amino acid catabolic process	The chemical reactions and pathways resulting in the breakdown of D-amino acids, the D-enantiomers of amino acids.
	GO:0046416	D-amino acid metabolic process	The chemical reactions and pathways involving D-amino acids, the D-enantiomers of amino acids.
	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/Biological Unit
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	Cis Peptide Bonds
		Pro A:279 - Leu A:280	[ RasMol ]

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	DAAA_BACYM \| P19938	:	1a0g 1daa 1g2w 2daa 2dab 3daa 4daa 5daa

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