2QBT - JenaLib

Title :   STRUCTURAL STUDIES REVEAL THE INACTIVATION OF E. COLI L-ASPARTATE AMINOTRANSFERASE BY (S)-4,5-AMINO-DIHYDRO-2-THIOPHENECARBOXYLIC ACID (SADTA) VIA TWO MECHANISMS (AT PH 8.0)

Authors :   D. Liu, E. Pozharski, B. Lepore, M. Fu, R. B. Silverman, G. A. Petsko, D. R

Date :   18 Jun 07 (Deposition) - 04 Sep 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Mechanism-Based Inactivator, Ph Dependence, Aspartate Aminotransferase, Sadta, Plp, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Liu, E. Pozharski, B. W. Lepore, M. Fu, R. B. Silverman, G. A. Petsko, D. Ringe
Inactivation Of Escherichia Coli L-Aspartate Aminotransferase By (S)-4-Amino-4, 5-Dihydro-2-Thiophenecarboxylic Acid Reveals "A Tale Of Two Mechanisms".
Biochemistry V. 46 10517 2007
PubMed-ID: 17713924 | Reference-DOI: 10.1021/BI700663N

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 14)

Sites (13, 13)

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:134 , ASN A:138 , GLU A:143 , VAL A:144 , ARG A:145 , GOL A:806 , HOH A:1121	BINDING SITE FOR RESIDUE SO4 A 501
02	AC2	SOFTWARE	PRO A:72 , ARG A:76 , HOH A:894	BINDING SITE FOR RESIDUE SO4 A 502
03	AC3	SOFTWARE	THR A:312 , ARG A:315 , GLN A:316 , GOL A:804 , HOH A:941	BINDING SITE FOR RESIDUE SO4 A 503
04	AC4	SOFTWARE	GLY A:34 , TYR A:65 , GLY A:102 , GLY A:103 , THR A:104 , TRP A:130 , ASN A:183 , ASP A:211 , TYR A:214 , SER A:243 , SER A:245 , KST A:246 , ARG A:254 , PHE A:348 , ARG A:374 , GOL A:808 , HOH A:1021 , HOH A:1206	BINDING SITE FOR RESIDUE PSZ A 600
05	AC5	SOFTWARE	TYR A:65 , GLY A:103 , THR A:104 , TRP A:130 , ASN A:183 , ASP A:211 , TYR A:214 , SER A:243 , SER A:245 , KST A:246 , ARG A:254 , HOH A:814	BINDING SITE FOR RESIDUE PMP A 700
06	AC6	SOFTWARE	GLY A:216 , GLY A:220 , LEU A:221 , GLU A:308 , THR A:312 , ARG A:315 , HOH A:1085 , HOH A:1199	BINDING SITE FOR RESIDUE GOL A 801
07	AC7	SOFTWARE	TYR A:36 , THR A:43 , PRO A:44 , LEU A:46 , KST A:246 , GLY A:249 , TYR A:251 , MET A:314 , HOH A:1192	BINDING SITE FOR RESIDUE GOL A 802
08	AC8	SOFTWARE	PRO A:72 , GLY A:75 , ARG A:76 , GLN A:79 , ALA A:95 , ARG A:96 , THR A:97 , HOH A:809 , HOH A:1103 , HOH A:1140	BINDING SITE FOR RESIDUE GOL A 803
09	AC9	SOFTWARE	ARG A:315 , GLN A:316 , GLN A:319 , SO4 A:503	BINDING SITE FOR RESIDUE GOL A 804
10	BC1	SOFTWARE	TYR A:55 , ASN A:300 , LEU A:303 , HOH A:966	BINDING SITE FOR RESIDUE GOL A 805
11	BC2	SOFTWARE	ASN A:138 , GLY A:141 , LEU A:142 , SO4 A:501	BINDING SITE FOR RESIDUE GOL A 806
12	BC3	SOFTWARE	PRO A:189 , THR A:190 , LEU A:191 , ARG A:219 , ASN A:345 , HOH A:833 , HOH A:855 , HOH A:918 , HOH A:1001	BINDING SITE FOR RESIDUE GOL A 807
13	BC4	SOFTWARE	TYR A:65 , KST A:246 , ARG A:280 , PSZ A:600 , HOH A:1024 , HOH A:1163 , HOH A:1190	BINDING SITE FOR RESIDUE GOL A 808

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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:396
 aligned with AAT_ECOLI | P00509 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:396
                                    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      
            AAT_ECOLI     1 MFENITAAPADPILGLADLFRADERPGKINLGIGVYKDETGKTPVLTSVKKAEQYLLENETTKNYLGIDGIPEFGRCTQELLFGKGSALINDKRARTAQTPGGTGALRVAADFLAKNTSVKRVWVSNPSWPNHKSVFNSAGLEVREYAYYDAENHTLDFDALINSLNEAQAGDVVLFHGCCHNPTGIDPTLEQWQTLAQLSVEKGWLPLFDFAYQGFARGLEEDAEGLRAFAAMHKELIVASSYSKNFGLYNERVGACTLVAADSETVDRAFSQMKAAIRANYSNPPAHGASVVATILSNDALRAIWEQELTDMRQRIQRMRQLFVNTLQEKGANRDFSFIIKQNGMFSFSGLTKEQVLRLREEFGVYAVASGRVNVAGMTPDNMAPLCEAIVAVL 396
               SCOP domains d2qbta_ A: Aspartate aminotransferase, AAT                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------2qbtA02 A:45-314 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                          ---------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------Aminotran_1_2-2qbtA01 A:26-392                                                                                                                                                                                                                                                                                                                                                 ---- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhh.....ee...............hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh..hhhhhh..eeeeeehhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhh..eeeeee.ee....eehhhhhhhhhh......eeeee...........hhhhhhhhhhhhhhhh.eeeeee.......hhhhhhhhhhhhhhhh..eeeeee......hhhhh.eeeeee..hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh...eee...hhhhhhhhhhhhhee.....eee.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CL-------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qbt A   1 MFENITAAPADPILGLADLFRADERPGKINLGIGVYKDETGKTPVLTSVKKAEQYLLENETTKNYLGIDGIPEFGRCTQELLFGKGSALINDKRARTAQTPGGTGALRVAADFLAKNTSVKRVWVSNPSWPNHKSVFNSAGLEVREYAYYDAENHTLDFDALINSLNEAQAGDVVLFHGCCHNPTGIDPTLEQWQTLAQLSVEKGWLPLFDFAYQGFARGLEEDAEGLRAFAAMHKELIVASSYSkNFGLYNERVGACTLVAADSETVDRAFSQMKAAIRANYSNPPAHGASVVATILSNDALRAIWEQELTDMRQRIQRMRQLFVNTLQEKGANRDFSFIIKQNGMFSFSGLTKEQVLRLREEFGVYAVASGRVNVAGMTPDNMAPLCEAIVAVL 396
                                    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      
                                                                                                                                                                                                                                                                               246-KST

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (14, 14)

Asymmetric Unit(hide GO term definitions)

Chain A (AAT_ECOLI | P00509)

molecular function
	GO:0004069	L-aspartate:2-oxoglutarate aminotransferase activity	Catalysis of the reaction: L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate.
	GO:0080130	L-phenylalanine:2-oxoglutarate aminotransferase activity	Catalysis of the reaction: L-phenylalanine + 2-oxoglutarate = phenylpyruvate + L-glutamate.
	GO:0004838	L-tyrosine:2-oxoglutarate aminotransferase activity	Catalysis of the reaction: L-tyrosine + 2-oxoglutarate = 4-hydroxyphenylpyruvate + L-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: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:0009094	L-phenylalanine biosynthetic process	The chemical reactions and pathways resulting in the formation of L-phenylalanine, the L-enantiomer of 2-amino-3-phenylpropanoic acid, i.e. (2S)-2-amino-3-phenylpropanoic acid.
	GO:0033585	L-phenylalanine biosynthetic process from chorismate via phenylpyruvate	The chemical reactions and pathways resulting in the formation of L-phenylalanine from other compounds, including chorismate, via the intermediate phenylpyruvate.
	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:0006520	cellular amino acid metabolic process	The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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