2A1H - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   X-RAY CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH GABAPENTIN

Authors :   M. Goto, I. Miyahara, K. Hirotsu, M. Conway, N. Yennawar, M. M. Islam, S.

Date :   20 Jun 05 (Deposition) - 06 Sep 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Fold Type Iv, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Goto, I. Miyahara, K. Hirotsu, M. Conway, N. Yennawar, M. M. Islam, S. M. Hutson
Structural Determinants For Branched-Chain Aminotransferase Isozyme-Specific Inhibition By The Anticonvulsant Drug Gabapentin.
J. Biol. Chem. V. 280 37246 2005
PubMed-ID: 16141215 | Reference-DOI: 10.1074/JBC.M506486200

Molecule 1 - BRANCHED CHAIN AMINOTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.6.1.42
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	MITOCHONDRIAL BCAT
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	GBN	2	Ligand/Ion	[1-(AMINOMETHYL)CYCLOHEXYL]ACETIC ACID
3	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:99 , ARG A:192 , LYS A:202 , TYR A:207 , GLU A:237 , THR A:240 , ASN A:242 , GLY A:268 , VAL A:269 , VAL A:270 , GLY A:312 , THR A:313 , GBN A:502 , HOH A:513 , HOH A:525 , HOH A:533	BINDING SITE FOR RESIDUE PLP A 400
2	AC2	SOFTWARE	ARG B:99 , ARG B:192 , LYS B:202 , TYR B:207 , GLU B:237 , THR B:240 , ASN B:242 , GLY B:268 , VAL B:269 , VAL B:270 , GLY B:312 , THR B:313 , GBN B:501 , HOH B:1005 , HOH B:1009 , HOH B:1024	BINDING SITE FOR RESIDUE PLP B 400
3	AC3	SOFTWARE	TYR A:70 , VAL A:155 , TYR B:141 , ARG B:143 , THR B:240 , GLY B:312 , THR B:313 , ALA B:314 , PLP B:400 , HOH B:1096	BINDING SITE FOR RESIDUE GBN B 501
4	AC4	SOFTWARE	TYR A:141 , ARG A:143 , THR A:240 , GLY A:312 , THR A:313 , ALA A:314 , PLP A:400 , HOH A:544 , TYR B:70 , VAL B:155	BINDING SITE FOR RESIDUE GBN A 502
5	AC5	SOFTWARE	LEU B:59 , THR B:60 , HOH B:1170	BINDING SITE FOR RESIDUE ACY B 1001

(no "SS Bond" information available for 2A1H)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:338	-	Pro A:339
2	Gly B:338	-	Pro B:339

Asymmetric/Biological Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_048234	T	186	R	BCAT2_HUMAN	Polymorphism	11548193	A/B	R	159	R

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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.	BCAT2_HUMAN	264-298	2	A:237-271 B:237-271

Asymmetric/Biological Unit (10, 20)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000316273	1a	ENSE00001342922	chr19:49314301-49314241	61	BCAT2_HUMAN	1-8	8	0	-	-
1.3	ENST00000316273	3	ENSE00001609474	chr19:49310331-49310257	75	BCAT2_HUMAN	9-33	25	2	A:3-6 B:3-6	4 4
1.4	ENST00000316273	4	ENSE00001707807	chr19:49309974-49309774	201	BCAT2_HUMAN	34-100	67	2	A:7-73 B:7-73	67 67
1.5	ENST00000316273	5	ENSE00000718215	chr19:49303554-49303444	111	BCAT2_HUMAN	101-137	37	2	A:74-110 B:74-110	37 37
1.6	ENST00000316273	6	ENSE00000718210	chr19:49303357-49303238	120	BCAT2_HUMAN	138-177	40	2	A:111-150 B:111-150	40 40
1.7	ENST00000316273	7	ENSE00000718205	chr19:49303095-49302932	164	BCAT2_HUMAN	178-232	55	2	A:151-205 B:151-205	55 55
1.8	ENST00000316273	8	ENSE00000718200	chr19:49300590-49300448	143	BCAT2_HUMAN	232-280	49	2	A:205-253 B:205-253	49 49
1.9	ENST00000316273	9	ENSE00000718196	chr19:49300279-49300194	86	BCAT2_HUMAN	280-308	29	2	A:253-281 B:253-281	29 29
1.10	ENST00000316273	10	ENSE00000853352	chr19:49299975-49299835	141	BCAT2_HUMAN	309-355	47	2	A:282-328 B:282-328	47 47
1.11	ENST00000316273	11	ENSE00000853351	chr19:49299759-49299685	75	BCAT2_HUMAN	356-380	25	2	A:329-353 B:329-353	25 25
1.12	ENST00000316273	12	ENSE00001236079	chr19:49298721-49298322	400	BCAT2_HUMAN	381-392	12	2	A:354-365 B:354-365	12 12

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 BCAT2_HUMAN | O15382 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:363
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389   
          BCAT2_HUMAN    30 SSFKAADLQLEMTQKPHKKPGPGEPLVFGKTFTDHMLMVEWNDKGWGQPRIQPFQNLTLHPASSSLHYSLQLFEGMKAFKGKDQQVRLFRPWLNMDRMLRSAMRLCLPSFDKLELLECIRRLIEVDKDWVPDAAGTSLYVRPVLIGNEPSLGVSQPTRALLFVILCPVGAYFPGGSVTPVSLLADPAFIRAWVGGVGNYKLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPLNGVILPGVVRQSLLDMAQTWGEFRVVERTITMKQLLRALEEGRVREVFGSGTACQVCPVHRILYKDRNLHIPTMENGPELILRFQKELKEIQYGIRAHEWMFPV 392
               SCOP domains d2a1ha_ A: automated matches                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2a1hA01 A:3-174,A:351-365  [code=3.30.470.10, no name defined]                                                                                                              2a1hA02 A:175-350 D-amino Acid Aminotransferase, subunit A, domain 2                                                                                                            2a1hA01         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhee........................eeeeeeee..ee...eeee...eee...hhhhhh..eee..eeeee.....eeeehhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh......eeeeeeeeee...........eeeeeeeeeee...........eeeee................hhhhhhhhhhhhhhhhhh...eeeeee....eeeee..eeeeeeee.....eeeee.........hhhhhhhhhhhhhhh..eeee...hhhhhhhhhhh..eeeeeeee...eeeeeeeeee..eeee..hhhhhhhhhhhhhhhhhhhhh.......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------R-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_4  PDB: A:237-271---------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.3 Exon 1.4  PDB: A:7-73 UniProt: 34-100                              Exon 1.5  PDB: A:74-110              Exon 1.6  PDB: A:111-150                Exon 1.7  PDB: A:151-205 UniProt: 178-232              -----------------------------------------------Exon 1.9  PDB: A:253-281     Exon 1.10  PDB: A:282-328 UniProt: 309-355     Exon 1.11  PDB: A:329-353Exon 1.12    Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: A:205-253 UniProt: 232-280        ---------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2a1h A   3 SSFKAADLQLEMTQKPHKKPGPGEPLVFGKTFTDHMLMVEWNDKGWGQPRIQPFQNLTLHPASSSLHYSLQLFEGMKAFKGKDQQVRLFRPWLNMDRMLRSAMRLCLPSFDKLELLECIRRLIEVDKDWVPDAAGTSLYVRPVLIGNEPSLGVSQPRRALLFVILCPVGAYFPGGSVTPVSLLADPAFIRAWVGGVGNYKLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPLNGVILPGVVRQSLLDMAQTWGEFRVVERTITMKQLLRALEEGRVREVFGSGTACQVCPVHRILYKDRNLHIPTMENGPELILRFQKELKEIQYGIRAHEWMFPV 365
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362

Chain B from PDB  Type:PROTEIN  Length:363
 aligned with BCAT2_HUMAN | O15382 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:363
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389   
          BCAT2_HUMAN    30 SSFKAADLQLEMTQKPHKKPGPGEPLVFGKTFTDHMLMVEWNDKGWGQPRIQPFQNLTLHPASSSLHYSLQLFEGMKAFKGKDQQVRLFRPWLNMDRMLRSAMRLCLPSFDKLELLECIRRLIEVDKDWVPDAAGTSLYVRPVLIGNEPSLGVSQPTRALLFVILCPVGAYFPGGSVTPVSLLADPAFIRAWVGGVGNYKLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPLNGVILPGVVRQSLLDMAQTWGEFRVVERTITMKQLLRALEEGRVREVFGSGTACQVCPVHRILYKDRNLHIPTMENGPELILRFQKELKEIQYGIRAHEWMFPV 392
               SCOP domains d2a1hb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2a1hB01 B:3-174,B:351-365  [code=3.30.470.10, no name defined]                                                                                                              2a1hB02 B:175-350 D-amino Acid Aminotransferase, subunit A, domain 2                                                                                                            2a1hB01         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhee........................eeeeeeee..ee...eeee...eee...hhhhhh..eee..eeeee.....eeeehhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh......eeeeeeeeee............eeeeeeeeee...........eeeee................hhhhhhhhhhhhhhhhhh...eeeeee....eeeee..eeeeeeee.....eeeee.........hhhhhhhhhhhhhhh..eeee...hhhhhhhhhhh..eeeeeeee...eeeeeeeeee..eeee.......hhhhhhhhhhhhhhhh.......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------R-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_4  PDB: B:237-271---------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.3 Exon 1.4  PDB: B:7-73 UniProt: 34-100                              Exon 1.5  PDB: B:74-110              Exon 1.6  PDB: B:111-150                Exon 1.7  PDB: B:151-205 UniProt: 178-232              -----------------------------------------------Exon 1.9  PDB: B:253-281     Exon 1.10  PDB: B:282-328 UniProt: 309-355     Exon 1.11  PDB: B:329-353Exon 1.12    Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: B:205-253 UniProt: 232-280        ---------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2a1h B   3 SSFKAADLQLEMTQKPHKKPGPGEPLVFGKTFTDHMLMVEWNDKGWGQPRIQPFQNLTLHPASSSLHYSLQLFEGMKAFKGKDQQVRLFRPWLNMDRMLRSAMRLCLPSFDKLELLECIRRLIEVDKDWVPDAAGTSLYVRPVLIGNEPSLGVSQPRRALLFVILCPVGAYFPGGSVTPVSLLADPAFIRAWVGGVGNYKLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPLNGVILPGVVRQSLLDMAQTWGEFRVVERTITMKQLLRALEEGRVREVFGSGTACQVCPVHRILYKDRNLHIPTMENGPELILRFQKELKEIQYGIRAHEWMFPV 365
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: D-amino Acid Aminotransferase; Chain A, domain 1 (175)

Homologous Superfamily: [code=3.30.470.10, no name defined] (39)

Human (Homo sapiens) (15)

1a	2a1hA01	A:3-174,A:351-365
1b	2a1hB01	B:3-174,B:351-365

Architecture: Alpha-Beta Barrel (2994)

Topology: D-amino Acid Aminotransferase; Chain A, domain 2 (39)

Homologous Superfamily: D-amino Acid Aminotransferase, subunit A, domain 2 (39)

Human (Homo sapiens) (15)

2a	2a1hA02	A:175-350
2b	2a1hB02	B:175-350

(no "Pfam Domain" information available for 2A1H)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (BCAT2_HUMAN | O15382)

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: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:0009083	branched-chain amino acid catabolic process	The chemical reactions and pathways resulting in the breakdown 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: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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:338 - Pro A:339	[ RasMol ]
		Gly B:338 - Pro B:339	[ RasMol ]

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	2a1h
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1ekf	THE SAME PROTEIN WITHOUT SUBSTRATE OR INHIBITOR - ORTHORHOMBIC FORM.
1ekp	THE SAME PROTEIN WITHOUT SUBSTRATE OR INHIBITOR - MONOCLINIC FORM.
1ekv	SAME PROTEIN INACTIVATED BY TRIS.
1kt8	SAME PROTEIN IN ITS KETIMINE FORM WITH SUBSTRATE, ISOLEUCINE.
1kta	SAME PROTEIN WITH ITS COFACTOR IN THE PYRIDOXAMINE FORM. COFACTOR

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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Exons (10, 20)

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