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Title :   CRYSTAL STRUCTURE OF OXIDIZED HUMAN CYTOSOLIC BRANCHED-CHAIN AMINOTRANSFERASE COMPLEXED WITH 4-METHYLVALERATE

Authors :   M. Goto

Date :   17 May 05 (Deposition) - 30 Aug 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Plp-Dependent Enzyme, 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 1, CYTOSOLIC
	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
	Mutation	:	YES
	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	4MV	2	Ligand/Ion	4-METHYL VALERIC ACID
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:133 , GLU B:274 , HOH B:453 , HOH B:454 , HOH B:578	BINDING SITE FOR RESIDUE MG B 430
2	AC2	SOFTWARE	ARG A:119 , ARG A:212 , LYS A:222 , TYR A:227 , GLU A:257 , THR A:260 , ASN A:262 , LEU A:286 , GLY A:288 , VAL A:289 , THR A:290 , THR A:333 , HOH A:443 , HOH A:459	BINDING SITE FOR RESIDUE PLP A 410
3	AC3	SOFTWARE	ARG B:119 , ARG B:212 , LYS B:222 , TYR B:227 , GLU B:257 , THR B:260 , ASN B:262 , LEU B:286 , GLY B:288 , VAL B:289 , THR B:290 , THR B:333 , HOH B:434 , HOH B:445 , HOH B:483	BINDING SITE FOR RESIDUE PLP B 410
4	AC4	SOFTWARE	ARG A:163 , TYR A:193 , THR A:260 , MET A:261 , THR A:333 , ALA A:334 , TYR B:90	BINDING SITE FOR RESIDUE 4MV A 420
5	AC5	SOFTWARE	TYR A:90 , VAL A:175 , TYR B:193 , THR B:260 , MET B:261 , GLY B:332 , THR B:333 , ALA B:334 , HOH B:521	BINDING SITE FOR RESIDUE 4MV B 420

Asymmetric/Biological Unit

No.	Residues
1	A:335	-	A:338
2	B:335	-	B:338

Asymmetric/Biological Unit

No.	Residues
1	Gly A:358	-	Pro A:359
2	Gly B:358	-	Pro B:359

Asymmetric/Biological Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_047681	T	59	M	BCAT1_HUMAN	Polymorphism	17374285	A/B	T	59	M
2	UniProt	VAR_019614	E	321	K	BCAT1_HUMAN	Polymorphism	7313020	A/B	E	321	K
3	UniProt	VAR_047682	G	330	S	BCAT1_HUMAN	Polymorphism	1057204	A/B	G	330	S

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.	BCAT1_HUMAN	257-291	2	A:257-291 B:257-291

Asymmetric/Biological Unit (10, 20)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000261192	1	ENSE00001535251	chr12:25102308-25101861	448	BCAT1_HUMAN	1-2	2	0	-	-
1.2	ENST00000261192	2	ENSE00001306384	chr12:25054819-25054748	72	BCAT1_HUMAN	3-26	24	2	A:22-26 B:24-26	5 3
1.4	ENST00000261192	4	ENSE00000465783	chr12:25047409-25047209	201	BCAT1_HUMAN	27-93	67	2	A:27-93 (gaps) B:27-93	67 67
1.5	ENST00000261192	5	ENSE00001290230	chr12:25034345-25034235	111	BCAT1_HUMAN	94-130	37	2	A:94-130 B:94-130	37 37
1.6	ENST00000261192	6	ENSE00000797209	chr12:25031583-25031464	120	BCAT1_HUMAN	131-170	40	2	A:131-170 B:131-170	40 40
1.7	ENST00000261192	7	ENSE00000730302	chr12:25002883-25002720	164	BCAT1_HUMAN	171-225	55	2	A:171-225 (gaps) B:171-225 (gaps)	55 55
1.8	ENST00000261192	8	ENSE00000730341	chr12:24995158-24995016	143	BCAT1_HUMAN	225-273	49	2	A:225-273 B:225-273	49 49
1.9	ENST00000261192	9	ENSE00000730344	chr12:24989530-24989445	86	BCAT1_HUMAN	273-301	29	2	A:273-301 B:273-301	29 29
1.10	ENST00000261192	10	ENSE00001314201	chr12:24985797-24985657	141	BCAT1_HUMAN	302-348	47	2	A:302-348 B:302-348	47 47
1.11	ENST00000261192	11	ENSE00001292534	chr12:24982831-24982757	75	BCAT1_HUMAN	349-373	25	2	A:349-373 B:349-373	25 25
1.12	ENST00000261192	12	ENSE00001318494	chr12:24970983-24964281	6703	BCAT1_HUMAN	374-386	13	2	A:374-385 B:374-385	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:358
 aligned with BCAT1_HUMAN | P54687 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:364
                                    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       291       301       311       321       331       341       351       361       371       381    
          BCAT1_HUMAN    22 VGTFKAKDLIVTPATILKEKPDPNNLVFGTVFTDHMLTVEWSSEFGWEKPHIKPLQNLSLHPGSSALHYAVELFEGLKAFRGVDNKIRLFQPNLNMDRMYRSAVRATLPVFDKEELLECIQQLVKLDQEWVPYSTSASLYIRPTFIGTEPSLGVKKPTKALLFVLLSPVGPYFSSGTFNPVSLWANPKYVRAWKGGTGDCKMGGNYGSSLFAQCEAVDNGCQQVLWLYGEDHQITEVGTMNLFLYWINEDGEEELATPPLDGIILPGVTRRCILDLAHQWGEFKVSERYLTMDDLTTALEGNRVREMFGSGTACVVCPVSDILYKGETIHIPTMENGPKLASRILSKLTDIQYGREESDWTIVL 385
               SCOP domains d2coga_ A: automated mat ches                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2cogA01 A:22-193,A:374-3 85  [code=3.30.470.10, no name defined]                                                                                                                 2cogA02 A:199-373 D-amino Acid Aminotransferase, subunit A, domain 2                                                                                                           2cogA01      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhee.............-.........eeeeeeee...ee...eeee...eee...hhhhhh..eee..eeeee.....eeeehhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh......eeeeeeeeee...........eeeeeeeeeee...-----...eeeee.................hhhhhhhhhhhhhhhh....eeeeee....eeeee..eeeeeeee.....eeeee.........hhhhhhhhhhhhhhh..eeee...hhhhhhhhhh...eeeeeee......eeeeeeee..eeee..hhhhhhhhhhhhhhhhhhhhh.......eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------M---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------K--------S------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_4  PDB: A:257-291---------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.2  Exon 1.4  PDB: A:27-93 (gaps) UniProt: 27-93                       Exon 1.5  PDB: A:94-130              Exon 1.6  PDB: A:131-170                Exon 1.7  PDB: A:171-225 (gaps) UniProt: 171-225       -----------------------------------------------Exon 1.9  PDB: A:273-301     Exon 1.10  PDB: A:302-348 UniProt: 302-348     Exon 1.11  PDB: A:349-373Exon 1.12    Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: A:225-273 UniProt: 225-273        ---------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2cog A  22 VGTFKAKDLIVTPATILKEKPDPN-LVFGTVFTDHMLTVEWSSEFGWEKPHIKPLQNLSLHPGSSALHYAVELFEGLKAFRGVDNKIRLFQPNLNMDRMYRSAVRATLPVFDKEELLECIQQLVKLDQEWVPYSTSASLYIRPTFIGTEPSLGVKKPTKALLFVLLSPVGPY-----FNPVSLWANPKYVRAWKGGTGDCKMGGNYGSSLFAQCEAVDNGCQQVLWLYGEDHQITEVGTMNLFLYWINEDGEEELATPPLDGIILPGVTRRCILDLAHQWGEFKVSERYLTMDDLTTALEGNRVREMFGSGTACVVCPVSDILYKGETIHIPTMENGPKLASRILSKLTDIQYGREERDWTIVL 385
                                    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       291       301       311       321       331       341       351       361       371       381    
                                                  45 |                                                                                                                                               193   199                                                                                                                                                                                          
                                                    47

Chain B from PDB  Type:PROTEIN  Length:358
 aligned with BCAT1_HUMAN | P54687 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:362
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383  
          BCAT1_HUMAN    24 TFKAKDLIVTPATILKEKPDPNNLVFGTVFTDHMLTVEWSSEFGWEKPHIKPLQNLSLHPGSSALHYAVELFEGLKAFRGVDNKIRLFQPNLNMDRMYRSAVRATLPVFDKEELLECIQQLVKLDQEWVPYSTSASLYIRPTFIGTEPSLGVKKPTKALLFVLLSPVGPYFSSGTFNPVSLWANPKYVRAWKGGTGDCKMGGNYGSSLFAQCEAVDNGCQQVLWLYGEDHQITEVGTMNLFLYWINEDGEEELATPPLDGIILPGVTRRCILDLAHQWGEFKVSERYLTMDDLTTALEGNRVREMFGSGTACVVCPVSDILYKGETIHIPTMENGPKLASRILSKLTDIQYGREESDWTIVL 385
               SCOP domains d2cogb_ B: automated matches                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2cogB01 B:24-194,B:374-385  [code=3.30.470.10, no name defined]                                                                                                            ----2cogB02 B:199-373 D-amino Acid Aminotransferase, subunit A, domain 2                                                                                                           2cogB01      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhee.......................eeeeeeee...ee...eeee...eee...hhhhhh..eee..eeeee.....eeeehhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh......eeeeeeeeee...........eeeeeeeeeee....----...eeee..................hhhhhhhhhhhhhhhh....eeeeee....eeeee..eeeeeeee.....eeeee.........hhhhhhhhhhhhhhh..eeee...hhhhhhhhhhh..eeeeeeee..eeeeeeeeeee..eeee.hhhhhhhhhhhhhhhhhhhhhh.......eee. Sec.struct. author
                 SAPs(SNPs) -----------------------------------M---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------K--------S------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_4  PDB: B:257-291---------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.2Exon 1.4  PDB: B:27-93 UniProt: 27-93                              Exon 1.5  PDB: B:94-130              Exon 1.6  PDB: B:131-170                Exon 1.7  PDB: B:171-225 (gaps) UniProt: 171-225       -----------------------------------------------Exon 1.9  PDB: B:273-301     Exon 1.10  PDB: B:302-348 UniProt: 302-348     Exon 1.11  PDB: B:349-373Exon 1.12    Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: B:225-273 UniProt: 225-273        ---------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2cog B  24 TFKAKDLIVTPATILKEKPDPNNLVFGTVFTDHMLTVEWSSEFGWEKPHIKPLQNLSLHPGSSALHYAVELFEGLKAFRGVDNKIRLFQPNLNMDRMYRSAVRATLPVFDKEELLECIQQLVKLDQEWVPYSTSASLYIRPTFIGTEPSLGVKKPTKALLFVLLSPVGPYF----FNPVSLWANPKYVRAWKGGTGDCKMGGNYGSSLFAQCEAVDNGCQQVLWLYGEDHQITEVGTMNLFLYWINEDGEEELATPPLDGIILPGVTRRCILDLAHQWGEFKVSERYLTMDDLTTALEGNRVREMFGSGTACVVCPVSDILYKGETIHIPTMENGPKLASRILSKLTDIQYGREERDWTIVL 385
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193|    | 203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383  
                                                                                                                                                                                                    194  199

Legend:		→ Mismatch	(orange background)
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	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	2cogB01	B:24-194,B:374-385
1b	2cogA01	A:22-193,A:374-385

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	2cogA02	A:199-373
2b	2cogB02	B:199-373

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (BCAT1_HUMAN | P54687)

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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0000082	G1/S transition of mitotic cell cycle	The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated.
	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:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:358 - Pro A:359	[ RasMol ]
		Gly B:358 - Pro B:359	[ RasMol ]

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	2cog
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	BCAT1_HUMAN \| P54687	:	2abj 2coi 2coj

2coi	OXIDIZED CYTOSOLIC BRANCHED-CHAIN AMINOTRANSFERASE COMPLEXED WITH GABAPENTIN
2coj	REDUCED CYTOSOLIC BRANCHED-CHAIN AMINOTRANSFERASE COMPLEXED WITH GABAPENTIN

Description

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Ligands, Modified Residues, Ions (3, 5)

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SS Bonds (2, 2)

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