1KT8 - JenaLib

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Title :   HUMAN BRANCHED CHAIN AMINO ACID AMINOTRANSFERASE (MITOCHONDRIAL): THREE DIMENSIONAL STRUCTURE OF ENZYME IN ITS KETIMINE FORM WITH THE SUBSTRATE L-ISOLEUCINE

Authors :   N. H. Yennawar, M. E. Conway, H. P. Yennawar, G. K. Farber, S. M. Hutson

Date :   15 Jan 02 (Deposition) - 20 Nov 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

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

Reference :   N. H. Yennawar, M. E. Conway, H. P. Yennawar, G. K. Farber, S. M. Hutson
Crystal Structures Of Human Mitochondrial Branched Chain Aminotransferase Reaction Intermediates: Ketimine And Pyridoxamine Phosphate Forms
Biochemistry V. 41 11592 2002
PubMed-ID: 12269802 | Reference-DOI: 10.1021/BI020221C
(for further references see the PDB file header)

Molecule 1 - BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE, MITOCHONDRIAL
	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	:	BL21DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BCAT(M)

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 9)

No.	Name	Count	Type	Full Name
1	ACY	6	Ligand/Ion	ACETIC ACID
2	GOL	1	Ligand/Ion	GLYCEROL
3	ILP	2	Ligand/Ion	N-[O-PHOSPHONO-PYRIDOXYL]-ISOLEUCINE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:77 , ARG A:99 , TYR A:141 , ARG A:192 , LYS A:202 , TYR A:207 , GLU A:237 , THR A:240 , ASN A:242 , LEU A:266 , GLY A:268 , VAL A:269 , VAL A:270 , GLY A:312 , THR A:313 , HOH A:1032 , HOH A:1036	BINDING SITE FOR RESIDUE ILP A 400
2	AC2	SOFTWARE	TYR A:70 , VAL A:155 , HOH B:68 , HOH B:108 , HOH B:119 , PHE B:575 , GLY B:577 , ARG B:599 , TYR B:641 , ARG B:643 , ARG B:692 , LYS B:702 , TYR B:707 , GLU B:737 , THR B:740 , ASN B:742 , LEU B:766 , GLY B:768 , VAL B:769 , VAL B:770 , THR B:813	BINDING SITE FOR RESIDUE ILP B 900
3	AC3	SOFTWARE	MET B:540 , GLU B:542 , THR B:560 , LEU B:662	BINDING SITE FOR RESIDUE ACY B 1001
4	AC4	SOFTWARE	ASP B:776 , MET B:777 , THR B:780 , HIS B:859	BINDING SITE FOR RESIDUE ACY B 1002
5	AC5	SOFTWARE	ARG A:102 , ASN A:200 , LEU A:261 , PRO A:267	BINDING SITE FOR RESIDUE ACY A 1003
6	AC6	SOFTWARE	TRP A:94 , ACY A:1005	BINDING SITE FOR RESIDUE ACY A 1004
7	AC7	SOFTWARE	ARG A:92 , TRP A:94 , ACY A:1004	BINDING SITE FOR RESIDUE ACY A 1005
8	AC8	SOFTWARE	ARG B:592 , TRP B:594	BINDING SITE FOR RESIDUE ACY B 1006
9	AC9	SOFTWARE	HOH B:181 , PHE B:690 , LEU B:712 , VAL B:713	BINDING SITE FOR RESIDUE GOL B 2001

(no "SS Bond" information available for 1KT8)

(no "Cis Peptide Bond" information available for 1KT8)

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	159 659	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:737-771

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:1-6 B:501-506	6 6
1.4	ENST00000316273	4	ENSE00001707807	chr19:49309974-49309774	201	BCAT2_HUMAN	34-100	67	2	A:7-73 B:507-573	67 67
1.5	ENST00000316273	5	ENSE00000718215	chr19:49303554-49303444	111	BCAT2_HUMAN	101-137	37	2	A:74-110 B:574-610	37 37
1.6	ENST00000316273	6	ENSE00000718210	chr19:49303357-49303238	120	BCAT2_HUMAN	138-177	40	2	A:111-150 B:611-650	40 40
1.7	ENST00000316273	7	ENSE00000718205	chr19:49303095-49302932	164	BCAT2_HUMAN	178-232	55	2	A:151-205 (gaps) B:651-705	55 55
1.8	ENST00000316273	8	ENSE00000718200	chr19:49300590-49300448	143	BCAT2_HUMAN	232-280	49	2	A:205-253 B:705-753	49 49
1.9	ENST00000316273	9	ENSE00000718196	chr19:49300279-49300194	86	BCAT2_HUMAN	280-308	29	2	A:253-281 B:753-781	29 29
1.10	ENST00000316273	10	ENSE00000853352	chr19:49299975-49299835	141	BCAT2_HUMAN	309-355	47	2	A:282-328 B:782-828	47 47
1.11	ENST00000316273	11	ENSE00000853351	chr19:49299759-49299685	75	BCAT2_HUMAN	356-380	25	2	A:329-353 B:829-853	25 25
1.12	ENST00000316273	12	ENSE00001236079	chr19:49298721-49298322	400	BCAT2_HUMAN	381-392	12	2	A:354-365 B:854-865	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:360
 aligned with BCAT2_HUMAN | O15382 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:365
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387     
          BCAT2_HUMAN    28 ASSSFKAADLQLEMTQKPHKKPGPGEPLVFGKTFTDHMLMVEWNDKGWGQPRIQPFQNLTLHPASSSLHYSLQLFEGMKAFKGKDQQVRLFRPWLNMDRMLRSAMRLCLPSFDKLELLECIRRLIEVDKDWVPDAAGTSLYVRPVLIGNEPSLGVSQPTRALLFVILCPVGAYFPGGSVTPVSLLADPAFIRAWVGGVGNYKLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPLNGVILPGVVRQSLLDMAQTWGEFRVVERTITMKQLLRALEEGRVREVFGSGTACQVCPVHRILYKDRNLHIPTMENGPELILRFQKELKEIQYGIRAHEWMFPV 392
               SCOP domains d1kt8a_ A: Branched-chain aminoacid aminotransferase                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1kt8A01 A:1-179,A:351-364  [code=3.30.470.10, no name defined]                                                                                                                     1kt8A02 A:180-350 D-amino Acid Aminotransferase, subunit A, domain 2                                                                                                       1kt8A01       - 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..eeeeeee.....eeeeeeeee..eeee.hhhhhhhhhhhhhhhhhhhhhh.......eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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 (gaps) 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)
                 1kt8 A   1 ASSSFKAADLQLEMTQKPHKKPGPGEPLVFGKTFTDHMLMVEWNDKGWGQPRIQPFQNLTLHPASSSLHYSLQLFEGMKAFKGKDQQVRLFRPWLNMDRMLRSAMRLCLPSFDKLELLECIRRLIEVDKDWVPDAAGTSLYVRPVLIGNEPSLGVSQPRRALLFVILCPVGAY-----VTPVSLLADPAFIRAWVGGVGNYKLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPLNGVILPGVVRQSLLDMAQTWGEFRVVERTITMKQLLRALEEGRVREVFGSGTACQVCPVHRILYKDRNLHIPTMENGPELILRFQKELKEIQYGIRAHEWMFPV 365
                                    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     
                                                                                                                                                                                                      173   179

Chain B from PDB  Type:PROTEIN  Length:365
 aligned with BCAT2_HUMAN | O15382 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:365
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387     
          BCAT2_HUMAN    28 ASSSFKAADLQLEMTQKPHKKPGPGEPLVFGKTFTDHMLMVEWNDKGWGQPRIQPFQNLTLHPASSSLHYSLQLFEGMKAFKGKDQQVRLFRPWLNMDRMLRSAMRLCLPSFDKLELLECIRRLIEVDKDWVPDAAGTSLYVRPVLIGNEPSLGVSQPTRALLFVILCPVGAYFPGGSVTPVSLLADPAFIRAWVGGVGNYKLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPLNGVILPGVVRQSLLDMAQTWGEFRVVERTITMKQLLRALEEGRVREVFGSGTACQVCPVHRILYKDRNLHIPTMENGPELILRFQKELKEIQYGIRAHEWMFPV 392
               SCOP domains d1kt8b_ B: Branched-chain aminoacid aminotransferase                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1kt8B01 B:501-674,B:851-865  [code=3.30.470.10, no name defined]                                                                                                              1kt8B02 B:675-850 D-amino Acid Aminotransferase, subunit A, domain 2                                                                                                            1kt8B01         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh..........................eeeeeeee..ee...eeee...eee...hhhhhh..eee..eeeee.....eeeehhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh......eeeeeeeeee............eeeeeeeeee...........eeee.................hhhhhhhhhhhhhhhhhh...eeeeee....eeeee...eeeeeee.....eeeee.........hhhhhhhhhhhhhhh..eeee...hhhhhhhhhhh..eeeeeee.....eeeeeeee....eee.hhhhhhhhhhhhhhhhhhhhhh.......eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------R-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_4  PDB: B:737-771---------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.3   Exon 1.4  PDB: B:507-573 UniProt: 34-100                           Exon 1.5  PDB: B:574-610             Exon 1.6  PDB: B:611-650                Exon 1.7  PDB: B:651-705 UniProt: 178-232              -----------------------------------------------Exon 1.9  PDB: B:753-781     Exon 1.10  PDB: B:782-828 UniProt: 309-355     Exon 1.11  PDB: B:829-853Exon 1.12    Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: B:705-753 UniProt: 232-280        ---------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1kt8 B 501 ASSSFKAADLQLEMTQKPHKKPGPGEPLVFGKTFTDHMLMVEWNDKGWGQPRIQPFQNLTLHPASSSLHYSLQLFEGMKAFKGKDQQVRLFRPWLNMDRMLRSAMRLCLPSFDKLELLECIRRLIEVDKDWVPDAAGTSLYVRPVLIGNEPSLGVSQPRRALLFVILCPVGAYFPGGSVTPVSLLADPAFIRAWVGGVGNYKLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPLNGVILPGVVRQSLLDMAQTWGEFRVVERTITMKQLLRALEEGRVREVFGSGTACQVCPVHRILYKDRNLHIPTMENGPELILRFQKELKEIQYGIRAHEWMFPV 865
                                   510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860

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	1kt8B01	B:501-674,B:851-865
1b	1kt8A01	A:1-179,A:351-364

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	1kt8A02	A:180-350
2b	1kt8B02	B:675-850

(no "Pfam Domain" information available for 1KT8)

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
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1ekf	CRYSTALLOGRAPHIC STRUCTURE OF HUMAN BRANCHED CHAIN AMINO ACID AMINOTRANSFERASE (MITOCHONDRIAL) COMPLEXED WITH PYRIDOXAL-5'-PHOSPHATE AT 1.95 ANGSTROMS (ORTHORHOMBIC FORM)
1ekp	CRYSTAL STRUCTURE OF HUMAN BRANCHED CHAIN AMINO ACID AMINOTRANSFERASE (MITOCHONDRIAL) COMPLEXED WITH PYRIDOXAL- 5'-PHOSPHATE AT 2.5 ANGSTROMS (MONOCLINIC FORM)
1ekv	HUMAN BRANCHED CHAIN AMINO ACID AMINOTRANSFERASE (MITOCHONDRIAL): THREE DIMENSIONAL STRUCTURE OF ENZYME INACTIVATED BY TRIS BOUND TO THE PYRIDOXAL-5'-PHOSPHATE ON ONE END AND ACTIVE SITE LYS202 NZ ON THE OTHER
1kta	HUMAN BRANCHED CHAIN AMINO ACID AMINOTRANSFERASE : THREE DIMENSIONAL STRUCTURE OF THE ENZYME IN ITS PYRIDOXAMINE PHOSPHATE FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (1, 2)

Exons (10, 20)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (2, 4)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

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