3FVX - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   HUMAN KYNURENINE AMINOTRANSFERASE I IN COMPLEX WITH TRIS

Authors :   Q. Han, H. Robinson, T. Cai, D. A. Tagle, J. Li

Date :   16 Jan 09 (Deposition) - 19 May 09 (Release) - 19 May 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Alpha Beta Protein Plp Dependent Protein Aminotransferase Lyase Pyridoxal Phosphate Transferase, Alternative Splicing, Aminotransferase, Cytoplasm, Lyase, Pyridoxal Phosphate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Q. Han, H. Robinson, T. Cai, D. A. Tagle, J. Li
Structural Insight Into The Inhibition Of Human Kynurenine Aminotransferase I/Glutamine Transaminase K
J. Med. Chem. V. 52 2786 2009
PubMed-ID: 19338303 | Reference-DOI: 10.1021/JM9000874
(for further references see the PDB file header)

Molecule 1 - KYNURENINE--OXOGLUTARATE TRANSAMINASE 1
	Chains	:	A, B
	EC Number	:	2.6.1.7, 2.6.1.64, 4.4.1.13
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Plasmid	:	PBLUEBAC4.5
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Gene	:	CCBL1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	KYNURENINE--OXOGLUTARATE TRANSAMINASE I, KYNURENINE AMINOTRANSFERASE I, KATI, GLUTAMINE-- PHENYLPYRUVATE TRANSAMINASE, GLUTAMINE TRANSAMINASE K, GTK, CYSTEINE-S-CONJUGATE BETA-LYASE

		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	LLP	2	Mod. Amino Acid	2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
2	NA	2	Ligand/Ion	SODIUM ION
3	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:36 , PHE A:125 , ASN A:185 , TYR A:216 , LLP A:247 , PHE A:339 , ARG A:398 , HOH A:456 , HOH A:661 , HOH A:760 , TYR B:63	BINDING SITE FOR RESIDUE TRS A 423
2	AC2	SOFTWARE	HIS A:206 , HOH A:449 , HOH A:469 , HOH A:471 , HOH A:600 , HOH A:616	BINDING SITE FOR RESIDUE NA A 424
3	AC3	SOFTWARE	HIS B:206 , HOH B:464 , HOH B:562 , HOH B:609 , HOH B:707 , HOH B:716	BINDING SITE FOR RESIDUE NA B 423

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

Asymmetric/Biological Unit

No.	Residues
1	Glu A:122	-	Pro A:123
2	Thr A:182	-	Pro A:183
3	Asn A:185	-	Pro A:186
4	Glu B:122	-	Pro B:123
5	Thr B:182	-	Pro B:183
6	Asn B:185	-	Pro B:186

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

(no "PROSITE Motif" information available for 3FVX)

Asymmetric/Biological Unit (12, 24)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2c	ENST00000302586	2c	ENSE00001851283	chr9:131644332-131644176	157	KAT1_HUMAN	-	0	0	-	-
1.5b	ENST00000302586	5b	ENSE00002195023	chr9:131607690-131607632	59	KAT1_HUMAN	1-18	18	2	A:4-18 B:4-18	15 15
1.6	ENST00000302586	6	ENSE00001143432	chr9:131605080-131604933	148	KAT1_HUMAN	18-67	50	2	A:18-67 B:18-67	50 50
1.9b	ENST00000302586	9b	ENSE00002146235	chr9:131600646-131600497	150	KAT1_HUMAN	68-117	50	2	A:68-117 B:68-117	50 50
1.10	ENST00000302586	10	ENSE00001626071	chr9:131600416-131600330	87	KAT1_HUMAN	118-146	29	2	A:118-146 B:118-146	29 29
1.11c	ENST00000302586	11c	ENSE00001784290	chr9:131600092-131599964	129	KAT1_HUMAN	147-189	43	2	A:147-189 B:147-189	43 43
1.12	ENST00000302586	12	ENSE00001761291	chr9:131599201-131599081	121	KAT1_HUMAN	190-230	41	2	A:190-230 B:190-230	41 41
1.13c	ENST00000302586	13c	ENSE00001704435	chr9:131598352-131598276	77	KAT1_HUMAN	230-255	26	2	A:230-255 B:230-255	26 26
1.14	ENST00000302586	14	ENSE00001738063	chr9:131598147-131598058	90	KAT1_HUMAN	256-285	30	2	A:256-285 B:256-285	30 30
1.15a	ENST00000302586	15a	ENSE00001595628	chr9:131597946-131597760	187	KAT1_HUMAN	286-348	63	2	A:286-348 B:286-348	63 63
1.16a	ENST00000302586	16a	ENSE00001756602	chr9:131597681-131597602	80	KAT1_HUMAN	348-374	27	2	A:348-374 B:348-374	27 27
1.17	ENST00000302586	17	ENSE00001781922	chr9:131596105-131596019	87	KAT1_HUMAN	375-403	29	2	A:375-403 B:375-403	29 29
1.18d	ENST00000302586	18d	ENSE00001709974	chr9:131595922-131595392	531	KAT1_HUMAN	404-422	19	2	A:404-422 B:404-422	19 19

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:419
 aligned with KAT1_HUMAN | Q16773 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:419
                                    13        23        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       393       403       413         
           KAT1_HUMAN     4 QLQARRLDGIDYNPWVEFVKLASEHDVVNLGQGFPDFPPPDFAVEAFQHAVSGDFMLNQYTKTFGYPPLTKILASFFGELLGQEIDPLRNVLVTVGGYGALFTAFQALVDEGDEVIIIEPFFDCYEPMTMMAGGRPVFVSLKPGPIQNGELGSSSNWQLDPMELAGKFTSRTKALVLNTPNNPLGKVFSREELELVASLCQQHDVVCITDEVYQWMVYDGHQHISIASLPGMWERTLTIGSAGKTFSATGWKVGWVLGPDHIMKHLRTVHQNSVFHCPTQSQAAVAESFEREQLLFRQPSSYFVQFPQAMQRCRDHMIRSLQSVGLKPIIPQGSYFLITDISDFKRKMPDLPGAVDEPYDRRFVKWMIKNKGLVAIPVSIFYSVPHQKHFDHYIRFCFVKDEATLQAMDEKLRKWKVEL 422
               SCOP domains d3fvxa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh....hhhhhhhhhhhh...ee..........hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...hhhhheeeehhhhhhhhhhhhhhh....eeeeee....hhhhhhhhh..eeeeee............hhhhh..hhhhhhh.....eeeeeee..........hhhhhhhhhhhhhhhh.eeeee..............hhhhh..hhh.eeeeeehhhhhhhhhhh.eeee.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eee......eeeeehhhhhhhh.........hhhhhhhhhhhhhhhee.ee.hhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5b      -------------------------------------------------Exon 1.9b  PDB: A:68-117 UniProt: 68-117          Exon 1.10  PDB: A:118-146    Exon 1.11c  PDB: A:147-189 UniProt: 147-189Exon 1.12  PDB: A:190-230                -------------------------Exon 1.14  PDB: A:256-285     Exon 1.15a  PDB: A:286-348 UniProt: 286-348                    --------------------------Exon 1.17  PDB: A:375-403    Exon 1.18d          Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.6  PDB: A:18-67 UniProt: 18-67             ------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.13c  PDB: A:230-255--------------------------------------------------------------------------------------------Exon 1.16a  PDB: A:348-374 ------------------------------------------------ Transcript 1 (2)
                 3fvx A   4 QLQARRLDGIDYNPWVEFVKLASEHDVVNLGQGFPDFPPPDFAVEAFQHAVSGDFMLNQYTKTFGYPPLTKILASFFGELLGQEIDPLRNVLVTVGGYGALFTAFQALVDEGDEVIIIEPFFDCYEPMTMMAGGRPVFVSLKPGPIQNGELGSSSNWQLDPMELAGKFTSRTKALVLNTPNNPLGKVFSREELELVASLCQQHDVVCITDEVYQWMVYDGHQHISIASLPGMWERTLTIGSAGkTFSATGWKVGWVLGPDHIMKHLRTVHQNSVFHCPTQSQAAVAESFEREQLLFRQPSSYFVQFPQAMQRCRDHMIRSLQSVGLKPIIPQGSYFLITDISDFKRKMPDLPGAVDEPYDRRFVKWMIKNKGLVAIPVSIFYSVPHQKHFDHYIRFCFVKDEATLQAMDEKLRKWKVEL 422
                                    13        23        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       393       403       413         
                                                                                                                                                                                                                                                                             247-LLP

Chain B from PDB  Type:PROTEIN  Length:419
 aligned with KAT1_HUMAN | Q16773 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:419
                                    13        23        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       393       403       413         
           KAT1_HUMAN     4 QLQARRLDGIDYNPWVEFVKLASEHDVVNLGQGFPDFPPPDFAVEAFQHAVSGDFMLNQYTKTFGYPPLTKILASFFGELLGQEIDPLRNVLVTVGGYGALFTAFQALVDEGDEVIIIEPFFDCYEPMTMMAGGRPVFVSLKPGPIQNGELGSSSNWQLDPMELAGKFTSRTKALVLNTPNNPLGKVFSREELELVASLCQQHDVVCITDEVYQWMVYDGHQHISIASLPGMWERTLTIGSAGKTFSATGWKVGWVLGPDHIMKHLRTVHQNSVFHCPTQSQAAVAESFEREQLLFRQPSSYFVQFPQAMQRCRDHMIRSLQSVGLKPIIPQGSYFLITDISDFKRKMPDLPGAVDEPYDRRFVKWMIKNKGLVAIPVSIFYSVPHQKHFDHYIRFCFVKDEATLQAMDEKLRKWKVEL 422
               SCOP domains d3fvxb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh....hhhhhhhhhhhh...ee..........hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh........eeeehhhhhhhhhhhhhhh....eeeeee....hhhhhhhhh..eeeeee...........ee.hhh..hhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhhhh.eeeee..............hhhhh..hhh.eeeeeehhhhh.hhhhh.eeee.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeee.....eeeeehhhhhhhh.........hhhhhhhhhhhhhhhee.ee.hhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5b      -------------------------------------------------Exon 1.9b  PDB: B:68-117 UniProt: 68-117          Exon 1.10  PDB: B:118-146    Exon 1.11c  PDB: B:147-189 UniProt: 147-189Exon 1.12  PDB: B:190-230                -------------------------Exon 1.14  PDB: B:256-285     Exon 1.15a  PDB: B:286-348 UniProt: 286-348                    --------------------------Exon 1.17  PDB: B:375-403    Exon 1.18d          Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.6  PDB: B:18-67 UniProt: 18-67             ------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.13c  PDB: B:230-255--------------------------------------------------------------------------------------------Exon 1.16a  PDB: B:348-374 ------------------------------------------------ Transcript 1 (2)
                 3fvx B   4 QLQARRLDGIDYNPWVEFVKLASEHDVVNLGQGFPDFPPPDFAVEAFQHAVSGDFMLNQYTKTFGYPPLTKILASFFGELLGQEIDPLRNVLVTVGGYGALFTAFQALVDEGDEVIIIEPFFDCYEPMTMMAGGRPVFVSLKPGPIQNGELGSSSNWQLDPMELAGKFTSRTKALVLNTPNNPLGKVFSREELELVASLCQQHDVVCITDEVYQWMVYDGHQHISIASLPGMWERTLTIGSAGkTFSATGWKVGWVLGPDHIMKHLRTVHQNSVFHCPTQSQAAVAESFEREQLLFRQPSSYFVQFPQAMQRCRDHMIRSLQSVGLKPIIPQGSYFLITDISDFKRKMPDLPGAVDEPYDRRFVKWMIKNKGLVAIPVSIFYSVPHQKHFDHYIRFCFVKDEATLQAMDEKLRKWKVEL 422
                                    13        23        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       393       403       413         
                                                                                                                                                                                                                                                                             247-LLP

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: PLP-dependent transferase-like (627)

Superfamily: PLP-dependent transferases (625)

Family: AAT-like (184)

Protein domain: automated matches (16)

Human (Homo sapiens) [TaxId: 9606] (3)

1a	d3fvxa_	A:
1b	d3fvxb_	B:

(no "CATH Domain" information available for 3FVX)

(no "Pfam Domain" information available for 3FVX)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (KAT1_HUMAN | Q16773)

molecular function
	GO:0047945	L-glutamine:pyruvate aminotransferase activity	Catalysis of the reaction: L-glutamine + pyruvate = 2-oxoglutaramate + L-alanine.
	GO:0047312	L-phenylalanine:pyruvate aminotransferase activity	Catalysis of the reaction: pyruvate + L-phenylalanine = phenylpyruvate + L-alanine.
	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:0047804	cysteine-S-conjugate beta-lyase activity	Catalysis of the reaction: RS-CH2-CH(NH3+)COO- = RSH + NH3 + pyruvate.
	GO:0047316	glutamine-phenylpyruvate transaminase activity	Catalysis of the reaction: keto-phenylpyruvate + L-glutamine = 2-oxoglutaramate + L-phenylalanine.
	GO:0016212	kynurenine-oxoglutarate transaminase activity	Catalysis of the reaction: L-kynurenine + 2-oxoglutarate = 4-(2-aminophenyl)-2,4-dioxobutanoate + L-glutamate.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	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:0097053	L-kynurenine catabolic process	The chemical reactions and pathways resulting in the breakdown of L-kynurenine, the L-enantiomer of the amino acid kynurenine (3-(2-aminobenzoyl)-alanine).
	GO:0006559	L-phenylalanine catabolic process	The chemical reactions and pathways resulting in the breakdown of phenylalanine, 2-amino-3-phenylpropanoic acid.
	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: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:0006575	cellular modified amino acid metabolic process	The chemical reactions and pathways involving compounds derived from amino acids, organic acids containing one or more amino substituents.
	GO:0070189	kynurenine metabolic process	The chemical reactions and pathways involving kynurenine, the amino acid 3-(2-aminobenzoyl)-alanine.
	GO:0006569	tryptophan catabolic process	The chemical reactions and pathways resulting in the breakdown of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid.
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.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.

Asymmetric/Biological Unit
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		Asn A:185 - Pro A:186	[ RasMol ]
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		Glu A:122 - Pro A:123	[ RasMol ]
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		Thr A:182 - Pro A:183	[ RasMol ]
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	3fvx
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	KAT1_HUMAN \| Q16773
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	2.6.1.64
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	2.6.1.7
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	KAT1_HUMAN \| Q16773	:	1w7l 1w7m 1w7n 3fvs 3fvu 4wlh 4wlj 4wp0

(no "Related Entries Specified in the PDB File" available for 3FVX)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (12, 24)

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