2EJ3 - JenaLib

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Title :   CRYSTAL STRUCTURE OF T.TH.HB8 BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE COMPLEXED WITH GABAPENTIN

Authors :   M. Goto

Date :   14 Mar 07 (Deposition) - 18 Mar 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Plp-Dependent Enzyme, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Goto
Crystal Structure Of T. Th. Hb8 Branched-Chain Amino Acid Aminotransferase Complexed With Gabapentin
To Be Published
PubMed: search

Molecule 1 - BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE
	Chains	:	A, B, C
	EC Number	:	2.6.1.42
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8
	Synonym	:	ILVE

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (2x)	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 11)

No.	Name	Count	Type	Full Name
1	GBN	3	Ligand/Ion	[1-(AMINOMETHYL)CYCLOHEXYL]ACETIC ACID
2	MPD	5	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	PLP	3	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Biological Unit 1 (3, 22)

No.	Name	Count	Type	Full Name
1	GBN	6	Ligand/Ion	[1-(AMINOMETHYL)CYCLOHEXYL]ACETIC ACID
2	MPD	10	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	PLP	6	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:59 , ARG A:148 , LYS A:159 , TYR A:164 , GLU A:193 , GLY A:196 , LEU A:216 , GLY A:218 , ILE A:219 , THR A:220 , GLY A:255 , THR A:256 , HOH A:2443 , HOH A:2446	BINDING SITE FOR RESIDUE PLP A 413
02	AC2	SOFTWARE	ARG B:59 , LYS B:159 , TYR B:164 , GLU B:193 , GLY B:196 , LEU B:216 , GLY B:218 , ILE B:219 , THR B:220 , GLY B:255 , THR B:256 , HOH B:928 , HOH B:958	BINDING SITE FOR RESIDUE PLP B 913
03	AC3	SOFTWARE	ARG C:59 , ARG C:148 , LYS C:159 , TYR C:164 , GLU C:193 , GLY C:196 , LEU C:216 , GLY C:218 , ILE C:219 , THR C:220 , GLY C:255 , THR C:256 , HOH C:1425 , HOH C:1447	BINDING SITE FOR RESIDUE PLP C 1413
04	AC4	SOFTWARE	ARG A:97 , GLY A:196 , GLU A:197 , GLY A:255 , THR A:256 , ALA A:257 , ALA A:258 , HOH A:2539 , HOH A:2554 , TYR C:31	BINDING SITE FOR RESIDUE GBN A 2414
05	AC5	SOFTWARE	ARG B:97 , GLY B:196 , GLU B:197 , GLY B:255 , THR B:256 , ALA B:257 , ALA B:258 , HOH B:983 , HOH B:984 , HOH B:1091	BINDING SITE FOR RESIDUE GBN B 914
06	AC6	SOFTWARE	TYR A:31 , ARG C:97 , GLY C:196 , GLU C:197 , GLY C:255 , THR C:256 , ALA C:257 , ALA C:258 , HOH C:1457 , HOH C:1469 , HOH C:1572	BINDING SITE FOR RESIDUE GBN C 1414
07	AC7	SOFTWARE	ASP A:230 , GLU A:297 , HOH A:2472 , HOH A:2502 , GLU C:289 , ARG C:294 , ARG C:295	BINDING SITE FOR RESIDUE MPD A 2416
08	AC8	SOFTWARE	ARG A:52 , GLU A:55 , GLU A:217 , ILE A:219 , ASP A:222 , HOH A:2524 , HOH A:2532 , ARG C:203 , ASP C:204	BINDING SITE FOR RESIDUE MPD A 1417
09	AC9	SOFTWARE	LEU B:107 , TRP B:124 , TRP B:126	BINDING SITE FOR RESIDUE MPD B 915
10	BC1	SOFTWARE	ARG A:203 , ASP A:204 , ARG B:52 , GLU B:55 , GLU B:217 , GLY B:218 , ASP B:222 , HOH B:967	BINDING SITE FOR RESIDUE MPD B 917
11	BC2	SOFTWARE	ARG B:203 , ASP B:204 , ARG C:52 , GLU C:55 , GLU C:217 , ASP C:222 , HOH C:1521 , HOH C:1569	BINDING SITE FOR RESIDUE MPD C 1416

(no "SS Bond" information available for 2EJ3)

Asymmetric Unit

No.	Residues
1	Asn A:115	-	Pro A:116
2	Asn B:115	-	Pro B:116
3	Asn C:115	-	Pro C:116

(no "SAP(SNP)/Variant" information available for 2EJ3)

(no "PROSITE Motif" information available for 2EJ3)

(no "Exon" information available for 2EJ3)

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
	(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:297
 aligned with Q5SM19_THET8 | Q5SM19 from UniProtKB/TrEMBL  Length:308

    Alignment length:305
                                    11        21        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     
         Q5SM19_THET8     2 QIKAGLIWMNGAFVPQEEAKTSVLSHALHYGTSVFEGIRAYETAKGPAIFRLKEHVKRFYNSAKVLRMEIPFAPEELEEAIKEVVRRNGYRSCYIRPLAWMGAKALGVNPLPNNPAEVMVAAWEWGAYLGEEAVRKGARLITSSWARFPANVMPGKAKVGGNYVNSALAKMEAVAAGADEALLLDEEGYVAEGSGENLFFVRDGVIYALEHSVNLEGITRDSVIRIAKDLGYEVQVVRATRDQLYMADEVFMTGTAAEVTPVSMIDWRPIGKGTAGPVALRLREVYLEAVTGRRPEYEGWLTYVN 306
               SCOP domains d2ej3a_ A: automated matches                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ---2ej3A01 A:5-126  [code=3.30.470.10, no name defined]                                                                      --------2ej3A02 A:135-294 D-amino Acid Aminotransferase, subunit A, domain 2                                                                                            ------------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeehhhhh.....hhhhhhh.eee..eeeeee..eeeeehhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh....eeeeeeee.........hhhhh..eeeeeeee.--------....eeeee................hhhhhhhhhhhhhhhhhh...eeeee.....eeee...eeeeee..eeeee.......hhhhhhhhhhhhhh...eeee..hhhhhhh..eeeeee...eeeeeeee..ee......hhhhhhhhhhhhhhhh..hhhhhh.eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ej3 A   2 QIKAGLIWMNGAFVPQEEAKTSVLSHALHYGTSVFEGIRAYETAKGPAIFRLKEHVKRFYNSAKVLRMEIPFAPEELEEAIKEVVRRNGYRSCYIRPLAWMGAKALGVNPLPNNPAEVMVAAWEW--------VRKGARLITSSWARFPANVMPGKAKVGGNYVNSALAKMEAVAAGADEALLLDEEGYVAEGSGENLFFVRDGVIYALEHSVNLEGITRDSVIRIAKDLGYEVQVVRATRDQLYMADEVFMTGTAAEVTPVSMIDWRPIGKGTAGPVALRLREVYLEAVTGRRPEYEGWLTYVN 306
                                    11        21        31        41        51        61        71        81        91       101       111       121    |    -   |   141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301     
                                                                                                                                                      126      135

Chain B from PDB  Type:PROTEIN  Length:304
 aligned with Q5SM19_THET8 | Q5SM19 from UniProtKB/TrEMBL  Length:308

    Alignment length:304
                                    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    
         Q5SM19_THET8     3 IKAGLIWMNGAFVPQEEAKTSVLSHALHYGTSVFEGIRAYETAKGPAIFRLKEHVKRFYNSAKVLRMEIPFAPEELEEAIKEVVRRNGYRSCYIRPLAWMGAKALGVNPLPNNPAEVMVAAWEWGAYLGEEAVRKGARLITSSWARFPANVMPGKAKVGGNYVNSALAKMEAVAAGADEALLLDEEGYVAEGSGENLFFVRDGVIYALEHSVNLEGITRDSVIRIAKDLGYEVQVVRATRDQLYMADEVFMTGTAAEVTPVSMIDWRPIGKGTAGPVALRLREVYLEAVTGRRPEYEGWLTYVN 306
               SCOP domains d2ej3b_ B: automated matches                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains --2ej3B01 B:5-130  [code=3.30.470.10, no name defined]                                                                          2ej3B02 B:131-294 D-amino Acid Aminotransferase, subunit A, domain 2                                                                                                ------------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeee.hhh.....hhhhhhh.eee..eeeeee..eeeeehhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh....eeeeeeee.........hhhhh..eeeeeee......hhhhhhhheeeee................hhhhhhhhhhhhhhhhhhh..eeeee.....eeee...eeeeee..eeeee.......hhhhhhhhhhhhhh..eeeee..hhhhhhh..eeeeee...eeeeeeee..ee......hhhhhhhhhhhhhhhh..hhhhhh.eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ej3 B   3 IKAGLIWMNGAFVPQEEAKTSVLSHALHYGTSVFEGIRAYETAKGPAIFRLKEHVKRFYNSAKVLRMEIPFAPEELEEAIKEVVRRNGYRSCYIRPLAWMGAKALGVNPLPNNPAEVMVAAWEWGAYLGEEAVRKGARLITSSWARFPANVMPGKAKVGGNYVNSALAKMEAVAAGADEALLLDEEGYVAEGSGENLFFVRDGVIYALEHSVNLEGITRDSVIRIAKDLGYEVQVVRATRDQLYMADEVFMTGTAAEVTPVSMIDWRPIGKGTAGPVALRLREVYLEAVTGRRPEYEGWLTYVN 306
                                    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

Chain C from PDB  Type:PROTEIN  Length:294
 aligned with Q5SM19_THET8 | Q5SM19 from UniProtKB/TrEMBL  Length:308

    Alignment length:304
                                    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    
         Q5SM19_THET8     3 IKAGLIWMNGAFVPQEEAKTSVLSHALHYGTSVFEGIRAYETAKGPAIFRLKEHVKRFYNSAKVLRMEIPFAPEELEEAIKEVVRRNGYRSCYIRPLAWMGAKALGVNPLPNNPAEVMVAAWEWGAYLGEEAVRKGARLITSSWARFPANVMPGKAKVGGNYVNSALAKMEAVAAGADEALLLDEEGYVAEGSGENLFFVRDGVIYALEHSVNLEGITRDSVIRIAKDLGYEVQVVRATRDQLYMADEVFMTGTAAEVTPVSMIDWRPIGKGTAGPVALRLREVYLEAVTGRRPEYEGWLTYVN 306
               SCOP domains d2ej3c_ C: automated matches                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains --2ej3C01 C:5-126  [code=3.30.470.10, no name defined]                                                                      ----------2ej3C02 C:137-294 D-amino Acid Aminotransferase, subunit A, domain 2                                                                                          ------------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eeehhhhh.....hhhhhhh.eee..eeeeee..eeeeehhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.....eeeeeeee.........hhhhh..eeeeeeee.----------..eeeee................hhhhhhhhhhhhhhhhhh...eeeee.....eeee...eeeeee..eeeee.......hhhhhhhhhhhhhhh.eeeee..hhhhhhh..eeeeee...eeeeeeee..ee......hhhhhhhhhhhhhhhh..hhhhhh.eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ej3 C   3 IKAGLIWMNGAFVPQEEAKTSVLSHALHYGTSVFEGIRAYETAKGPAIFRLKEHVKRFYNSAKVLRMEIPFAPEELEEAIKEVVRRNGYRSCYIRPLAWMGAKALGVNPLPNNPAEVMVAAWEW----------KGARLITSSWARFPANVMPGKAKVGGNYVNSALAKMEAVAAGADEALLLDEEGYVAEGSGENLFFVRDGVIYALEHSVNLEGITRDSVIRIAKDLGYEVQVVRATRDQLYMADEVFMTGTAAEVTPVSMIDWRPIGKGTAGPVALRLREVYLEAVTGRRPEYEGWLTYVN 306
                                    12        22        32        42        52        62        72        82        92       102       112       122   |     -    |  142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302    
                                                                                                                                                     126        137

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Multi-domain proteins (alpha and beta) (2421)

Fold: D-aminoacid aminotransferase-like PLP-dependent enzymes (46)

Superfamily: D-aminoacid aminotransferase-like PLP-dependent enzymes (46)

Family: automated matches (13)

Protein domain: automated matches (13)

Thermus thermophilus HB8 [TaxId: 300852] (4)

1a	d2ej3a_	A:
1b	d2ej3b_	B:
1c	d2ej3c_	C:

(no "Pfam Domain" information available for 2EJ3)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (Q5SM19_THET8 | Q5SM19)

molecular function
	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: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: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.

Asymmetric Unit
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	Cis Peptide Bonds
		Asn A:115 - Pro A:116	[ RasMol ]
		Asn B:115 - Pro B:116	[ RasMol ]
		Asn C:115 - Pro C:116	[ RasMol ]

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	2ej3
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	2.6.1.42
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	Q5SM19_THET8 \| Q5SM19	:	1wrv 2eiy 2ej0 2ej2

Description

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Ligands, Modified Residues, Ions (3, 11)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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