2JJH - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   E243 MUTANT OF M. TUBERCULOSIS RV3290C

Authors :   S. M. Tripathi, R. Ramachandran

Date :   04 Apr 08 (Deposition) - 30 Jun 09 (Release) - 25 Jan 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Rv3290C, Transferase, E243A Mutant, M. Tuberculosis, Lysine Epsilon Aminotransferase, Aminotransferase, Pyridoxal Phosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. M. Tripathi, A. Agarwal, R. Ramachandran
Mutational Analysis Of Mycobacterium Tuberculosis Lysine Epsilon-Aminotransferase And Inhibitor Co-Crystal Structures, Reveals Distinct Binding Modes.
Biochem. Biophys. Res. Commun. V. 463 154 2015
PubMed-ID: 26003725 | Reference-DOI: 10.1016/J.BBRC.2015.05.055

Molecule 1 - L-LYSINE EPSILON AMINOTRANSFERASE
	Chains	:	A
	EC Number	:	2.6.1.36
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector	:	PET
	Mutation	:	YES
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Synonym	:	L-LYSINE AMINOTRANSFERASE, LYSINE 6-AMINOTRANSFERASE, LYSINE EPSILON AMINOTRANSFERASE

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	AKG	1	Ligand/Ion	2-OXOGLUTARIC ACID
2	PLP	1	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	AKG	2	Ligand/Ion	2-OXOGLUTARIC ACID
2	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:128 , ALA A:129 , PHE A:167 , HIS A:168 , GLU A:238 , ASP A:271 , VAL A:273 , GLN A:274 , LYS A:300 , SER A:329 , THR A:330 , AKG A:1451 , HOH A:2021 , HOH A:2060 , HOH A:2061	BINDING SITE FOR RESIDUE PLP A1450
2	AC2	SOFTWARE	PHE A:167 , ARG A:170 , ILE A:184 , ALA A:243 , GLN A:274 , LYS A:300 , ASN A:328 , ARG A:422 , PLP A:1450 , HOH A:2062 , HOH A:2063	BINDING SITE FOR RESIDUE AKG A1451

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

(no "Cis Peptide Bond" information available for 2JJH)

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRANSFER_CLASS_3	PS00600	Aminotransferases class-III pyridoxal-phosphate attachment site.	LAT_MYCTU	268-305	1	A:268-305
1	AA_TRANSFER_CLASS_3	PS00600		LAT_MYCTO	268-305	1	A:268-305

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRANSFER_CLASS_3	PS00600	Aminotransferases class-III pyridoxal-phosphate attachment site.	LAT_MYCTU	268-305	2	A:268-305
1	AA_TRANSFER_CLASS_3	PS00600		LAT_MYCTO	268-305	2	A:268-305

(no "Exon" information available for 2JJH)

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:435
 aligned with LAT_MYCTO | P9WQ76 from UniProtKB/Swiss-Prot  Length:449

    Alignment length:435
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444     
            LAT_MYCTO    15 TTPDRVHEVLGRSMLVDGLDIVLDLTRSGGSYLVDAITGRRYLDMFTFVASSALGMNPPALVDDREFHAELMQAALNKPSNSDVYSVAMARFVETFARVLGDPALPHLFFVEGGALAVENALKAAFDWKSRHNQAHGIDPALGTQVLHLRGAFHGRSGYTLSLTNTKPTITARFPKFDWPRIDAPYMRPGLDEPAMAALEAEALRQARAAFETRPHDIACFVAEPIQGEGGDRHFRPEFFAAMRELCDEFDALLIFDEVQTGCGLTGTAWAYQQLDVAPDIVAFGKKTQVCGVMAGRRVDEVADNVFAVPSRLNSTWGGNLTDMVRARRILEVIEAEGLFERAVQHGKYLRARLDELAADFPAVVLDPRGRGLMCAFSLPTTADRDELIRQLWQRAVIVLPAGADTVRFRPPLTVSTAEIDAAIAAVRSALPVVT 449
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------Aminotran_3-2jjhA01 A:38-395                                                                                                                                                                                                                                                                                                                                          ------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh...................eee......eeee.hhhhhh......hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhhhhhh.........eeeee.........hhhhh...hhhhhh........ee.........hhhhhhhhhhhhhhhhhhhhhhh...eeeeee..ee.....ee.hhhhhhhhhhhhhhh..eeeee.............hhhhhh....eeeehhhhh.eeeee.hhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee..eeeee..hhhhhhhhhhhhhhh.ee.eee...eeee......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_3  PDB: A:268-305   ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jjh A  15 TTPDRVHEVLGRSMLVDGLDIVLDLTRSGGSYLVDAITGRRYLDMFTFVASSALGMNPPALVDDREFHAELMQAALNKPSNSDVYSVAMARFVETFARVLGDPALPHLFFVEGGALAVENALKAAFDWKSRHNQAHGIDPALGTQVLHLRGAFHGRSGYTLSLTNTKPTITARFPKFDWPRIDAPYMRPGLDEPAMAALEAEALRQARAAFETRPHDIACFVAEPIQGAGGDRHFRPEFFAAMRELCDEFDALLIFDEVQTGCGLTGTAWAYQQLDVAPDIVAFGKKTQVCGVMAGRRVDEVADNVFAVPSRLNSTWGGNLTDMVRARRILEVIEAEGLFERAVQHGKYLRARLDELAADFPAVVLDPRGRGLMCAFSLPTTADRDELIRQLWQRAVIVLPAGADTVRFRPPLTVSTAEIDAAIAAVRSALPVVT 449
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444

Chain A from PDB  Type:PROTEIN  Length:435
 aligned with LAT_MYCTU | P9WQ77 from UniProtKB/Swiss-Prot  Length:449

    Alignment length:435
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444     
            LAT_MYCTU    15 TTPDRVHEVLGRSMLVDGLDIVLDLTRSGGSYLVDAITGRRYLDMFTFVASSALGMNPPALVDDREFHAELMQAALNKPSNSDVYSVAMARFVETFARVLGDPALPHLFFVEGGALAVENALKAAFDWKSRHNQAHGIDPALGTQVLHLRGAFHGRSGYTLSLTNTKPTITARFPKFDWPRIDAPYMRPGLDEPAMAALEAEALRQARAAFETRPHDIACFVAEPIQGEGGDRHFRPEFFAAMRELCDEFDALLIFDEVQTGCGLTGTAWAYQQLDVAPDIVAFGKKTQVCGVMAGRRVDEVADNVFAVPSRLNSTWGGNLTDMVRARRILEVIEAEGLFERAVQHGKYLRARLDELAADFPAVVLDPRGRGLMCAFSLPTTADRDELIRQLWQRAVIVLPAGADTVRFRPPLTVSTAEIDAAIAAVRSALPVVT 449
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------Aminotran_3-2jjhA01 A:38-395                                                                                                                                                                                                                                                                                                                                          ------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh...................eee......eeee.hhhhhh......hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhhhhhh.........eeeee.........hhhhh...hhhhhh........ee.........hhhhhhhhhhhhhhhhhhhhhhh...eeeeee..ee.....ee.hhhhhhhhhhhhhhh..eeeee.............hhhhhh....eeeehhhhh.eeeee.hhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee..eeeee..hhhhhhhhhhhhhhh.ee.eee...eeee......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_3  PDB: A:268-305   ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jjh A  15 TTPDRVHEVLGRSMLVDGLDIVLDLTRSGGSYLVDAITGRRYLDMFTFVASSALGMNPPALVDDREFHAELMQAALNKPSNSDVYSVAMARFVETFARVLGDPALPHLFFVEGGALAVENALKAAFDWKSRHNQAHGIDPALGTQVLHLRGAFHGRSGYTLSLTNTKPTITARFPKFDWPRIDAPYMRPGLDEPAMAALEAEALRQARAAFETRPHDIACFVAEPIQGAGGDRHFRPEFFAAMRELCDEFDALLIFDEVQTGCGLTGTAWAYQQLDVAPDIVAFGKKTQVCGVMAGRRVDEVADNVFAVPSRLNSTWGGNLTDMVRARRILEVIEAEGLFERAVQHGKYLRARLDELAADFPAVVLDPRGRGLMCAFSLPTTADRDELIRQLWQRAVIVLPAGADTVRFRPPLTVSTAEIDAAIAAVRSALPVVT 449
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444

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 '\|'

(no "SCOP Domain" information available for 2JJH)

(no "CATH Domain" information available for 2JJH)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PLP_aminotran (240)

Family: Aminotran_3 (44)

Mycobacterium tuberculosis (5)

Aminotran_3-2jjhA01

A:38-395

Asymmetric Unit(hide GO term definitions)

Chain A (LAT_MYCTU | P9WQ77)

molecular function
	GO:0003867	4-aminobutyrate transaminase activity	Catalysis of the reaction: 4-aminobutanoate + amino group acceptor = succinate semialdehyde + amino acid.
	GO:0045484	L-lysine 6-transaminase activity	Catalysis of the reaction: 2-oxoglutarate + L-lysine = L-glutamate + allysine.
	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: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:0017000	antibiotic biosynthetic process	The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
	GO:0009450	gamma-aminobutyric acid catabolic process	The chemical reactions and pathways resulting in the breakdown of gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms.

Chain A (LAT_MYCTO | P9WQ76)

molecular function
	GO:0045484	L-lysine 6-transaminase activity	Catalysis of the reaction: 2-oxoglutarate + L-lysine = L-glutamate + allysine.
	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: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:0017000	antibiotic biosynthetic process	The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Sites
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		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2jjh)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Access by PDB/NDB ID
	2jjh
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
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	LAT_MYCTO \| P9WQ76
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	LAT_MYCTU \| P9WQ77
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.6.1.36
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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	(no 'MIM ID' available)
		Disease Information	:	OMIM

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		Age Related Information	:	GenAge

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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Access by UniProt ID/Accession number
	LAT_MYCTO \| P9WQ76
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	LAT_MYCTU \| P9WQ77
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	LAT_MYCTO \| P9WQ76	:	2cin 2cjd 2cjg 2cjh 2jje 2jjf 2jjg
	LAT_MYCTU \| P9WQ77	:	2cin 2cjd 2cjg 2cjh 2jje 2jjf 2jjg

2jje	CRYSTAL STRUCTURE OF T330S MUTANT OF RV3290C FROM M. TUBERCULOSIS
2jjf	N328A MUTANT OF M. TUBERCULOSIS RV3290C
2jjg	CRYSTAL STRUCTURE OF THE M. TUBERCULOSIS LYSINE-EPSILON AMINOTRANSFERASE (RV3290C) COMPLEXED TO AN INHIBITOR

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (9, 15)

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