1W66 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF A LIPOATE-PROTEIN LIGASE B FROM MYCOBACTERIUM TUBERCULOSIS

Authors :   Q. Ma, M. Wilmanns

Date :   13 Aug 04 (Deposition) - 08 Dec 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.08

Chains :   Asym./Biol. Unit : A

Keywords :   Lipoate-Protein Ligase B, Lipoyltransferase, Lipoic Acid, Acyltransferase, Transferase, Mycobacterium Tuberculosis Structural Proteomics Project, Xmtb, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Q. Ma, X. Zhao, A. N. Eddine, A. Geerlof, X. Li, J. E. Cronan, S. H. Kaufmann, M. Wilmanns
The Mycobacterium Tuberculosis Lipb Enzyme Functions As A Cysteine/Lysine Dyad Acyltransferase.
Proc. Natl. Acad. Sci. Usa V. 103 8662 2006
PubMed-ID: 16735476 | Reference-DOI: 10.1073/PNAS.0510436103

Molecule 1 - LIPOYLTRANSFERASE
	Chains	:	A
	EC Number	:	2.3.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETM11
	Expression System Strain	:	ROSETTA(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	83332
	Strain	:	H37RV
	Synonym	:	LIPOATE-PROTEIN LIGASE B, LIPOYL-[ACYL-CARRIER PROTEIN]-PROTEIN-N-LIPOYLTRANSFERASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	DKA	1	Ligand/Ion	DECANOIC ACID

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:76 , GLY A:78 , LYS A:79 , TYR A:91 , GLY A:147 , GLY A:158 , PHE A:159 , CYS A:176 , HOH A:2134 , HOH A:2246 , HOH A:2348 , HOH A:2349	BINDING SITE FOR RESIDUE DKA A 301

(no "SS Bond" information available for 1W66)

Asymmetric/Biological Unit

No.	Residues
1	Glu A:98	-	Pro A:99
2	Arg A:138	-	Pro A:139

(no "SAP(SNP)/Variant" information available for 1W66)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BPL_LPL_CATALYTIC	PS51733	Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile.	LIPB_MYCTO	38-215	1	A:38-215
1	BPL_LPL_CATALYTIC	PS51733		LIPB_MYCTU	38-215	1	A:38-215
2	LIPB	PS01313	Lipoate-protein ligase B signature.	LIPB_MYCTO	76-91	1	A:76-91
2	LIPB	PS01313	Lipoate-protein ligase B signature.	LIPB_MYCTU	76-91	1	A:76-91

(no "Exon" information available for 1W66)

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:218
 aligned with LIPB_MYCTO | P9WK82 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:218
                              1                                                                                                                                                                                                                       
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208        
           LIPB_MYCTO     - --MTGSIRSKLSAIDVRQLGTVDYRTAWQLQRELADARVAGGADTLLLLEHPAVYTAGRRTETHERPIDGTPVVDTDRGGKITWHGPGQLVGYPIIGLAEPLDVVNYVRRLEESLIQVCADLGLHAGRVDGRSGVWLPGRPARKVAAIGVRVSRATTLHGFALNCDCDLAAFTAIVPCGISDAAVTSLSAELGRTVTVDEVRATVAAAVCAALDGVLP 216
               SCOP domains --d1w66a1 A:1-216 Lipoyltransferase LipB                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------BPL_LplA_LipB-1w66A01 A:56-166                                                                                 -------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.hhhhhhhhhhhhhhhhhh....eeeeee...eeee....hhhhh.......ee......eeee...eeeeeee.......hhhhhhhhhhhhhhhhhhhh....eee..eeeeee.....eeeeeeeeeee..eeeeeeeee....hhhhhhhhhhhh...ee.hhhhhhh...hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------BPL_LPL_CATALYTIC  PDB: A:38-215 UniProt: 38-215                                                                                                                                  - PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) -----------------------------------------------------------------------------LIPB            ----------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w66 A  -1 GAMAGSIRSKLSAIDVRQLGTVDYRTAWQLQRELADARVAGGADTLLLLEHPAVYTAGRRTETHERPIDGTPVVDTDRGGKITWHGPGQLVGYPIIGLAEPLDVVNYVRRLEESLIQVCADLGLHAGRVDGRSGVWLPGRPARKVAAIGVRVSRATTLHGFALNCDCDLAAFTAIVPCGISDAAVTSLSAELGRTVTVDEVRATVAAAVCAALDGVLP 216
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208

Chain A from PDB  Type:PROTEIN  Length:218
 aligned with LIPB_MYCTU | P9WK83 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:218
                              1                                                                                                                                                                                                                       
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208        
           LIPB_MYCTU     - --MTGSIRSKLSAIDVRQLGTVDYRTAWQLQRELADARVAGGADTLLLLEHPAVYTAGRRTETHERPIDGTPVVDTDRGGKITWHGPGQLVGYPIIGLAEPLDVVNYVRRLEESLIQVCADLGLHAGRVDGRSGVWLPGRPARKVAAIGVRVSRATTLHGFALNCDCDLAAFTAIVPCGISDAAVTSLSAELGRTVTVDEVRATVAAAVCAALDGVLP 216
               SCOP domains --d1w66a1 A:1-216 Lipoyltransferase LipB                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------BPL_LplA_LipB-1w66A01 A:56-166                                                                                 -------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.hhhhhhhhhhhhhhhhhh....eeeeee...eeee....hhhhh.......ee......eeee...eeeeeee.......hhhhhhhhhhhhhhhhhhhh....eee..eeeeee.....eeeeeeeeeee..eeeeeeeee....hhhhhhhhhhhh...ee.hhhhhhh...hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------BPL_LPL_CATALYTIC  PDB: A:38-215 UniProt: 38-215                                                                                                                                  - PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -----------------------------------------------------------------------------LIPB            ----------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w66 A  -1 GAMAGSIRSKLSAIDVRQLGTVDYRTAWQLQRELADARVAGGADTLLLLEHPAVYTAGRRTETHERPIDGTPVVDTDRGGKITWHGPGQLVGYPIIGLAEPLDVVNYVRRLEESLIQVCADLGLHAGRVDGRSGVWLPGRPARKVAAIGVRVSRATTLHGFALNCDCDLAAFTAIVPCGISDAAVTSLSAELGRTVTVDEVRATVAAAVCAALDGVLP 216
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Class II aaRS and biotin synthetases (165)

Superfamily: Class II aaRS and biotin synthetases (165)

Family: LplA-like (14)

Protein domain: Lipoyltransferase LipB (1)

Mycobacterium tuberculosis [TaxId: 1773] (1)

d1w66a1

A:1-216

(no "CATH Domain" information available for 1W66)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: tRNA_synt_II (64)

Family: BPL_LplA_LipB (10)

Mycobacterium tuberculosis (1)

BPL_LplA_LipB-1w66A01

A:56-166

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (LIPB_MYCTO | P9WK82)

molecular function
	GO:0033819	lipoyl(octanoyl) transferase activity	Catalysis of the reaction: octanoyl-[acyl-carrier protein] + protein = protein N6-(octanoyl)lysine + acyl-carrier protein.
	GO:0016415	octanoyltransferase activity	Catalysis of the transfer of an octanoyl (CH3-[CH2]6-CO-) group to an acceptor molecule.
	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.
	GO:0016746	transferase activity, transferring acyl groups	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
	GO:0006464	cellular protein modification process	The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
	GO:0009107	lipoate biosynthetic process	The chemical reactions and pathways resulting in the formation of lipoate, 1,2-dithiolane-3-pentanoate, the anion derived from lipoic acid.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A (LIPB_MYCTU | P9WK83)

molecular function
	GO:0033819	lipoyl(octanoyl) transferase activity	Catalysis of the reaction: octanoyl-[acyl-carrier protein] + protein = protein N6-(octanoyl)lysine + acyl-carrier protein.
	GO:0016415	octanoyltransferase activity	Catalysis of the transfer of an octanoyl (CH3-[CH2]6-CO-) group to an acceptor molecule.
	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.
	GO:0016746	transferase activity, transferring acyl groups	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
	GO:0006464	cellular protein modification process	The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
	GO:0040007	growth	The increase in size or mass of an entire organism, a part of an organism or a cell.
	GO:0009107	lipoate biosynthetic process	The chemical reactions and pathways resulting in the formation of lipoate, 1,2-dithiolane-3-pentanoate, the anion derived from lipoic acid.
	GO:0009249	protein lipoylation	The addition of a lipoyl group to an amino acid residue in a protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Arg A:138 - Pro A:139	[ RasMol ]
		Glu A:98 - Pro A:99	[ RasMol ]

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	1w66
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
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	LIPB_MYCTO \| P9WK82
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	LIPB_MYCTU \| P9WK83
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	2.3.1.-
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		Disease Information	:	OMIM

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	LIPB_MYCTO \| P9WK82
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	LIPB_MYCTU \| P9WK83
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1W66)

(no "Related Entries Specified in the PDB File" available for 1W66)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

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SCOP Domains (1, 1)

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Gene Ontology (10, 17)

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