2C8M - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   STRUCTURE OF PROTEIN TA0514, PUTATIVE LIPOATE PROTEIN LIGASE FROM T. ACIDOPHILUM WITH BOUND LIPOIC ACID

Authors :   E. Mcmanus, R. N. Perham, B. F. Luisi

Date :   06 Dec 05 (Deposition) - 15 Dec 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.89

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Lipoylation, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Mcmanus, B. F. Luisi, R. N. Perham
Structure Of A Putative Lipoate Protein Ligase From Thermoplasma Acidophilum And The Mechanism Of Target Selection For Post-Translational Modification.
J. Mol. Biol. V. 356 625 2006
PubMed-ID: 16384580 | Reference-DOI: 10.1016/J.JMB.2005.11.057

Molecule 1 - LIPOATE-PROTEIN LIGASE A
	Chains	:	A, B, C, D
	EC Number	:	6.3.2.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET 3A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	THERMOPLASMA ACIDOPHILUM
	Organism Taxid	:	273075
	Strain	:	DSM 1728

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	LPA	4	Ligand/Ion	LIPOIC ACID

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	LPA	1	Ligand/Ion	LIPOIC ACID

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	LPA	1	Ligand/Ion	LIPOIC ACID

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	LPA	1	Ligand/Ion	LIPOIC ACID

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	LPA	1	Ligand/Ion	LIPOIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:39 , ARG A:72 , VAL A:79 , HIS A:81 , LYS A:145 , GLY A:148 , ALA A:149 , HOH A:2134 , HOH A:2189 , HOH A:2190 , HOH A:2191	BINDING SITE FOR RESIDUE LPA A 900
2	AC2	SOFTWARE	TYR B:39 , ARG B:72 , VAL B:79 , HIS B:81 , LYS B:145 , GLY B:148 , ALA B:149 , HOH B:2104 , HOH B:2161 , HOH B:2162	BINDING SITE FOR RESIDUE LPA B 900
3	AC3	SOFTWARE	TYR C:39 , ARG C:72 , VAL C:79 , HIS C:81 , LYS C:145 , GLY C:148 , ALA C:149 , ALA C:162 , HOH C:2045 , HOH C:2064 , HOH C:2065	BINDING SITE FOR RESIDUE LPA C 900
4	AC4	SOFTWARE	TYR D:39 , ARG D:72 , VAL D:79 , HIS D:81 , LYS D:145 , GLY D:148 , ALA D:149 , HOH D:2024 , HOH D:2048	BINDING SITE FOR RESIDUE LPA D 900

(no "SS Bond" information available for 2C8M)

(no "Cis Peptide Bond" information available for 2C8M)

(no "SAP(SNP)/Variant" information available for 2C8M)

Asymmetric Unit (1, 4)

	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.	LPLAN_THEAC	30-226	4	A:30-226 B:30-226 C:30-226 D:30-226

Biological Unit 1 (1, 1)

	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.	LPLAN_THEAC	30-226	1	A:30-226 - - -

Biological Unit 2 (1, 1)

	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.	LPLAN_THEAC	30-226	1	- B:30-226 - -

Biological Unit 3 (1, 1)

	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.	LPLAN_THEAC	30-226	1	- - C:30-226 -

Biological Unit 4 (1, 1)

	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.	LPLAN_THEAC	30-226	1	- - - D:30-226

(no "Exon" information available for 2C8M)

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:241
 aligned with LPLAN_THEAC | Q9HKT1 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:256
                                    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      
          LPLAN_THEAC     1 MEGRLLLLETPGNTRMSLAYDEAIYRSFQYGDKPILRFYRHDRSVIIGYFQVAEEEVDLDYMKKNGIMLARRYTGGGAVYHDLGDLNFSVVRSSDDMDITSMFRTMNEAVVNSLRILGLDARPGELNDVSIPVNKKTDIMAGEKKIMGAAGAMRKGAKLWHAAMLVHTDLDMLSAVLKVPDEKFRDKIAKSTRERVANVTDFVDVSIDEVRNALIRGFSETLHIDFREDTITEKEESLARELFDKKYSTEEWNMGL 256
               SCOP domains d2c8ma_ A: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhhhhh......eeeee....eeee....hhhhhhhhhhhhhh..eeee.......eee...eeeeeeeee....hhhhhhhhhhhhhhhhhhhh....ee...............eee..eeeeeeeeeee..eeeeeeeee...hhhhhhhhh.---------------....hhhhh...hhhhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhh..hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------BPL_LPL_CATALYTIC  PDB: A:30-226 UniProt: 30-226                                                                                                                                                     ------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c8m A   1 MEGRLLLLETPGNTRMSLAYDEAIYRSFQYGDKPILRFYRHDRSVIIGYFQVAEEEVDLDYMKKNGIMLARRYTGGGAVYHDLGDLNFSVVRSSDDMDITSMFRTMNEAVVNSLRILGLDARPGELNDVSIPVNKKTDIMAGEKKIMGAAGAMRKGAKLWHAAMLVHTDLDMLSAVLK---------------ERVANVTDFVDVSIDEVRNALIRGFSETLHIDFREDTITEKEESLARELFDKKYSTEEWNMGL 256
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       | -         -   |   200       210       220       230       240       250      
                                                                                                                                                                                                           178             194

Chain B from PDB  Type:PROTEIN  Length:245
 aligned with LPLAN_THEAC | Q9HKT1 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:257
                                    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       
          LPLAN_THEAC     1 MEGRLLLLETPGNTRMSLAYDEAIYRSFQYGDKPILRFYRHDRSVIIGYFQVAEEEVDLDYMKKNGIMLARRYTGGGAVYHDLGDLNFSVVRSSDDMDITSMFRTMNEAVVNSLRILGLDARPGELNDVSIPVNKKTDIMAGEKKIMGAAGAMRKGAKLWHAAMLVHTDLDMLSAVLKVPDEKFRDKIAKSTRERVANVTDFVDVSIDEVRNALIRGFSETLHIDFREDTITEKEESLARELFDKKYSTEEWNMGLL 257
               SCOP domains d2c8mb_ B: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhhhhh......eeeee....eeee....hhhhhhhhhhhhhh..eeee.......eee...eeeeeeeeee...hhhhhhhhhhhhhhhhhhhh....ee...............eee..eeeeeeeeeee.eeeeeeeeee...hhhhhhhhh.------------.hhhh..hhhhh...hhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh..hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------BPL_LPL_CATALYTIC  PDB: B:30-226 UniProt: 30-226                                                                                                                                                     ------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c8m B   1 MEGRLLLLETPGNTRMSLAYDEAIYRSFQYGDKPILRFYRHDRSVIIGYFQVAEEEVDLDYMKKNGIMLARRYTGGGAVYHDLGDLNFSVVRSSDDMDITSMFRTMNEAVVNSLRILGLDARPGELNDVSIPVNKKTDIMAGEKKIMGAAGAMRKGAKLWHAAMLVHTDLDMLSAVLK------------STRERVANVTDFVDVSIDEVRNALIRGFSETLHIDFREDTITEKEESLARELFDKKYSTEEWNMGLL 257
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       | -         -|      200       210       220       230       240       250       
                                                                                                                                                                                                           178          191

Chain C from PDB  Type:PROTEIN  Length:245
 aligned with LPLAN_THEAC | Q9HKT1 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:257
                                    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       
          LPLAN_THEAC     1 MEGRLLLLETPGNTRMSLAYDEAIYRSFQYGDKPILRFYRHDRSVIIGYFQVAEEEVDLDYMKKNGIMLARRYTGGGAVYHDLGDLNFSVVRSSDDMDITSMFRTMNEAVVNSLRILGLDARPGELNDVSIPVNKKTDIMAGEKKIMGAAGAMRKGAKLWHAAMLVHTDLDMLSAVLKVPDEKFRDKIAKSTRERVANVTDFVDVSIDEVRNALIRGFSETLHIDFREDTITEKEESLARELFDKKYSTEEWNMGLL 257
               SCOP domains d2c8mc_ C: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhhhh......eeeee....eeee....hhhhhhhhhhhhhhh.eeee.......eee...eeeeeeeee....hhhhhhhhhhhhhhhhhhhh....ee...............eee..eeeeeeeeeee..eeeeeeeee...hhhhhhhhh.------------hhhhhh.hhhhh...hhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh..hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------BPL_LPL_CATALYTIC  PDB: C:30-226 UniProt: 30-226                                                                                                                                                     ------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c8m C   1 MEGRLLLLETPGNTRMSLAYDEAIYRSFQYGDKPILRFYRHDRSVIIGYFQVAEEEVDLDYMKKNGIMLARRYTGGGAVYHDLGDLNFSVVRSSDDMDITSMFRTMNEAVVNSLRILGLDARPGELNDVSIPVNKKTDIMAGEKKIMGAAGAMRKGAKLWHAAMLVHTDLDMLSAVLK------------STRERVANVTDFVDVSIDEVRNALIRGFSETLHIDFREDTITEKEESLARELFDKKYSTEEWNMGLL 257
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       | -         -|      200       210       220       230       240       250       
                                                                                                                                                                                                           178          191

Chain D from PDB  Type:PROTEIN  Length:241
 aligned with LPLAN_THEAC | Q9HKT1 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:255
                                    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     
          LPLAN_THEAC     1 MEGRLLLLETPGNTRMSLAYDEAIYRSFQYGDKPILRFYRHDRSVIIGYFQVAEEEVDLDYMKKNGIMLARRYTGGGAVYHDLGDLNFSVVRSSDDMDITSMFRTMNEAVVNSLRILGLDARPGELNDVSIPVNKKTDIMAGEKKIMGAAGAMRKGAKLWHAAMLVHTDLDMLSAVLKVPDEKFRDKIAKSTRERVANVTDFVDVSIDEVRNALIRGFSETLHIDFREDTITEKEESLARELFDKKYSTEEWNMG 255
               SCOP domains d2c8md_ D: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhhh.......eeeee....eeee....hhhhhhhhhhhhhh..eeee.......eee...eeeeeeeee....hhhhhhhhhhhhhhhhhhhhh...ee...............eee..eeeeeeeeeee..eeeeeeeee...hhhhhhhhh.--------------.....hhhhh...hhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh..hhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------BPL_LPL_CATALYTIC  PDB: D:30-226 UniProt: 30-226                                                                                                                                                     ----------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c8m D   1 MEGRLLLLETPGNTRMSLAYDEAIYRSFQYGDKPILRFYRHDRSVIIGYFQVAEEEVDLDYMKKNGIMLARRYTGGGAVYHDLGDLNFSVVRSSDDMDITSMFRTMNEAVVNSLRILGLDARPGELNDVSIPVNKKTDIMAGEKKIMGAAGAMRKGAKLWHAAMLVHTDLDMLSAVLK--------------RERVANVTDFVDVSIDEVRNALIRGFSETLHIDFREDTITEKEESLARELFDKKYSTEEWNMG 255
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       | -         -  |    200       210       220       230       240       250     
                                                                                                                                                                                                           178            193

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: 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: automated matches (3)

Thermoplasma acidophilum [TaxId: 273075] (3)

1a	d2c8ma_	A:
1b	d2c8mb_	B:
1c	d2c8mc_	C:
1d	d2c8md_	D:

(no "CATH Domain" information available for 2C8M)

(no "Pfam Domain" information available for 2C8M)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (LPLAN_THEAC | Q9HKT1)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0016979	lipoate-protein ligase activity	Catalysis of the formation of carbon-nitrogen bonds between lipoate (5-(1,2-dithiolan-3-yl)pentanoate) and a protein.
	GO:0017118	lipoyltransferase activity	Catalysis of the transfer of the lipoyl group from lipoyl-AMP to the lysine residue of lipoate-dependent enzyme.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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).
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: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.

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	LPLAN_THEAC \| Q9HKT1	:	2ars 2art 2aru 2c7i 3r07

2ars	CRYSTAL STRUCTURE OF LIPOATE-PROTEIN LIGASE A FROMTHERMOPLASMA ACIDOPHILUM
2art	CRYSTAL STRUCTURE OF LIPOATE-PROTEIN LIGASE A BOUND WITHLIPOYL-AMP
2aru	CRYSTAL STRUCTURE OF LIPOATE-PROTEIN LIGASE A BOUND WITH ATP
2c7i	STRUCTURE OF PROTEIN TA0514, PUTATIVE LIPOATE PROTEIN LIGASE FROM T. ACIDOPHILUM.

Description

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Ligands, Modified Residues, Ions (1, 4)

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