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(-) Description

Title :  STRUCTURE OF PROTEIN TA0514, PUTATIVE LIPOATE PROTEIN LIGASE FROM T. ACIDOPHILUM.
 
Authors :  E. Mcmanus, R. N. Perham, B. F. Luisi
Date :  24 Nov 05  (Deposition) - 15 Dec 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
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

(-) Compounds

Molecule 1 - PUTATIVE LIPOATE PROTEIN LIGASE
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET 3A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Organism ScientificTHERMOPLASMA ACIDOPHILUM
    Organism Taxid273075
    StrainDSM 1728
    SynonymLIPOATE-PROTEIN LIGASE A

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
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)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2C7I)

(-) Sites  (0, 0)

(no "Site" information available for 2C7I)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C7I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2C7I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C7I)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BPL_LPL_CATALYTICPS51733 Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile.LPLAN_THEAC30-226
 
 
 
  4A:30-226
B:30-226
C:30-226
D:30-226
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BPL_LPL_CATALYTICPS51733 Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile.LPLAN_THEAC30-226
 
 
 
  1A:30-226
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BPL_LPL_CATALYTICPS51733 Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile.LPLAN_THEAC30-226
 
 
 
  1-
B:30-226
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BPL_LPL_CATALYTICPS51733 Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile.LPLAN_THEAC30-226
 
 
 
  1-
-
C:30-226
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BPL_LPL_CATALYTICPS51733 Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile.LPLAN_THEAC30-226
 
 
 
  1-
-
-
D:30-226

(-) Exons   (0, 0)

(no "Exon" information available for 2C7I)

(-) Sequences/Alignments

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:244
 aligned with LPLAN_THEAC | Q9HKT1 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:258
                                    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 MEGRLLLLETPGNTRMSLAYDEAIYRSFQYGDKPILRFYRHDRSVIIGYFQVAEEEVDLDYMKKNGIMLARRYTGGGAVYHDLGDLNFSVVRSSDDMDITSMFRTMNEAVVNSLRILGLDARPGELNDVSIPVNKKTDIMAGEKKIMGAAGAMRKGAKLWHAAMLVHTDLDMLSAVLKVPDEKFRDKIAKSTRERVANVTDFVDVSIDEVRNALIRGFSETLHIDFREDTITEKEESLARELFDKKYSTEEWNMGLLR 258
               SCOP domains d2c7ia_ A: automated matches                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhhhhh......eeeee....eeee..........hhhhhhhh..eeee.......eee...eeeeeeeeee...hhhhhhhhhhhhhhhhhhhh....ee...............eee..eeeeeeeeeee.eeeeeeeeee...hhhhhhhhh.--------------.....hhhhh...hhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh..hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------BPL_LPL_CATALYTIC  PDB: A:30-226 UniProt: 30-226                                                                                                                                                     -------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2c7i A   1 MEGRLLLLETPGNTRMSLAYDEAIYRSFQYGDKPILRFYRHDRSVIIGYFQVAEEEVDLDYMKKNGIMLARRYTGGGAVYHDLGDLNFSVVRSSDDMDITSMFRTMNEAVVNSLRILGLDARPGELNDVSIPVNKKTDIMAGEKKIMGAAGAMRKGAKLWHAAMLVHTDLDMLSAVLK--------------RERVANVTDFVDVSIDEVRNALIRGFSETLHIDFREDTITEKEESLARELFDKKYSTEEWNMGLLR 258
                                    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                                                                 

Chain B from PDB  Type:PROTEIN  Length:240
 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 d2c7ib_ B: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhhhh......eeeee....eeee....hhhhhhhhhhhhhhh.eeee.......eee...eeeeeeeee....hhhhhhhhhhhhhhhhhhhhh...ee...............eee..eeeeeeeeeee..eeeeeeeee...hhhhhhhhh----------------....hhhhh...hhhhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhh..hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------BPL_LPL_CATALYTIC  PDB: B:30-226 UniProt: 30-226                                                                                                                                                     ------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c7i B   1 MEGRLLLLETPGNTRMSLAYDEAIYRSFQYGDKPILRFYRHDRSVIIGYFQVAEEEVDLDYMKKNGIMLARRYTGGGAVYHDLGDLNFSVVRSSDDMDITSMFRTMNEAVVNSLRILGLDARPGELNDVSIPVNKKTDIMAGEKKIMGAAGAMRKGAKLWHAAMLVHTDLDMLSAVL----------------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      
                                                                                                                                                                                                          177              194                                                              

Chain C from PDB  Type:PROTEIN  Length:240
 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 d2c7ic_ C: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhhhhh......eeeee....eeee....hhhhhhhhhhhh-...eeee.......eee...eeeeeeeee....hhhhhhhhhhhhhhhhhhhh....ee...............eee..eeeeeeeeeee..eeeeeeeee............---------------.....hhhhhh..hhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh..hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------BPL_LPL_CATALYTIC  PDB: C:30-226 UniProt: 30-226                                                                                                                                                     ------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c7i C   1 MEGRLLLLETPGNTRMSLAYDEAIYRSFQYGDKPILRFYRHDRSVIIGYFQVAEEEVDLDYMK-NGIMLARRYTGGGAVYHDLGDLNFSVVRSSDDMDITSMFRTMNEAVVNSLRILGLDARPGELNDVSIPVNKKTDIMAGEKKIMGAAGAMRKGAKLWHAAMLVHTDLDMLSAVL---------------RERVANVTDFVDVSIDEVRNALIRGFSETLHIDFREDTITEKEESLARELFDKKYSTEEWNMGL 256
                                    10        20        30        40        50        60  | |   70        80        90       100       110       120       130       140       150       160       170      |  -         -  |    200       210       220       230       240       250      
                                                                                         63 |                                                                                                             177             193                                                               
                                                                                           65                                                                                                                                                                                               

Chain D from PDB  Type:PROTEIN  Length:240
 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 d2c7id_ D: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhhh.......eeeee...eeeee....hhhhhh..-.......eeee.......eeee..eeeeeeeee....hhhhhhhhhhhhhhhhhhhhh...ee...............eee..eeeeeeeeee...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
                 2c7i D   1 MEGRLLLLETPGNTRMSLAYDEAIYRSFQYGDKPILRFYRHDRSVIIGYFQVAEEEVDL-YMKKNGIMLARRYTGGGAVYHDLGDLNFSVVRSSDDMDITSMFRTMNEAVVNSLRILGLDARPGELNDVSIPVNKKTDIMAGEKKIMGAAGAMRKGAKLWHAAMLVHTDLDMLSAVL----------------ERVANVTDFVDVSIDEVRNALIRGFSETLHIDFREDTITEKEESLARELFDKKYSTEEWNMGLL 257
                                    10        20        30        40        50        |-|       70        80        90       100       110       120       130       140       150       160       170      |  -         -   |   200       210       220       230       240       250       
                                                                                     59 |                                                                                                                 177              194                                                               
                                                                                       61                                                                                                                                                                                                    

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2C7I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C7I)

(-) Gene Ontology  (10, 10)

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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        LPLAN_THEAC | Q9HKT12ars 2art 2aru 2c8m 3r07

(-) Related Entries Specified in the PDB File

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
2c8m STRUCTURE OF PROTEIN TA0514, PUTATIVE LIPOATE PROTEIN LIGASE FROM T. ACIDOPHILUM WITH BOUND LIPOIC ACID