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(-) Description

Title :  CRYSTAL STRUCTURE OF LIPOATE-PROTEIN LIGASE A BOUND WITH ATP
 
Authors :  D. J. Kim, K. H. Kim, H. H. Lee, S. J. Lee, J. Y. Ha, H. J. Yoon, S. W. Suh
Date :  22 Aug 05  (Deposition) - 04 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. J. Kim, K. H. Kim, H. H. Lee, S. J. Lee, J. Y. Ha, H. J. Yoon, S. W. Suh
Crystal Structure Of Lipoate-Protein Ligase A Bound With The Activated Intermediate: Insights Into Interaction With Lipoyl Domains
J. Biol. Chem. V. 280 38081 2005
PubMed-ID: 16141198  |  Reference-DOI: 10.1074/JBC.M507284200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LIPOATE-PROTEIN LIGASE A
    Chains: A
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TA0514
    Organism Scientific: THERMOPLASMA ACIDOPHILUM
    Organism Taxid: 2303

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:137 , ASP A:138 , GLY A:148 , ALA A:149 , ATP A:1065BINDING SITE FOR RESIDUE MG A 1301
2AC2SOFTWAREARG A:72 , GLY A:77 , ALA A:78 , VAL A:79 , TYR A:80 , HIS A:81 , ASP A:85 , PRO A:132 , LYS A:135 , ASP A:138 , LYS A:145 , GLY A:148 , ALA A:149 , ALA A:150 , ALA A:163 , LEU A:165 , LEU A:173 , MG A:1301BINDING SITE FOR RESIDUE ATP A 1065

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (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

(-) Exons   (0, 0)

(no "Exon" information available for 2ARU)

(-) Sequences/Alignments

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:247
 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 d2arua_ A: Lipoate-protein ligase A                                                                                                                                                                                                                               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.hhhhhh..hhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh..hhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------BPL_LPL_CATALYTIC  PDB: A:30-226 UniProt: 30-226                                                                                                                                                     ------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aru A   1 MEGRLLLLETPGNTRMSLAYDEAIYRSFQYGDKPILRFYRHDRSVIIGYFQVAEEEVDLDYMKKNGIMLARRYTGGGAVYHDLGDLNFSVVRSSDDMDITSMFRTMNEAVVNSLRILGLDARPGELNDVSIPVNKKTDIMAGEKKIMGAAGAMRKGAKLWHAAMLVHTDLDMLSAVLKVP----------STRERVANVTDFVDVSIDEVRNALIRGFSETLHIDFREDTITEKEESLARELFDKKYSTEEWNMGLL 257
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         -|      200       210       220       230       240       250       
                                                                                                                                                                                                             180        191
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  - → Gap (green background, '-', border residues have a numbering label)
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  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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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 | Q9HKT1: 2ars 2art 2c7i 2c8m 3r07

(-) Related Entries Specified in the PDB File

2ars THE SAME PROTEIN
2art THE SAME PROTEIN BOUND WITH LIPOYL-AMP