Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURAL ANALYSIS OF AN ARCHAEAL LIPOYLATION SYSTEM. A BI-PARTITE LIPOATE PROTEIN LIGASE AND ITS E2 LIPOYL DOMAIN FROM THERMOPLASMA ACIDOPHILUM
 
Authors :  M. G. Posner, U. Upadhyay, S. Crennell
Date :  07 Mar 11  (Deposition) - 25 Apr 12  (Release) - 23 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Adenylate-Forming Enzyme, Ligase, Bi-Partite, Atp-Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. G. Posner, A. Upadhyay, S. Crennell, M. J. Danson, S. Bagby
Structural Analysis Of An Archaeal Lipoylation System. A Bi-Partite Lipoate Protein Ligase And Its E2 Lipoyl Domain From Thermoplasma Acidophilum
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LIPOATE-PROTEIN LIGASE A SUBUNIT 1
    Chains: A
    EC Number: 2.7.7.63
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET19B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LPLA, TA0514
    Organism Scientific: THERMOPLASMA ACIDOPHILUM DSM 1728
    Organism Taxid: 273075
    Strain: ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165
    Synonym: LIPOATE--PROTEIN LIGASE SUBUNIT 1
 
Molecule 2 - PUTATIVE LIPOATE-PROTEIN LIGASE A SUBUNIT 2
    Chains: C
    EC Number: 2.7.7.63
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TA0513, TA0513M
    Organism Scientific: THERMOPLASMA ACIDOPHILUM DSM 1728
    Organism Taxid: 273075
    Strain: ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165
    Synonym: LIPOATE--PROTEIN LIGASE SUBUNIT 2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:9 , PHE A:38 , LEU A:86 , ARG A:211BINDING SITE FOR RESIDUE MPD A 263
2AC2SOFTWAREARG A:72 , GLY A:77 , VAL A:79 , GLY A:148 , ALA A:149 , HIS A:161BINDING SITE FOR RESIDUE MPD A 264
3AC3SOFTWAREARG A:227BINDING SITE FOR RESIDUE ACT C 89

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R07)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Pro A:123 -Gly A:124
2Phe C:39 -Pro C:40
3Arg C:52 -Gly C:53

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R07)

(-) 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 3R07)

(-) 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:255
 aligned with LPLAN_THEAC | Q9HKT1 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:263
                             1                                                                                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259   
          LPLAN_THEAC     - -MEGRLLLLETPGNTRMSLAYDEAIYRSFQYGDKPILRFYRHDRSVIIGYFQVAEEEVDLDYMKKNGIMLARRYTGGGAVYHDLGDLNFSVVRSSDDMDITSMFRTMNEAVVNSLRILGLDARPGELNDVSIPVNKKTDIMAGEKKIMGAAGAMRKGAKLWHAAMLVHTDLDMLSAVLKVPDEKFRDKIAKSTRERVANVTDFVDVSIDEVRNALIRGFSETLHIDFREDTITEKEESLARELFDKKYSTEEWNMGLLRKEVV 262
               SCOP domains d3r07a_ A: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhh.......eeeee....eeee....hhhhhhhhhhhhhh..eeee.......eee...eeeeeeeee....hhhhhhhhhhhhhhhhhhhh....ee....eeee..--------..eeeeeeeeeee..eeeeeeeee.....hhhhhh....hhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhhheeeee...hhhhhhhhhhhhhhh..hhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------BPL_LPL_CATALYTIC  PDB: A:30-226 UniProt: 30-226                                                                                                                                                     ------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r07 A   0 HMEGRLLLLETPGNTRMSLAYDEAIYRSFQYGDKPILRFYRHDRSVIIGYFQVAEEEVDLDYMKKNGIMLARRYTGGGAVYHDLGDLNFSVVRSSDDMDITSMFRTMNEAVVNSLRILGLDARPGELNDVSIPV--------GEKKIMGAAGAMRKGAKLWHAAMLVHTDLDMLSAVLKVPDEKFRDKIAKSTRERVANVTDFVDVSIDEVRNALIRGFSETLHIDFREDTITEKEESLARELFDKKYSTEEWNMGLLRKEVV 262
                                     9        19        29        39        49        59        69        79        89        99       109       119       129   |     -  |    149       159       169       179       189       199       209       219       229       239       249       259   
                                                                                                                                                               133      142                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:88
 aligned with LPLAC_THEAC | Q9HKT2 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:88
                                    16        26        36        46        56        66        76        86        
          LPLAC_THEAC     7 MHMMYSKNWKAKKGLIRVTLDLDGNRIKDIHISGDFFMFPEDSINRLEDMLRGSSIEKINDIIRDFYNQGVITPGVEPEDFIQALRVI  94
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....eeeeeeeee..eeeeeeeeee......hhhhhhhhhhh.....hhhhhhhhhhh..........hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 3r07 C   1 MHMMYSKNWKAKKGLIRVTLDLDGNRIKDIHISGDFFMFPEDSINRLEDMLRGSSIEKINDIIRDFYNQGVITPGVEPEDFIQALRVI  88
                                    10        20        30        40        50        60        70        80
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R07)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3R07)

(-) Gene Ontology  (10, 17)

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.

Chain C   (LPLAC_THEAC | Q9HKT2)
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: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:0009249    protein lipoylation    The addition of a lipoyl group to an amino acid residue in a protein.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MPD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg C:52 - Gly C:53   [ RasMol ]  
    Phe C:39 - Pro C:40   [ RasMol ]  
    Pro A:123 - Gly A:124   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3r07
    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)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  LPLAC_THEAC | Q9HKT2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  LPLAN_THEAC | Q9HKT1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.7.63
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  LPLAC_THEAC | Q9HKT2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  LPLAN_THEAC | Q9HKT1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        LPLAN_THEAC | Q9HKT1: 2ars 2art 2aru 2c7i 2c8m

(-) Related Entries Specified in the PDB File

2l5t