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(-) Description

Title :  CRYSTAL STRUCTURE OF LPRG FROM MYCOBACTERIUM TUBERCULOSIS
 
Authors :  H. -C. Tsai, J. C. Sacchettini, Tb Structural Genomics Consortium
Date :  07 Apr 10  (Deposition) - 01 Sep 10  (Release) - 22 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Lipoprotein, Lprg, Glycolipid Binding Protein, Structural Genomics, Tb Structural Genomics Consortium, Tbsgc, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. G. Drage, H. C. Tsai, N. D. Pecora, T. Y. Cheng, A. R. Arida, S. Shukla, R. E. Rojas, C. Seshadri, D. B. Moody, W. H. Boom, J. C. Sacchettini, C. V. Harding
Mycobacterium Tuberculosis Lipoprotein Lprg (Rv1411C) Binds Triacylated Glycolipid Agonists Of Toll-Like Receptor 2.
Nat. Struct. Mol. Biol. V. 17 1088 2010
PubMed-ID: 20694006  |  Reference-DOI: 10.1038/NSMB.1869

(-) Compounds

Molecule 1 - LIPOPROTEIN LPRG
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LPP-27, LPRG, MT1455, MTCY21B4.28C, RV1411C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV
    Synonym: 27 KDA LIPOPROTEIN, ANTIGEN P27

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3MH8)

(-) Sites  (0, 0)

(no "Site" information available for 3MH8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MH8)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:83 -Pro A:84
2Asn B:83 -Pro B:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MH8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MH8)

(-) Exons   (0, 0)

(no "Exon" information available for 3MH8)

(-) 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:196
 aligned with LPRG_MYCTO | P9WK44 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:196
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225      
           LPRG_MYCTO    36 GPLPDAKPLVEEATAQTKALKSAHMVLTVNGKIPGLSLKTLSGDLTTNPTAATGNVKLTLGGSDIDADFVVFDGILYATLTPNQWSDFGPAADIYDPAQVLNPDTGLANVLANFADAKAEGRDTINGQNTIRISGKVSAQAVNQIAPPFNATQPVPATVWIQETGDHQLAQAQLDRGSGNSVQMTLSKWGEKVQVT 231
               SCOP domains d3mh8a_ A: automated matches                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh..eeeeeeeee.......eeeeeeeee....eeeeeeeee....eeeeeeeee..eeeeeee..eeeeeee.hhh.hhhhhhh...hhhhhhhheeeeeeeeeeee..eeeeeeeeeehhhhhhhhhhhhh....eeeeeeee......eeeeeee.....eeeeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mh8 A  36 GPLPDAKPLVEEATAQTKALKSAHMVLTVNGKIPGLSLKTLSGDLTTNPTAATGNVKLTLGGSDIDADFVVFDGILYATLTPNQWSDFGPAADIYDPAQVLNPDTGLANVLANFADAKAEGRDTINGQNTIRISGKVSAQAVNQIAPPFNATQPVPATVWIQETGDHQLAQAQLDRGSGNSVQMTLSKWGEKVQVT 231
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225      


Chain A from PDB  Type:PROTEIN  Length:196
 aligned with LPRG_MYCTU | P9WK45 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:196
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225      
           LPRG_MYCTU    36 GPLPDAKPLVEEATAQTKALKSAHMVLTVNGKIPGLSLKTLSGDLTTNPTAATGNVKLTLGGSDIDADFVVFDGILYATLTPNQWSDFGPAADIYDPAQVLNPDTGLANVLANFADAKAEGRDTINGQNTIRISGKVSAQAVNQIAPPFNATQPVPATVWIQETGDHQLAQAQLDRGSGNSVQMTLSKWGEKVQVT 231
               SCOP domains d3mh8a_ A: automated matches                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh..eeeeeeeee.......eeeeeeeee....eeeeeeeee....eeeeeeeee..eeeeeee..eeeeeee.hhh.hhhhhhh...hhhhhhhheeeeeeeeeeee..eeeeeeeeeehhhhhhhhhhhhh....eeeeeeee......eeeeeee.....eeeeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mh8 A  36 GPLPDAKPLVEEATAQTKALKSAHMVLTVNGKIPGLSLKTLSGDLTTNPTAATGNVKLTLGGSDIDADFVVFDGILYATLTPNQWSDFGPAADIYDPAQVLNPDTGLANVLANFADAKAEGRDTINGQNTIRISGKVSAQAVNQIAPPFNATQPVPATVWIQETGDHQLAQAQLDRGSGNSVQMTLSKWGEKVQVT 231
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225      


Chain B from PDB  Type:PROTEIN  Length:194
 aligned with LPRG_MYCTO | P9WK44 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:196
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225      
           LPRG_MYCTO    36 GPLPDAKPLVEEATAQTKALKSAHMVLTVNGKIPGLSLKTLSGDLTTNPTAATGNVKLTLGGSDIDADFVVFDGILYATLTPNQWSDFGPAADIYDPAQVLNPDTGLANVLANFADAKAEGRDTINGQNTIRISGKVSAQAVNQIAPPFNATQPVPATVWIQETGDHQLAQAQLDRGSGNSVQMTLSKWGEKVQVT 231
               SCOP domains d3mh8b_ B: automated matches                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----DUF1396-3mh8B01 B:40-230                                                                                                                                                                       - Pfam domains (1)
           Pfam domains (2) ----DUF1396-3mh8B02 B:40-230                                                                                                                                                                       - Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhhhh..eeeeeee......--.eeeeeeeee....eeeeeeeee....eeeeeeeee..eeeeeee..eeeeeee.hhh.hhhhhhh...hhhhhhhheeeeeeeeeeee..eeeeeeeeeehhhhhhhhh........eeeeeeee......eeeeeee.....eeeeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mh8 B  36 GPLPDAKPLVEEATAQTKALKSAHMVLTVNGKIP--SLKTLSGDLTTNPTAATGNVKLTLGGSDIDADFVVFDGILYATLTPNQWSDFGPAADIYDPAQVLNPDTGLANVLANFADAKAEGRDTINGQNTIRISGKVSAQAVNQIAPPFNATQPVPATVWIQETGDHQLAQAQLDRGSGNSVQMTLSKWGEKVQVT 231
                                    45        55        65   |  | 75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225      
                                                            69 72                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:194
 aligned with LPRG_MYCTU | P9WK45 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:196
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225      
           LPRG_MYCTU    36 GPLPDAKPLVEEATAQTKALKSAHMVLTVNGKIPGLSLKTLSGDLTTNPTAATGNVKLTLGGSDIDADFVVFDGILYATLTPNQWSDFGPAADIYDPAQVLNPDTGLANVLANFADAKAEGRDTINGQNTIRISGKVSAQAVNQIAPPFNATQPVPATVWIQETGDHQLAQAQLDRGSGNSVQMTLSKWGEKVQVT 231
               SCOP domains d3mh8b_ B: automated matches                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----DUF1396-3mh8B01 B:40-230                                                                                                                                                                       - Pfam domains (1)
           Pfam domains (2) ----DUF1396-3mh8B02 B:40-230                                                                                                                                                                       - Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhhhh..eeeeeee......--.eeeeeeeee....eeeeeeeee....eeeeeeeee..eeeeeee..eeeeeee.hhh.hhhhhhh...hhhhhhhheeeeeeeeeeee..eeeeeeeeeehhhhhhhhh........eeeeeeee......eeeeeee.....eeeeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mh8 B  36 GPLPDAKPLVEEATAQTKALKSAHMVLTVNGKIP--SLKTLSGDLTTNPTAATGNVKLTLGGSDIDADFVVFDGILYATLTPNQWSDFGPAADIYDPAQVLNPDTGLANVLANFADAKAEGRDTINGQNTIRISGKVSAQAVNQIAPPFNATQPVPATVWIQETGDHQLAQAQLDRGSGNSVQMTLSKWGEKVQVT 231
                                    45        55        65   |  | 75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225      
                                                            69 72
   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, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MH8)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: DUF1396] (3)

(-) Gene Ontology  (12, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (LPRG_MYCTU | P9WK45)
molecular function
    GO:0051861    glycolipid binding    Interacting selectively and non-covalently with a glycolipid, any compound containing one or more monosaccharide residues bound by a glycosidic linkage to a hydrophobic group such as an acylglycerol, a sphingoid, a ceramide (N-acylsphingoid) or a prenyl phosphate.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0035091    phosphatidylinositol binding    Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
biological process
    GO:0006869    lipid transport    The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0097691    bacterial extracellular vesicle    Small membrane vesicle (< 1 um) that buds off a prokaryotic cell plasma membrane, able to carry proteins, phospholipids, lipopolysaccharides, nucleic acids, viruses, and more. Important in intercellular communication and pathogenesis; can exist within host cells.
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

Chain A,B   (LPRG_MYCTO | P9WK44)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
biological process
    GO:0006869    lipid transport    The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LPRG_MYCTO | P9WK44: 3mh9 3mha
        LPRG_MYCTU | P9WK45: 3mh9 3mha 4zra

(-) Related Entries Specified in the PDB File

3mh9 CRYSTAL STRUCTURE OF LPRG MUTANT V91W FROM MYCOBACTERIUM TUBERCULOSIS
3mha CRYSTAL STRUCTURE OF LPRG FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO PIM RELATED ID: RV1411C RELATED DB: TARGETDB