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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PERIPLASMIC LIPOPOLYSACCHARIDE TRANSPORT PROTEIN LPTA (YHBN), TRIGONAL FORM
 
Authors :  M. D. L. Suits, A. Polissi, Z. Jia, Montreal-Kingston Bacterial Stru Genomics Initiative (Bsgi)
Date :  22 Aug 07  (Deposition) - 29 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.26
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Keywords :  Mainly Beta, Beta-Jellyroll, Beta-Taco, Structural Genomics, Bacterial Structural Genomics Initiative, Montreal-Kingston Bacterial Structural Genomics Initiative, Bsgi, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. D. Suits, P. Sperandeo, G. Deho, A. Polissi, Z. Jia
Novel Structure Of The Conserved Gram-Negative Lipopolysaccharide Transport Protein A And Mutagenesis Analysis.
J. Mol. Biol. V. 380 476 2008
PubMed-ID: 18534617  |  Reference-DOI: 10.1016/J.JMB.2008.04.045

(-) Compounds

Molecule 1 - PROTEIN YHBN
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: YHBN, B3200, JW3167
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x):     EFGH

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2R1A)

(-) Sites  (0, 0)

(no "Site" information available for 2R1A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R1A)

(-) Cis Peptide Bonds  (15, 15)

Asymmetric Unit
No.Residues
1Lys A:91 -Pro A:92
2Val A:132 -Asp A:133
3Gly B:49 -Asn B:50
4Lys B:91 -Pro B:92
5Gly B:125 -Asn B:126
6Lys C:91 -Pro C:92
7Val C:165 -Pro C:166
8Lys D:91 -Pro D:92
9Thr D:124 -Gly D:125
10Lys E:91 -Pro E:92
11Ala E:117 -Lys E:118
12Lys F:91 -Pro F:92
13Met F:98 -Gln F:99
14Lys G:91 -Pro G:92
15Lys H:91 -Pro H:92

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R1A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R1A)

(-) Exons   (0, 0)

(no "Exon" information available for 2R1A)

(-) 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:131
 aligned with LPTA_ECOLI | P0ADV1 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:138
                                    37        47        57        67        77        87        97       107       117       127       137       147       157        
           LPTA_ECOLI    28 VTGDTDQPIHIESDQQSLDMQGNVVTFTGNVIVTQGTIKINADKVVVTRPGGEQGKEVIDGYGKPATFYQMQDNGKPVEGHASQMHYELAKDFVVLTGNAYLQQVDSNIKGDKITYLVKEQKMQAFSDKGKRVTTVLV 165
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2r1aA00 A:28-165 Lip  opolysaccharide (LPS) transp     ort protein A like domain                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh..eee........--.........eee....eee.........-----.............ee.......ee.............eeeeeeeeee......eeeeeeeee.......ee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2r1a A  28 VTGDTDQPIHIESDQQSLDM--NVVTFTGNVIVTQGTIKINADKVVVTRP-----KEVIDGYGKPATFYQMQDNGKPVEGHASQMHYELAKDFVVLTGNAYLQQVDSNIKGDKITYLVKEQKMQAFSDKGKRVTTVLV 165
                                    37        47  |     57        67        77     |  87        97       107       117       127       137       147       157        
                                              47 50                         77    83                                                                                  


Chain B from PDB  Type:PROTEIN  Length:134
 aligned with LPTA_ECOLI | P0ADV1 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:138
                                    38        48        58        68        78        88        98       108       118       128       138       148       158        
           LPTA_ECOLI    29 TGDTDQPIHIESDQQSLDMQGNVVTFTGNVIVTQGTIKINADKVVVTRPGGEQGKEVIDGYGKPATFYQMQDNGKPVEGHASQMHYELAKDFVVLTGNAYLQQVDSNIKGDKITYLVKEQKMQAFSDKGKRVTTVLVP 166
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2r1aB00 B:29-166 Lipopolysaccharide (LPS) transpor    t protein A like domain                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........ee...eee......eeeee..eeeee..eeeee...eee...----.....ee....eeee.......eeee..ee.......ee..eeeeeee...eeeeeee.eee....eeeee.....eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2r1a B  29 TGDTDQPIHIESDQQSLDMQGNVVTFTGNVIVTQGTIKINADKVVVTRPG----KEVIDGYGKPATFYQMQDNGKPVEGHASQMHYELAKDFVVLTGNAYLQQVDSNIKGDKITYLVKEQKMQAFSDKGKRVTTVLVP 166
                                    38        48        58        68        78    |   88        98       108       118       128       138       148       158        
                                                                            78   83                                                                                   


Chain C from PDB  Type:PROTEIN  Length:135
 aligned with LPTA_ECOLI | P0ADV1 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:138
                                    38        48        58        68        78        88        98       108       118       128       138       148       158        
           LPTA_ECOLI    29 TGDTDQPIHIESDQQSLDMQGNVVTFTGNVIVTQGTIKINADKVVVTRPGGEQGKEVIDGYGKPATFYQMQDNGKPVEGHASQMHYELAKDFVVLTGNAYLQQVDSNIKGDKITYLVKEQKMQAFSDKGKRVTTVLVP 166
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2r1aC00 C:29-166 Lipopolysaccharide (LPS) transport    protein A like domain                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeee...ee........eeeeeeeee.....eeeeeee......---..eeee.......................eeee....eeee...eeeee..eeeee.eeeee....eeeee......eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2r1a C  29 TGDTDQPIHIESDQQSLDMQGNVVTFTGNVIVTQGTIKINADKVVVTRPGG---KEVIDGYGKPATFYQMQDNGKPVEGHASQMHYELAKDFVVLTGNAYLQQVDSNIKGDKITYLVKEQKMQAFSDKGKRVTTVLVP 166
                                    38        48        58        68        78|   |   88        98       108       118       128       138       148       158        
                                                                             79  83                                                                                   


Chain D from PDB  Type:PROTEIN  Length:136
 aligned with LPTA_ECOLI | P0ADV1 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:139
                                    37        47        57        67        77        87        97       107       117       127       137       147       157         
           LPTA_ECOLI    28 VTGDTDQPIHIESDQQSLDMQGNVVTFTGNVIVTQGTIKINADKVVVTRPGGEQGKEVIDGYGKPATFYQMQDNGKPVEGHASQMHYELAKDFVVLTGNAYLQQVDSNIKGDKITYLVKEQKMQAFSDKGKRVTTVLVP 166
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2r1aD00 D:28-166 Lipopolysaccharide (LPS) transport    protein A like domain                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee.eeeee....eeeee..eeee.....eee...eee....---..eee...................................ee...........ee..ee..................ee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r1a D  28 VTGDTDQPIHIESDQQSLDMQGNVVTFTGNVIVTQGTIKINADKVVVTRPGG---KEVIDGYGKPATFYQMQDNGKPVEGHASQMHYELAKDFVVLTGNAYLQQVDSNIKGDKITYLVKEQKMQAFSDKGKRVTTVLVP 166
                                    37        47        57        67        77 |   |  87        97       107       117       127       137       147       157         
                                                                              79  83                                                                                   


Chain E from PDB  Type:PROTEIN  Length:132
 aligned with LPTA_ECOLI | P0ADV1 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:137
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       
           LPTA_ECOLI    31 DTDQPIHIESDQQSLDMQGNVVTFTGNVIVTQGTIKINADKVVVTRPGGEQGKEVIDGYGKPATFYQMQDNGKPVEGHASQMHYELAKDFVVLTGNAYLQQVDSNIKGDKITYLVKEQKMQAFSDKGKRVTTVLVPS 167
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2r1aE00 E:31-167 Lipopolysaccharide (LPS) trans     port protein A like domain                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee....eeeeeeee..........eeeeeee..-----..eeeee.....................eeeee....eeeee...............eeeee....ee................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r1a E  31 DTDQPIHIESDQQSLDMQGNVVTFTGNVIVTQGTIKINADKVVVTRP-----KEVIDGYGKPATFYQMQDNGKPVEGHASQMHYELAKDFVVLTGNAYLQQVDSNIKGDKITYLVKEQKMQAFSDKGKRVTTVLVPS 167
                                    40        50        60        70      |  -  |     90       100       110       120       130       140       150       160       
                                                                         77    83                                                                                    


Chain F from PDB  Type:PROTEIN  Length:132
 aligned with LPTA_ECOLI | P0ADV1 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:138
                                    37        47        57        67        77        87        97       107       117       127       137       147       157        
           LPTA_ECOLI    28 VTGDTDQPIHIESDQQSLDMQGNVVTFTGNVIVTQGTIKINADKVVVTRPGGEQGKEVIDGYGKPATFYQMQDNGKPVEGHASQMHYELAKDFVVLTGNAYLQQVDSNIKGDKITYLVKEQKMQAFSDKGKRVTTVLV 165
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2r1aF00 F:28-165 Lipopolysaccharide (LPS) transpo      rt protein A like domain                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........ee....eeee......eeee..eeeee....eee.......------..ee...........................ee............................................eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2r1a F  28 VTGDTDQPIHIESDQQSLDMQGNVVTFTGNVIVTQGTIKINADKVVVTR------KEVIDGYGKPATFYQMQDNGKPVEGHASQMHYELAKDFVVLTGNAYLQQVDSNIKGDKITYLVKEQKMQAFSDKGKRVTTVLV 165
                                    37        47        57        67        |-     |  87        97       107       117       127       137       147       157        
                                                                           76     83                                                                                  


Chain G from PDB  Type:PROTEIN  Length:135
 aligned with LPTA_ECOLI | P0ADV1 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:138
                                    37        47        57        67        77        87        97       107       117       127       137       147       157        
           LPTA_ECOLI    28 VTGDTDQPIHIESDQQSLDMQGNVVTFTGNVIVTQGTIKINADKVVVTRPGGEQGKEVIDGYGKPATFYQMQDNGKPVEGHASQMHYELAKDFVVLTGNAYLQQVDSNIKGDKITYLVKEQKMQAFSDKGKRVTTVLV 165
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2r1aG00 G:28-165 Lipopolysaccharide (LPS) transport    protein A like domain                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............eeeee......eeeeeeee..ee..ee......eee....---..eee..........................ee........................ee.........eee........ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2r1a G  28 VTGDTDQPIHIESDQQSLDMQGNVVTFTGNVIVTQGTIKINADKVVVTRPGG---KEVIDGYGKPATFYQMQDNGKPVEGHASQMHYELAKDFVVLTGNAYLQQVDSNIKGDKITYLVKEQKMQAFSDKGKRVTTVLV 165
                                    37        47        57        67        77 |   |  87        97       107       117       127       137       147       157        
                                                                              79  83                                                                                  


Chain H from PDB  Type:PROTEIN  Length:131
 aligned with LPTA_ECOLI | P0ADV1 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:137
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       
           LPTA_ECOLI    28 VTGDTDQPIHIESDQQSLDMQGNVVTFTGNVIVTQGTIKINADKVVVTRPGGEQGKEVIDGYGKPATFYQMQDNGKPVEGHASQMHYELAKDFVVLTGNAYLQQVDSNIKGDKITYLVKEQKMQAFSDKGKRVTTVL 164
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2r1aH00 H:28-164 Lipopolysaccharide (LPS) transpo      rt protein A like domain                                                           CATH domains
           Pfam domains (1) ---------OstA-2r1aH01 H:37-149                                                                                            --------------- Pfam domains (1)
           Pfam domains (2) ---------OstA-2r1aH02 H:37-149                                                                                            --------------- Pfam domains (2)
           Pfam domains (3) ---------OstA-2r1aH03 H:37-149                                                                                            --------------- Pfam domains (3)
           Pfam domains (4) ---------OstA-2r1aH04 H:37-149                                                                                            --------------- Pfam domains (4)
           Pfam domains (5) ---------OstA-2r1aH05 H:37-149                                                                                            --------------- Pfam domains (5)
           Pfam domains (6) ---------OstA-2r1aH06 H:37-149                                                                                            --------------- Pfam domains (6)
           Pfam domains (7) ---------OstA-2r1aH07 H:37-149                                                                                            --------------- Pfam domains (7)
           Pfam domains (8) ---------OstA-2r1aH08 H:37-149                                                                                            --------------- Pfam domains (8)
         Sec.struct. author ..hhhhh.eeee....................eee..............------............eeee.....eeee.............eeee...........ee..eeeee....ee..........eeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r1a H  28 VTGDTDQPIHIESDQQSLDMQGNVVTFTGNVIVTQGTIKINADKVVVTR------KEVIDGYGKPATFYQMQDNGKPVEGHASQMHYELAKDFVVLTGNAYLQQVDSNIKGDKITYLVKEQKMQAFSDKGKRVTTVL 164
                                    37        47        57        67        |-     |  87        97       107       117       127       137       147       157       
                                                                           76     83
   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  (0, 0)

(no "SCOP Domain" information available for 2R1A)

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 8)

Asymmetric Unit
(-)
Clan: OstA (3)
(-)
Family: OstA (2)
(-)
Escherichia coli (strain K12) (2)
1aOstA-2r1aH01H:37-149
1bOstA-2r1aH02H:37-149
1cOstA-2r1aH03H:37-149
1dOstA-2r1aH04H:37-149
1eOstA-2r1aH05H:37-149
1fOstA-2r1aH06H:37-149
1gOstA-2r1aH07H:37-149
1hOstA-2r1aH08H:37-149

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H   (LPTA_ECOLI | P0ADV1)
molecular function
    GO:0017089    glycolipid transporter activity    Enables the directed movement of glycolipids, compounds containing (usually) 1-4 linked monosaccharide residues joined by a glycosyl linkage to a lipid, into, out of or within a cell, or between cells.
    GO:0001530    lipopolysaccharide binding    Interacting selectively and non-covalently with lipopolysaccharide.
    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:0043165    Gram-negative-bacterium-type cell outer membrane assembly    The assembly of an outer membrane of the type formed in Gram-negative bacteria. This membrane is enriched in polysaccharide and protein, and the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    GO:0046836    glycolipid transport    The directed movement of glycolipids, compounds containing (usually) 1-4 linked monosaccharide residues joined by a glycosyl linkage to a lipid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0015920    lipopolysaccharide transport    The directed movement of lipopolysaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A lipopolysaccharide is any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria. Lipopolysaccharides consist three covalently linked regions, lipid A, core oligosaccharide, and an O side chain. Lipid A is responsible for the toxicity of the lipopolysaccharide.
    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:0009279    cell outer membrane    A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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  Cis Peptide Bonds
    Ala E:117 - Lys E:118   [ RasMol ]  
    Gly B:125 - Asn B:126   [ RasMol ]  
    Gly B:49 - Asn B:50   [ RasMol ]  
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  2r1a
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 Related Entries

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

UniProtKB/Swiss-Prot
        LPTA_ECOLI | P0ADV1: 2r19

(-) Related Entries Specified in the PDB File

2r19 CRYSTAL STRUCTURE OF PERIPLASMIC LIPOPOLYSACCHARIDE TRANSPORT PROTEIN LPTA (YHBN), ORTHORHOMBIC FORM, TWO MOLECULES IN ASYMMETRIC UNIT