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(-) Description

Title :  THREE-DIMENSIONAL STRUCTURES OF THE PERIPLASMIC LYSINE-, ARGININE-, ORNITHINE-BINDING PROTEIN WITH AND WITHOUT A LIGAND
 
Authors :  S. -H. Kim, B. -H. Oh
Date :  25 Feb 93  (Deposition) - 22 Jun 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Amino-Acid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. H. Oh, J. Pandit, C. H. Kang, K. Nikaido, S. Gokcen, G. F. Ames, S. H. Kim
Three-Dimensional Structures Of The Periplasmic Lysine/Arginine/Ornithine-Binding Protein With And Without A Ligand.
J. Biol. Chem. V. 268 11348 1993
PubMed-ID: 8496186
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LYSINE, ARGININE, ORNITHINE-BINDING PROTEIN
    Chains: A
    Engineered: YES
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1LYS1Mod. Amino AcidLYSINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:11 , TYR A:14 , PHE A:52 , SER A:69 , SER A:70 , SER A:72 , ARG A:77 , LEU A:117 , SER A:120 , THR A:121 , GLN A:122 , ASP A:161 , HOH A:426BINDING SITE FOR RESIDUE LYS A 240

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:38 -A:45

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:15 -Pro A:16

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LST)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SBP_BACTERIAL_3PS01039 Bacterial extracellular solute-binding proteins, family 3 signature.ARGT_SALTY50-63  1A:28-41

(-) Exons   (0, 0)

(no "Exon" information available for 1LST)

(-) 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:239
 aligned with ARGT_SALTY | P02911 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:239
                                                                                                                                                                                                                                                                       260 
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       | 
           ARGT_SALTY    23 ALPQTVRIGTDTTYAPFSSKDAKGEFIGFDIDLGNEMCKRMQVKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAKGSPIQPTLESLKGKHVGVLQGSTQEAYANDNWRTKGVDVVAYANQDLIYSDLTAGRLDAALQDEVAASEGFLKQPAGKEYAFAGPSVKDKKYFGDGTGVGLRKDDTELKAAFDKALTELRQDGTYDKMAKKYFDFNVYGD-   -
               SCOP domains d1lsta_ A: Lysine-,arginine-,ornithine-binding (LAO) protein                                                                                                                                                                                    SCOP domains
               CATH domains 1lstA01 A:1-90,A:192-238 Periplasmic binding protein-like II                              1lstA02 A:91-191 Periplasmic binding protein-like II                                                 1lstA01 A:1-90,A:192-238                       - CATH domains
               Pfam domains -----SBP_bac_3-1lstA01 A:6-233                                                                                                                                                                                                           ------ Pfam domains
         Sec.struct. author ....eeeeee..................hhhhhhhhhhhhh..eeeeee.....hhhhhh.....ee.......hhhhhh.eee.......eeeeee........hhhh...eeeee...hhhhhhhhh......eeeee..hhhhhhhhh.....eeeeehhhhhhh.........eeee......hhhh.....eee....hhhhhhhhhhhhhhhh..hhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------SBP_BACTERIAL_------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lst A   1 ALPQTVRIGTDTTYAPFSSKDAKGEFIGFDIDLGNEMCKRMQVKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAKGSPIQPTLESLKGKHVGVLQGSTQEAYANDNWRTKGVDVVAYANQDLIYSDLTAGRLDAALQDEVAASEGFLKQPAGKEYAFAGPSVKDKKYFGDGTGVGLRKDDTELKAAFDKALTELRQDGTYDKMAKKYFDFNVYGDK 240
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       ||
                                                                                                                                                                                                                                                                       238|
                                                                                                                                                                                                                                                                        240
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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) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ARGT_SALTY | P02911)
molecular function
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0006865    amino acid transport    The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        ARGT_SALTY | P02911: 1laf 1lag 1lah 2lao

(-) Related Entries Specified in the PDB File

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