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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF PERIPLASMIC LEU/ILE/VAL-BINDING PROTEIN WITH BOUND LIGAND ISOLEUCINE
 
Authors :  S. D. Trakhanov, N. K. Vyas, D. M. Kristensen, J. Ma, F. A. Quiocho
Date :  03 Mar 05  (Deposition) - 04 Oct 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym./Biol. Unit :  A
Keywords :  Periplasmic Binding Proteins, Alpha-Beta Fold, Aliphatic Amino Acid Binding Protein, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. D. Trakhanov, N. K. Vyas, H. Luecke, D. M. Kristensen, J. Ma, F. A. Quiocho
Ligand-Free And -Bound Structures Of The Binding Protein (Livj) Of The Escherichia Coli Abc Leucine/Isoleucine/Valin Transport System: Trajectory And Dynamics Of The Interdomai Rotation And Ligand Specificity.
Biochemistry V. 44 6597 2005
PubMed-ID: 15850393  |  Reference-DOI: 10.1021/BI047302O
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LEU/ILE/VAL-BINDING PROTEIN
    Chains: A
    Fragment: MATURED PROTEIN (RESIDUES 24-367)
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: LIV-BP

 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
1ILE1Mod. Amino AcidISOLEUCINE
2MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:18 , LEU A:77 , CYS A:78 , SER A:79 , ALA A:100 , ALA A:101 , THR A:102 , TYR A:150 , TYR A:202 , GLU A:226 , GLY A:227 , PHE A:276BINDING SITE FOR RESIDUE ILE A 400
2AC2SOFTWAREASP A:173 , THR A:184 , LEU A:185 , ARG A:188 , ALA A:298 , GLU A:299 , HOH A:824BINDING SITE FOR RESIDUE MRD A 410

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:53 -A:78

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Z17)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z17)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Z17)

(-) Exons   (0, 0)

(no "Exon" information available for 1Z17)

(-) 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:345
 aligned with LIVJ_ECO57 | P0AD98 from UniProtKB/Swiss-Prot  Length:367

    Alignment length:345
                                                                                                                                                                                                                                                                                                                                                                                 367 
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363   | 
           LIVJ_ECO57    24 EDIKVAVVGAMSGPVAQYGDQEFTGAEQAVADINAKGGIKGNKLQIVKYDDACDPKQAVAVANKVVNDGIKYVIGHLCSSSTQPASDIYEDEGILMITPAATAPELTARGYQLILRTTGLDSDQGPTAAKYILEKVKPQRIAIVHDKQQYGEGLARAVQDGLKKGNANVVFFDGITAGEKDFSTLVARLKKENIDFVYYGGYHPEMGQILRQARAAGLKTQFMGPEGVANVSLSNIAGESAEGLLVTKPKNYDQVPANKPIVDAIKAKKQDPSGAFVWTTYAALQSLQAGLNQSDDPAEIAKYLKANSVDTVMGPLTWDEKGDLKGFEFGVFDWHANGTATDAK-   -
               SCOP domains d1z17a_ A: automated matches                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1z17A01 A:1-120,A:250-328  [code=3.40.50.2300, no name defined]                                                         1z17A02 A:121-249,A:329-344  [code=3.40.50.2300, no name defined]                                                                1z17A01 A:1-120,A:250-328  [code=3.40.50.2300, no name defined]                1z17A02         - CATH domains
               Pfam domains -Peripla_BP_6-1z17A01 A:2-338                                                                                                                                                                                                                                                                                                                     ------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhhhhhhhhhhh.......eeeeeee...hhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhh.eeee....hhhhhh.....eee...hhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.eee..eee.............eeeee.....eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z17 A   1 EDIKVAVVGAMSGPVAQYGDQEFTGAEQAVADINAKGGIKGNKLQIVKYDDACDPKQAVAVANKVVNDGIKYVIGHLCSSSTQPASDIYEDEGILMITPAATAPELTARGYQLILRTTGLDSDQGPTAAKYILEKVKPQRIAIVHDKQQYGEGLARAVQDGLKKGNANVVFFDGITAGEKDFSTLVARLKKENIDFVYYGGYHPEMGQILRQARAAGLKTQFMGPEGVANVSLSNIAGESAEGLLVTKPKNYDQVPANKPIVDAIKAKKQDPSGAFVWTTYAALQSLQAGLNQSDDPAEIAKYLKANSVDTVMGPLTWDEKGDLKGFEFGVFDWHANGTATDAKI 400
                                    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       260       270       280       290       300       310       320       330       340   ||
                                                                                                                                                                                                                                                                                                                                                                                 344|
                                                                                                                                                                                                                                                                                                                                                                                  400


Chain A from PDB  Type:PROTEIN  Length:345
 aligned with LIVJ_ECOL6 | P0AD97 from UniProtKB/Swiss-Prot  Length:367

    Alignment length:345
                                                                                                                                                                                                                                                                                                                                                                                 367 
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363   | 
           LIVJ_ECOL6    24 EDIKVAVVGAMSGPVAQYGDQEFTGAEQAVADINAKGGIKGNKLQIVKYDDACDPKQAVAVANKVVNDGIKYVIGHLCSSSTQPASDIYEDEGILMITPAATAPELTARGYQLILRTTGLDSDQGPTAAKYILEKVKPQRIAIVHDKQQYGEGLARAVQDGLKKGNANVVFFDGITAGEKDFSTLVARLKKENIDFVYYGGYHPEMGQILRQARAAGLKTQFMGPEGVANVSLSNIAGESAEGLLVTKPKNYDQVPANKPIVDAIKAKKQDPSGAFVWTTYAALQSLQAGLNQSDDPAEIAKYLKANSVDTVMGPLTWDEKGDLKGFEFGVFDWHANGTATDAK-   -
               SCOP domains d1z17a_ A: automated matches                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1z17A01 A:1-120,A:250-328  [code=3.40.50.2300, no name defined]                                                         1z17A02 A:121-249,A:329-344  [code=3.40.50.2300, no name defined]                                                                1z17A01 A:1-120,A:250-328  [code=3.40.50.2300, no name defined]                1z17A02         - CATH domains
               Pfam domains -Peripla_BP_6-1z17A01 A:2-338                                                                                                                                                                                                                                                                                                                     ------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhhhhhhhhhhh.......eeeeeee...hhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhh.eeee....hhhhhh.....eee...hhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.eee..eee.............eeeee.....eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z17 A   1 EDIKVAVVGAMSGPVAQYGDQEFTGAEQAVADINAKGGIKGNKLQIVKYDDACDPKQAVAVANKVVNDGIKYVIGHLCSSSTQPASDIYEDEGILMITPAATAPELTARGYQLILRTTGLDSDQGPTAAKYILEKVKPQRIAIVHDKQQYGEGLARAVQDGLKKGNANVVFFDGITAGEKDFSTLVARLKKENIDFVYYGGYHPEMGQILRQARAAGLKTQFMGPEGVANVSLSNIAGESAEGLLVTKPKNYDQVPANKPIVDAIKAKKQDPSGAFVWTTYAALQSLQAGLNQSDDPAEIAKYLKANSVDTVMGPLTWDEKGDLKGFEFGVFDWHANGTATDAKI 400
                                    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       260       270       280       290       300       310       320       330       340   ||
                                                                                                                                                                                                                                                                                                                                                                                 344|
                                                                                                                                                                                                                                                                                                                                                                                  400


Chain A from PDB  Type:PROTEIN  Length:345
 aligned with LIVJ_ECOLI | P0AD96 from UniProtKB/Swiss-Prot  Length:367

    Alignment length:345
                                                                                                                                                                                                                                                                                                                                                                                 367 
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363   | 
           LIVJ_ECOLI    24 EDIKVAVVGAMSGPVAQYGDQEFTGAEQAVADINAKGGIKGNKLQIVKYDDACDPKQAVAVANKVVNDGIKYVIGHLCSSSTQPASDIYEDEGILMITPAATAPELTARGYQLILRTTGLDSDQGPTAAKYILEKVKPQRIAIVHDKQQYGEGLARAVQDGLKKGNANVVFFDGITAGEKDFSTLVARLKKENIDFVYYGGYHPEMGQILRQARAAGLKTQFMGPEGVANVSLSNIAGESAEGLLVTKPKNYDQVPANKPIVDAIKAKKQDPSGAFVWTTYAALQSLQAGLNQSDDPAEIAKYLKANSVDTVMGPLTWDEKGDLKGFEFGVFDWHANGTATDAK-   -
               SCOP domains d1z17a_ A: automated matches                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1z17A01 A:1-120,A:250-328  [code=3.40.50.2300, no name defined]                                                         1z17A02 A:121-249,A:329-344  [code=3.40.50.2300, no name defined]                                                                1z17A01 A:1-120,A:250-328  [code=3.40.50.2300, no name defined]                1z17A02         - CATH domains
               Pfam domains -Peripla_BP_6-1z17A01 A:2-338                                                                                                                                                                                                                                                                                                                     ------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhhhhhhhhhhh.......eeeeeee...hhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhh.eeee....hhhhhh.....eee...hhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.eee..eee.............eeeee.....eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z17 A   1 EDIKVAVVGAMSGPVAQYGDQEFTGAEQAVADINAKGGIKGNKLQIVKYDDACDPKQAVAVANKVVNDGIKYVIGHLCSSSTQPASDIYEDEGILMITPAATAPELTARGYQLILRTTGLDSDQGPTAAKYILEKVKPQRIAIVHDKQQYGEGLARAVQDGLKKGNANVVFFDGITAGEKDFSTLVARLKKENIDFVYYGGYHPEMGQILRQARAAGLKTQFMGPEGVANVSLSNIAGESAEGLLVTKPKNYDQVPANKPIVDAIKAKKQDPSGAFVWTTYAALQSLQAGLNQSDDPAEIAKYLKANSVDTVMGPLTWDEKGDLKGFEFGVFDWHANGTATDAKI 400
                                    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       260       270       280       290       300       310       320       330       340   ||
                                                                                                                                                                                                                                                                                                                                                                                 344|
                                                                                                                                                                                                                                                                                                                                                                                  400
   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) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Periplas_BP (97)

(-) Gene Ontology  (6, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LIVJ_ECOL6 | P0AD97)
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: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).

Chain A   (LIVJ_ECOLI | P0AD96)
molecular function
    GO:0015658    branched-chain amino acid transmembrane transporter activity    Enables the transfer of branched-chain amino acids from one side of a membrane to the other. Branched-chain amino acids are amino acids with a branched carbon skeleton without rings.
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:0015803    branched-chain amino acid transport    The directed movement of branched-chain amino acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Branched-chain amino acids are amino acids with a branched carbon skeleton without rings.
    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).

Chain A   (LIVJ_ECO57 | P0AD98)
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: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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  1z17
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  LIVJ_ECO57 | P0AD98
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  LIVJ_ECOL6 | P0AD97
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  LIVJ_ECOLI | P0AD96
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 Related Entries

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

UniProtKB/Swiss-Prot
        LIVJ_ECO57 | P0AD98: 1z15 1z16 1z18 2liv
        LIVJ_ECOL6 | P0AD97: 1z15 1z16 1z18 2liv
        LIVJ_ECOLI | P0AD96: 1z15 1z16 1z18 2liv

(-) Related Entries Specified in the PDB File

1z15
1z16
1z18
2lbp 2LBP IS A LEUCINE SPECIFIC PROTEIN BUT ITS OVERALL STRUCTURE IS SIMILAR TO 2LIV.
2liv 2LIV IS THE SAME STRUCTURE BUT IN LESS OPEN FORM.