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(-) Description

Title :  STRUCTURE OF A DI PEPTIDE BOUND POT FAMILY PEPTIDE TRANSPORTER
 
Authors :  J. A. Lyons, J. L. Parker, N. Solcan, A. Brinth, D. Li, S. T. A. Shah, M. Caf S. Newstead
Date :  09 May 14  (Deposition) - 25 Jun 14  (Release) - 13 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.47
Chains :  Asym./Biol. Unit :  A,D
Keywords :  Transport Protein, Major Facilitator Superfamily, Proton Oligopeptide Transporter (Pot) Family, Peptide Transporter, Peptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Lyons, J. L. Parker, N. Solcan, A. Brinth, D. Li, S. T. Shah, M. Caffrey, S. Newstead
Structural Basis For Polyspecificity In The Pot Family Of Proton-Coupled Oligopeptide Transporters.
Embo Rep. V. 15 886 2014
PubMed-ID: 24916388  |  Reference-DOI: 10.15252/EMBR.201338403

(-) Compounds

Molecule 1 - DI-OR TRIPEPTIDE:H+ SYMPORTER
    Atcc: BAA-250
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PWALDO-GFPD
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: C43
    Expression System Vector Type: PLASMID
    Organism Scientific: STREPTOCOCCUS THERMOPHILUS
    Organism Taxid: 264199
    Strain: LMG 18311
    Synonym: DI- OR TRIPEPTIDE PROTON SYMPORTER
 
Molecule 2 - L-ALANINE-L-PHENYLALANINE
    Chains: D
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
178M4Ligand/Ion(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
278N2Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:85 , PRO A:86 , PHE A:89 , TYR A:194 , LYS A:198BINDING SITE FOR RESIDUE 78M A1473
2AC2SOFTWAREALA A:248 , ASN A:251 , ALA A:259 , PHE A:263BINDING SITE FOR RESIDUE 78M A1474
3AC3SOFTWARELEU A:369 , ALA A:372 , ILE A:373 , 78M A:1476BINDING SITE FOR RESIDUE 78N A1475
4AC4SOFTWARELEU A:212 , LEU A:221 , ALA A:376 , 78N A:1475 , 78N A:1478BINDING SITE FOR RESIDUE 78M A1476
5AC5SOFTWARELEU A:370 , TYR A:378 , VAL A:384 , SER A:385 , LEU A:387 , TRP A:388 , GLY A:391BINDING SITE FOR RESIDUE 78M A1477
6AC6SOFTWARELEU A:212 , VAL A:217 , 78M A:1476BINDING SITE FOR RESIDUE 78N A1478
7AC7SOFTWAREASP A:48 , PHE A:106 , GLY A:107 , ALA A:108 , SER A:109BINDING SITE FOR RESIDUE PO4 A1479

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D2C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4D2C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4D2C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D2C)

(-) Exons   (0, 0)

(no "Exon" information available for 4D2C)

(-) 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:429
 aligned with Q5M4H8_STRT2 | Q5M4H8 from UniProtKB/TrEMBL  Length:483

    Alignment length:467
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       
         Q5M4H8_STRT2     6 KTFFGQPLGLSTLFMTEMWERFSYYGMRAILLYYMWFLISTGDLHITRATAASIMAIYASMVYLSGTIGGFVADRIIGARPAVFWGGVLIMLGHIVLALPFGASALFGSIILIIIGTGFLKPNVSTLVGTLYDEHDRRRDAGFSIFVFGINLGAFIAPLIVGAAQEAAGYHVAFSLAAIGMFIGLLVYYFGGKKTLDPHYLRPTDPLAPEEVKPLLVKVSLAVAGFIAIIVVMNLVGWNSLPAYINLLTIVAIAIPVFYFAWMISSVKVTSTEHLRVVSYIPLFIAAVLFWAIEEQGSVVLATFAAERVDSSWFPVSWFQSLNPLFIMLYTPFFAWLWTAWKKNQPSSPTKFAVGLMFAGLSFLLMAIPGALYGTSGKVSPLWLVGSWALVILGEMLISPVGLSVTTKLAPKAFNSQMMSMWFLSSSVGSALNAQLVTLYNAKSEVAYFSYFGLGSVVLGIVLVFLS 472
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh-----------------hhhhhhhhhhhhhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh-----..hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..----------------hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d2c A   6 KTFFGQPLGLSTLFMTEMWERFSYYGMRAILLYYMWFLISTGDLHITRATAASIMAIYASMVYLSGTIGGFVADRIIGARPAVFWGGVLIMLGHIVLALPFGASALFGSIILIIIGTGFLKPNVSTLVGTLYDEHDRRRDAGFSIFVFGINLGAFIAPLIVGAAQEAAGYHVAFSLAAIGMFIGLLVYYFGGKKTLDPHYLRPTDPLAPEEVKPLLVKVSLAVAGFIAIIVVMNLVGWNSLPAYINLLTIVAIAIPVFYFAW-----------------YIPLFIAAVLFWAIEEQGSVVLATFAAERVDSSWFPVSWFQSLNPLFIMLYTPFFAWLWTAW-----SSPTKFAVGLMFAGLSFLLMAIPGALYGTSGKVSPLWLVGSWALVILGEMLISPV----------------MMSMWFLSSSVGSALNAQLVTLYNAKSEVAYFSYFGLGSVVLGIVLVFLS 472
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265 |       -       285       295       305       315       325       335       345|     |355       365       375       385       395       405|        -       425       435       445       455       465       
                                                                                                                                                                                                                                                                                               267               285                                                          346   352                                                   406              423                                                 


Chain D from PDB  Type:PROTEIN  Length:2
                                  
               SCOP domains -- SCOP domains
               CATH domains -- CATH domains
               Pfam domains -- Pfam domains
         Sec.struct. author .. Sec.struct. author
                 SAPs(SNPs) -- SAPs(SNPs)
                    PROSITE -- PROSITE
                 Transcript -- Transcript
                 4d2c D  32 AF  33
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 4D2C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D2C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D2C)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q5M4H8_STRT2 | Q5M4H8)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0015197    peptide transporter activity    Enables the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells.
    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:0006857    oligopeptide transport    The directed movement of oligopeptides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Oligopeptides are molecules that contain a small number (2 to 20) of amino-acid residues connected by peptide linkages.
    GO:0015833    peptide transport    The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, 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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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        Q5M4H8_STRT2 | Q5M4H8: 4aps 4d2b 4d2d 4xni 4xnj 5d58 5d59 5d6k 5mmt

(-) Related Entries Specified in the PDB File

4d2b STRUCTURE OF A LIGAND FREE POT FAMILY PEPTIDE TRANSPORTER
4d2d STRUCTURE OF A TRI PEPTIDE BOUND POT FAMILY PEPTIDE TRANSPORTER