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(-) Description

Title :  PUTRESCINE RECEPTOR (POTF) FROM E. COLI
 
Authors :  D. G. Vassylyev, H. Tomitori, K. Kashiwagi, K. Morikawa, K. Igarashi
Date :  17 Apr 98  (Deposition) - 21 Oct 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Binding Protein, Transport, Periplasmic Putrescine Binding Protein (Potf) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. G. Vassylyev, H. Tomitori, K. Kashiwagi, K. Morikawa, K. Igarashi
Crystal Structure And Mutational Analysis Of The Escherichia Coli Putrescine Receptor. Structural Basis For Substrate Specificity.
J. Biol. Chem. V. 273 17604 1998
PubMed-ID: 9651355  |  Reference-DOI: 10.1074/JBC.273.28.17604
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTRESCINE-BINDING PROTEIN
    Cellular Location: PERIPLASM
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: PUCPOTF
    Expression System Plasmid: PMWPOTF
    Expression System Strain: KK313POTF::KM
    Expression System Taxid: 562
    Gene: PUCPOTF
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: KK313
    Synonym: POTF

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1PUT4Ligand/Ion1,4-DIAMINOBUTANE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PUT2Ligand/Ion1,4-DIAMINOBUTANE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1PUT2Ligand/Ion1,4-DIAMINOBUTANE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:37 , SER A:38 , ASP A:39 , TYR A:40 , TRP A:244 , ASP A:247 , PHE A:276 , ASP A:278 , TYR A:314 , HOH A:471 , HOH A:968BINDING SITE FOR RESIDUE PUT A 371
2AC2SOFTWARETRP B:37 , SER B:38 , ASP B:39 , TYR B:40 , TRP B:244 , ASP B:247 , PHE B:276 , ASP B:278 , TYR B:314 , HOH B:743 , HOH B:858BINDING SITE FOR RESIDUE PUT B 371
3AC3SOFTWARETRP C:37 , SER C:38 , ASP C:39 , TYR C:40 , TRP C:244 , ASP C:247 , PHE C:276 , ASP C:278 , TYR C:314 , HOH C:897 , HOH C:962BINDING SITE FOR RESIDUE PUT C 371
4AC4SOFTWARETRP D:37 , SER D:38 , ASP D:39 , TYR D:40 , TRP D:244 , ASP D:247 , PHE D:276 , ASP D:278 , TYR D:314 , HOH D:412 , HOH D:456BINDING SITE FOR RESIDUE PUT D 371

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:175 -A:239
2B:175 -B:239
3C:175 -C:239
4D:175 -D:239

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1A99)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1A99)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1A99)

(-) Exons   (0, 0)

(no "Exon" information available for 1A99)

(-) 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:341
 aligned with POTF_ECOLI | P31133 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:341
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368 
           POTF_ECOLI    29 QKTLHIYNWSDYIAPDTVANFEKETGIKVVYDVFDSNEVLEGKLMAGSTGFDLVVPSASFLERQLTAGVFQPLDKSKLPEWKNLDPELLKLVAKHDPDNKFAMPYMWATTGIGYNVDKVKAVLGENAPVDSWDLILKPENLEKLKSCGVSFLDAPEEVFATVLNYLGKDPNSTKADDYTGPATDLLLKLRPNIRYFHSSQYINDLANGDICVAIGWAGDVWQASNRAKEAKNGVNVSFSIPKEGAMAFFDVFAMPADAKNKDEAYQFLNYLLRPDVVAHISDHVFYANANKAATPLVSAEVRENPGIYPPADVRAKLFTLKVQDPKIDRVRTRAWTKVKSG 369
               SCOP domains d1a99a_ A: Putrescine receptor (PotF)                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1a99A01 A:29-135,A:277-336 Periplasmic binding protein-like II                                             1a99A02 A:136-276,A:337-369 Periplasmic binding protein-like II                                                                              1a99A01 A:29-135,A:277-336                                  1a99A02 A:136-276,A:337-369       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.......hhhhhhhhh..eeeeeee..hhhhhhhhhh...........hhhhhhhhh........hhh.hhhhh..hhhhhhhhh..hhh..eeeeeeeeeeeeeehhhhhhhh........hhhhh.hhhhhhhhhh.......hhhhhhhhhhh.........hhhhh.hhhhhhhhhhhh.......hhhhhhh.....eeeeehhhhhhhhhhhhhh.....eeee......eeeeeeee.......hhhhhhhhhhhh.hhhhhhhhhhh.........hhh..hhhh........hhhhhh........hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a99 A  29 QKTLHIYNWSDYIAPDTVANFEKETGIKVVYDVFDSNEVLEGKLMAGSTGFDLVVPSASFLERQLTAGVFQPLDKSKLPEWKNLDPELLKLVAKHDPDNKFAMPYMWATTGIGYNVDKVKAVLGENAPVDSWDLILKPENLEKLKSCGVSFLDAPEEVFATVLNYLGKDPNSTKADDYTGPATDLLLKLRPNIRYFHSSQYINDLANGDICVAIGWAGDVWQASNRAKEAKNGVNVSFSIPKEGAMAFFDVFAMPADAKNKDEAYQFLNYLLRPDVVAHISDHVFYANANKAATPLVSAEVRENPGIYPPADVRAKLFTLKVQDPKIDRVRTRAWTKVKSG 369
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368 


Chain B from PDB  Type:PROTEIN  Length:341
 aligned with POTF_ECOLI | P31133 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:341
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368 
           POTF_ECOLI    29 QKTLHIYNWSDYIAPDTVANFEKETGIKVVYDVFDSNEVLEGKLMAGSTGFDLVVPSASFLERQLTAGVFQPLDKSKLPEWKNLDPELLKLVAKHDPDNKFAMPYMWATTGIGYNVDKVKAVLGENAPVDSWDLILKPENLEKLKSCGVSFLDAPEEVFATVLNYLGKDPNSTKADDYTGPATDLLLKLRPNIRYFHSSQYINDLANGDICVAIGWAGDVWQASNRAKEAKNGVNVSFSIPKEGAMAFFDVFAMPADAKNKDEAYQFLNYLLRPDVVAHISDHVFYANANKAATPLVSAEVRENPGIYPPADVRAKLFTLKVQDPKIDRVRTRAWTKVKSG 369
               SCOP domains d1a99b_ B: Putrescine receptor (PotF)                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1a99B01 B:29-135,B:277-336 Periplasmic binding protein-like II                                             1a99B02 B:136-276,B:337-369 Periplasmic binding protein-like II                                                                              1a99B01 B:29-135,B:277-336                                  1a99B02 B:136-276,B:337-369       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.......hhhhhhhhh..eeeeeee..hhhhhhhhhh...........hhhhhhhhh........hhh.hhhhh..hhhhhhhhh..hhh..eeeeeeeeeeeeeehhhhhhhh........hhhhh.hhhhhhhhhh.......hhhhhhhhhhh.........hhhhh.hhhhhhhhhhhh.......hhhhhhhh....eeeeehhhhhhhhhhhhhh.....eeee......eeeeeeee.......hhhhhhhhhhhh.hhhhhhhhhhh.........hhh..hhhh........hhhhhh........hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a99 B  29 QKTLHIYNWSDYIAPDTVANFEKETGIKVVYDVFDSNEVLEGKLMAGSTGFDLVVPSASFLERQLTAGVFQPLDKSKLPEWKNLDPELLKLVAKHDPDNKFAMPYMWATTGIGYNVDKVKAVLGENAPVDSWDLILKPENLEKLKSCGVSFLDAPEEVFATVLNYLGKDPNSTKADDYTGPATDLLLKLRPNIRYFHSSQYINDLANGDICVAIGWAGDVWQASNRAKEAKNGVNVSFSIPKEGAMAFFDVFAMPADAKNKDEAYQFLNYLLRPDVVAHISDHVFYANANKAATPLVSAEVRENPGIYPPADVRAKLFTLKVQDPKIDRVRTRAWTKVKSG 369
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368 


Chain C from PDB  Type:PROTEIN  Length:341
 aligned with POTF_ECOLI | P31133 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:341
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368 
           POTF_ECOLI    29 QKTLHIYNWSDYIAPDTVANFEKETGIKVVYDVFDSNEVLEGKLMAGSTGFDLVVPSASFLERQLTAGVFQPLDKSKLPEWKNLDPELLKLVAKHDPDNKFAMPYMWATTGIGYNVDKVKAVLGENAPVDSWDLILKPENLEKLKSCGVSFLDAPEEVFATVLNYLGKDPNSTKADDYTGPATDLLLKLRPNIRYFHSSQYINDLANGDICVAIGWAGDVWQASNRAKEAKNGVNVSFSIPKEGAMAFFDVFAMPADAKNKDEAYQFLNYLLRPDVVAHISDHVFYANANKAATPLVSAEVRENPGIYPPADVRAKLFTLKVQDPKIDRVRTRAWTKVKSG 369
               SCOP domains d1a99c_ C: Putrescine receptor (PotF)                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1a99C01 C:29-135,C:277-336 Periplasmic binding protein-like II                                             1a99C02 C:136-276,C:337-369 Periplasmic binding protein-like II                                                                              1a99C01 C:29-135,C:277-336                                  1a99C02 C:136-276,C:337-369       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.......hhhhhhhhh..eeeeeee..hhhhhhhhhh...........hhhhhhhhh........hhh.hhhhh..hhhhhhhhh..hhh..eeeeeeeeeeeeeehhhhhhhh........hhhhh.hhhhhhhhhh.......hhhhhhhhhhh.........hhhhh.hhhhhhhhhhhh.......hhhhhhh.....eeeeehhhhhhhhhhhhhh.....eeee......eeeeeeee.......hhhhhhhhhhhh.hhhhhhhhhhh.........hhh..hhhh........hhhhhh........hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a99 C  29 QKTLHIYNWSDYIAPDTVANFEKETGIKVVYDVFDSNEVLEGKLMAGSTGFDLVVPSASFLERQLTAGVFQPLDKSKLPEWKNLDPELLKLVAKHDPDNKFAMPYMWATTGIGYNVDKVKAVLGENAPVDSWDLILKPENLEKLKSCGVSFLDAPEEVFATVLNYLGKDPNSTKADDYTGPATDLLLKLRPNIRYFHSSQYINDLANGDICVAIGWAGDVWQASNRAKEAKNGVNVSFSIPKEGAMAFFDVFAMPADAKNKDEAYQFLNYLLRPDVVAHISDHVFYANANKAATPLVSAEVRENPGIYPPADVRAKLFTLKVQDPKIDRVRTRAWTKVKSG 369
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368 


Chain D from PDB  Type:PROTEIN  Length:341
 aligned with POTF_ECOLI | P31133 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:341
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368 
           POTF_ECOLI    29 QKTLHIYNWSDYIAPDTVANFEKETGIKVVYDVFDSNEVLEGKLMAGSTGFDLVVPSASFLERQLTAGVFQPLDKSKLPEWKNLDPELLKLVAKHDPDNKFAMPYMWATTGIGYNVDKVKAVLGENAPVDSWDLILKPENLEKLKSCGVSFLDAPEEVFATVLNYLGKDPNSTKADDYTGPATDLLLKLRPNIRYFHSSQYINDLANGDICVAIGWAGDVWQASNRAKEAKNGVNVSFSIPKEGAMAFFDVFAMPADAKNKDEAYQFLNYLLRPDVVAHISDHVFYANANKAATPLVSAEVRENPGIYPPADVRAKLFTLKVQDPKIDRVRTRAWTKVKSG 369
               SCOP domains d1a99d_ D: Putrescine receptor (PotF)                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1a99D01 D:29-135,D:277-336 Periplasmic binding protein-like II                                             1a99D02 D:136-276,D:337-369 Periplasmic binding protein-like II                                                                              1a99D01 D:29-135,D:277-336                                  1a99D02 D:136-276,D:337-369       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.......hhhhhhhhh..eeeeeee..hhhhhhhhhh...........hhhhhhhhh........hhh.hhhhh..hhhhhhhhh..hhh..eeeeeeeeeeeeeehhhhhhhh........hhhhh.hhhhhhh..........hhhhhhhhhhh.........hhhhh.hhhhhhhhhhhh.......hhhhhhhh....eeeeehhhhhhhhhhhhhh.....eeee......eeeeeeee.......hhhhhhhhhhhh.hhhhhhhhhhh.........hhh..hhhh........hhhhhh........hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a99 D  29 QKTLHIYNWSDYIAPDTVANFEKETGIKVVYDVFDSNEVLEGKLMAGSTGFDLVVPSASFLERQLTAGVFQPLDKSKLPEWKNLDPELLKLVAKHDPDNKFAMPYMWATTGIGYNVDKVKAVLGENAPVDSWDLILKPENLEKLKSCGVSFLDAPEEVFATVLNYLGKDPNSTKADDYTGPATDLLLKLRPNIRYFHSSQYINDLANGDICVAIGWAGDVWQASNRAKEAKNGVNVSFSIPKEGAMAFFDVFAMPADAKNKDEAYQFLNYLLRPDVVAHISDHVFYANANKAATPLVSAEVRENPGIYPPADVRAKLFTLKVQDPKIDRVRTRAWTKVKSG 369
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368
   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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Architecture: 3-Layer(aba) Sandwich (12045)
(-)
Topology: D-Maltodextrin-Binding Protein; domain 2 (600)
(-)
Homologous Superfamily: Periplasmic binding protein-like II (486)
(-)
Escherichia coli. Organism_taxid: 562. Strain: kk313. (1)
1a1a99A01A:29-135,A:277-336
1b1a99B01B:29-135,B:277-336
1c1a99C01C:29-135,C:277-336
1d1a99D01D:29-135,D:277-336
1e1a99A02A:136-276,A:337-369
1f1a99B02B:136-276,B:337-369
1g1a99C02C:136-276,C:337-369
1h1a99D02D:136-276,D:337-369

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1A99)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (POTF_ECOLI | P31133)
molecular function
    GO:0019808    polyamine binding    Interacting selectively and non-covalently with polyamines, organic compounds containing two or more amino groups.
    GO:0015594    putrescine-importing ATPase activity    Catalysis of the reaction: ATP + H2O + putrescine(out) -> ADP + phosphate + putrescine(in).
biological process
    GO:0015846    polyamine transport    The directed movement of polyamines, organic compounds containing two or more amino groups, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0015847    putrescine transport    The directed movement of putrescine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Putrescine is 1,4-diaminobutane, the polyamine formed by decarboxylation of ornithine and the metabolic precursor of spermidine and spermine.
    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:0043190    ATP-binding cassette (ABC) transporter complex    A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
    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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  1a99
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  POTF_ECOLI | P31133
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 Related Entries

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

UniProtKB/Swiss-Prot
        POTF_ECOLI | P31133: 4jdf

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1A99)