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(-) Description

Title :  INWARD OPEN CONFORMATION OF THE XYLOSE TRANSPORTER XYLE FROM E. COLI
 
Authors :  E. M. Quistgaard, C. Low, P. Moberg, L. Tresaugues, P. Nordlund
Date :  18 Feb 13  (Deposition) - 01 May 13  (Release) - 17 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.20
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Mfs General Substrate Transporter, Xylose Transporter, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. M. Quistgaard, C. Low, P. Moberg, L. Tresaugues, P. Nordlund
Structural Basis For Substrate Transport In The Glut-Homology Family Of Monosaccharide Transporters.
Nat. Struct. Mol. Biol. V. 20 766 2013
PubMed-ID: 23624861  |  Reference-DOI: 10.1038/NSMB.2569

(-) Compounds

Molecule 1 - D-XYLOSE-PROTON SYMPORTER
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PTH27 VECTOR
    Expression System Strain: C41(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 2-485
    Gene: XYLE, B4031, JW3991
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: D-XYLOSE TRANSPORTER

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CD1Ligand/IonCADMIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:258 , HIS A:262 , HIS B:258 , HIS B:262 , HIS C:258 , HIS C:262BINDING SITE FOR RESIDUE CD A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JA4)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Leu A:227 -Met A:228
2Lys A:431 -Asn A:432
3Leu B:227 -Met B:228
4Lys B:431 -Asn B:432
5Leu C:227 -Met C:228

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JA4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JA4)

(-) Exons   (0, 0)

(no "Exon" information available for 4JA4)

(-) 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:442
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh.hhhhhh.hhhhhhhhhhhh............hhhhhhhhh....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhh......hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh......hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh..............hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ja4 A   9 YIFSITLVATLGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVASALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMQEQAEGILRKIMGNTLATQAVQEIKHSLDHGMFGVGVIVIGVMLSIFQQFVGINVVLYYAPEVLLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGTAFYTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLANYFVSWTFPMMDKNSWNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELEALWE 479
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228|      242       252       262||     280       290       300  ||   321       331       341       351       361       371       381       391       401       411       421       431  ||   447       457       467       477  
                                                                                                                                                                                                                                                     228|                           263|                            303|                                                                                                                    434|                                      
                                                                                                                                                                                                                                                      233                            272                             315                                                                                                                     441                                      


Chain B from PDB  Type:PROTEIN  Length:439
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh.hhhhhh.hhhhhhhhhhh.............hhhhhhhhh....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh......hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh..............hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ja4 B   9 YIFSITLVATLGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVASALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNPVYLAGYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMQEQAEGILRKIMGNTLATQAVQEIKHSLDHGMFGVGVIVIGVMLSIFQQFVGINVVLYYAPEVLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGTAFYTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLANYFVSWTFPMMDKNSWNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELEALWE 479
                                    18        28        38        48        58        68        78        88        98       108       120       130       140       150       160       170       180       190       200       210       220       234       244       254       272       282       292       302||     324       334       344       354       364       374       384       394       404       414       424       434|      450       460       470         
                                                                                                                                     116|                                                                                                          228|                           263|                            303|                                                                                                                   434|                                      
                                                                                                                                      119                                                                                                           233                            272                             316                                                                                                                    441                                      


Chain C from PDB  Type:PROTEIN  Length:436
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh.hhhhhh.hhhhhhhhhhh.............hhhhhhhhh....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh......hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..............hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ja4 C   9 YIFSITLVATLGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVASALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPTVPVYLAGYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMQEQAEGILRKIMGNTLATQAVQEIKHSLDHGMFGVGVIVIGVMLSIFQQFVGINVVLYYAPEVLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGTAFYTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLANYFVSWTFPMMDKNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELEALWE 479
                                    18        28        38        48        58        68        78        88        98       108     ||120       130       140       150       160       170       180       190       200       210       220       234       244       254       272       282       292       302||     324       334       344       354       364       374       384       394       404       414       424      |443       453       463       473      
                                                                                                                                   114|                                                                                                            228|                           263|                            303|                                                                                                                431|                                      
                                                                                                                                    117                                                                                                             233                            272                             316                                                                                                                 441
   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 4JA4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JA4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JA4)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)

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  4ja4
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  XYLE_ECOLI | P0AGF4
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 Related Entries

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

UniProtKB/Swiss-Prot
        XYLE_ECOLI | P0AGF4: 4gby 4gbz 4gc0 4ja3 4qiq

(-) Related Entries Specified in the PDB File

4ja3 PARTIALLY OCCLUDED INWARD OPEN CONFORMATION OF THE XYLOSE TRANSPORTER XYLE FROM E. COLI