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(-) Description

Title :  CRYSTAL STRUCTURE OF A PERIPLASMIC SUGAR ABC TRANSPORTER FROM THERMOTOGA MARITIMA
 
Authors :  K. Palani, D. Kumaran, S. K. Burley, S. Swaminathan, New York Sgx Res Center For Structural Genomics (Nysgxrc)
Date :  08 Aug 07  (Deposition) - 28 Aug 07  (Release) - 18 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A (1x),B (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Abc Sugar Transporter, Sugar-Binding Protein, Protein Structure Initiative Ii, Psi Ii, Nysgxrc, 11013Q, Structural Genomics, New York Sgx Research Center For Structural Genomics, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Palani, D. Kumaran, S. K. Burley, S. Swaminathan
Structure Of A Periplasmic Glucose-Binding Protein From Thermotoga Maritima.
Acta Crystallogr. , Sect. F V. 68 1460 2012
PubMed-ID: 23192024  |  Reference-DOI: 10.1107/S1744309112045241

(-) Compounds

Molecule 1 - SUGAR ABC TRANSPORTER, PERIPLASMIC SUGAR-BINDING PROTEIN
    Atcc43589
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPSGX3(BC)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 33-334
    GeneTM_0114
    Organism ScientificTHERMOTOGA MARITIMA MSB8
    Organism Taxid243274
    StrainMSB8, DSM 3109, JCM 10099

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A (1x)B (1x)  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 48)

Asymmetric Unit (2, 48)
No.NameCountTypeFull Name
1BGC4Ligand/IonBETA-D-GLUCOSE
2MSE44Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2MSE11Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 24)
No.NameCountTypeFull Name
1BGC2Ligand/IonBETA-D-GLUCOSE
2MSE22Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:39 , SER A:40 , TRP A:45 , ASP A:119 , ASN A:167 , ARG A:171 , GLU A:194 , TYR A:220 , ALA A:221 , TYR A:222 , ASP A:246 , GLN A:266BINDING SITE FOR RESIDUE BGC A 400
2AC2SOFTWARELYS B:39 , TYR B:44 , TRP B:45 , ASP B:119 , ASN B:167 , ARG B:171 , GLU B:194 , TYR B:220 , ALA B:221 , TYR B:222 , ASP B:246 , GLN B:266BINDING SITE FOR RESIDUE BGC B 400
3AC3SOFTWARELYS C:39 , SER C:40 , TYR C:44 , TRP C:45 , ASP C:119 , ASN C:167 , ARG C:171 , GLU C:194 , TYR C:220 , ALA C:221 , TYR C:222 , ASP C:246 , GLN C:266BINDING SITE FOR RESIDUE BGC C 400
4AC4SOFTWARELYS D:39 , SER D:40 , TYR D:44 , TRP D:45 , ASP D:119 , ASN D:167 , ARG D:171 , GLU D:194 , TYR D:220 , ALA D:221 , TYR D:222 , ASP D:246 , GLN D:266BINDING SITE FOR RESIDUE BGC D 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QVC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2QVC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QVC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QVC)

(-) Exons   (0, 0)

(no "Exon" information available for 2QVC)

(-) 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:302
 aligned with Q9WXW9_THEMA | Q9WXW9 from UniProtKB/TrEMBL  Length:335

    Alignment length:302
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331  
         Q9WXW9_THEMA    32 LTIGVIGKSVHPYWSQVEQGVKAAGKALGVDTKFFVPQKEDINAQLQMLESFIAEGVNGIAIAPSDPTAVIPTIKKALEMGIPVVTLDTDSPDSGRYVYIGTDNYQAGYTAGLIMKELLGGKGKVVIGTGSLTAMNSLQRIQGFKDAIKDSEIEIVDILNDEEDGARAVSLAEAALNAHPDLDAFFGVYAYNGPAQALVVKNAGKVGKVKIVCFDTTPDILQYVKEGVIQATMGQRPYMMGYLSVTVLYLMNKIGVQNTLMMLPKVKVDGKVDYVIDTGVDVVTPENLDEYLKKMEELGIPI 333
               SCOP domains d2qvca_ A: automated matches                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2qvcA01 A:32-133,A:266-310  [code=3.40.50.2300, no name defined]                                      2qvcA02 A:134-265,A:311-333  [code=3.40.50.2300, no name defined]                                                                   2qvcA01 A:32-133,A:266-310                   2qvcA02                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhh...eeee..........eeee.hhhhhhhhhhhhhhhhh..eeeeeeee....hhhhhhhhhhhhhhhh..eeeeeeeee...hhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhh......eeeee..hhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeeeeee...eee...hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qvc A  32 LTIGVIGKSVHPYWSQVEQGVKAAGKALGVDTKFFVPQKEDINAQLQmLESFIAEGVNGIAIAPSDPTAVIPTIKKALEmGIPVVTLDTDSPDSGRYVYIGTDNYQAGYTAGLImKELLGGKGKVVIGTGSLTAmNSLQRIQGFKDAIKDSEIEIVDILNDEEDGARAVSLAEAALNAHPDLDAFFGVYAYNGPAQALVVKNAGKVGKVKIVCFDTTPDILQYVKEGVIQATmGQRPYmmGYLSVTVLYLmNKIGVQNTLmmLPKVKVDGKVDYVIDTGVDVVTPENLDEYLKKmEELGIPI 333
                                    41        51        61        71       |81        91       101       111       121       131       141    |  151       161    |  171       181       191       201       211       221       231       241       251       261  |    271       281|      291||     301       311       321    |  331  
                                                                          79-MSE                         111-MSE                            146-MSE             166-MSE                                                                                           264-MSE ||        282-MSE   292-MSE                           326-MSE   
                                                                                                                                                                                                                                                                        270-MSE                293-MSE                                    
                                                                                                                                                                                                                                                                         271-MSE                                                          

Chain B from PDB  Type:PROTEIN  Length:302
 aligned with Q9WXW9_THEMA | Q9WXW9 from UniProtKB/TrEMBL  Length:335

    Alignment length:302
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331  
         Q9WXW9_THEMA    32 LTIGVIGKSVHPYWSQVEQGVKAAGKALGVDTKFFVPQKEDINAQLQMLESFIAEGVNGIAIAPSDPTAVIPTIKKALEMGIPVVTLDTDSPDSGRYVYIGTDNYQAGYTAGLIMKELLGGKGKVVIGTGSLTAMNSLQRIQGFKDAIKDSEIEIVDILNDEEDGARAVSLAEAALNAHPDLDAFFGVYAYNGPAQALVVKNAGKVGKVKIVCFDTTPDILQYVKEGVIQATMGQRPYMMGYLSVTVLYLMNKIGVQNTLMMLPKVKVDGKVDYVIDTGVDVVTPENLDEYLKKMEELGIPI 333
               SCOP domains d2qvcb_ B: automated matches                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2qvcB01 B:32-133,B:266-310  [code=3.40.50.2300, no name defined]                                      2qvcB02 B:134-265,B:311-333  [code=3.40.50.2300, no name defined]                                                                   2qvcB01 B:32-133,B:266-310                   2qvcB02                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhh...eeee..........eeee.hhhhhhhhhhhhhhhhh..eeeeeeee....hhhhhhhhhhhhhhh...eeeeeeeee...hhhhhhhhhh..........eeee...hhhhhhhhhhhhh......eeeee..hhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..eeeeeee...eee...hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qvc B  32 LTIGVIGKSVHPYWSQVEQGVKAAGKALGVDTKFFVPQKEDINAQLQmLESFIAEGVNGIAIAPSDPTAVIPTIKKALEmGIPVVTLDTDSPDSGRYVYIGTDNYQAGYTAGLImKELLGGKGKVVIGTGSLTAmNSLQRIQGFKDAIKDSEIEIVDILNDEEDGARAVSLAEAALNAHPDLDAFFGVYAYNGPAQALVVKNAGKVGKVKIVCFDTTPDILQYVKEGVIQATmGQRPYmmGYLSVTVLYLmNKIGVQNTLmmLPKVKVDGKVDYVIDTGVDVVTPENLDEYLKKmEELGIPI 333
                                    41        51        61        71       |81        91       101       111       121       131       141    |  151       161    |  171       181       191       201       211       221       231       241       251       261  |    271       281|      291||     301       311       321    |  331  
                                                                          79-MSE                         111-MSE                            146-MSE             166-MSE                                                                                           264-MSE ||        282-MSE   292-MSE                           326-MSE   
                                                                                                                                                                                                                                                                        270-MSE                293-MSE                                    
                                                                                                                                                                                                                                                                         271-MSE                                                          

Chain C from PDB  Type:PROTEIN  Length:302
 aligned with Q9WXW9_THEMA | Q9WXW9 from UniProtKB/TrEMBL  Length:335

    Alignment length:302
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331  
         Q9WXW9_THEMA    32 LTIGVIGKSVHPYWSQVEQGVKAAGKALGVDTKFFVPQKEDINAQLQMLESFIAEGVNGIAIAPSDPTAVIPTIKKALEMGIPVVTLDTDSPDSGRYVYIGTDNYQAGYTAGLIMKELLGGKGKVVIGTGSLTAMNSLQRIQGFKDAIKDSEIEIVDILNDEEDGARAVSLAEAALNAHPDLDAFFGVYAYNGPAQALVVKNAGKVGKVKIVCFDTTPDILQYVKEGVIQATMGQRPYMMGYLSVTVLYLMNKIGVQNTLMMLPKVKVDGKVDYVIDTGVDVVTPENLDEYLKKMEELGIPI 333
               SCOP domains d2qvcc_ C: automated matches                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2qvcC01 C:32-133,C:266-310  [code=3.40.50.2300, no name defined]                                      2qvcC02 C:134-265,C:311-333  [code=3.40.50.2300, no name defined]                                                                   2qvcC01 C:32-133,C:266-310                   2qvcC02                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhh....eee.......hhhhhhhhhhh...eeee..........eeee.hhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhh......eeeeeee...hhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhh......eeeee..hhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeeeeee...eee...hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qvc C  32 LTIGVIGKSVHPYWSQVEQGVKAAGKALGVDTKFFVPQKEDINAQLQmLESFIAEGVNGIAIAPSDPTAVIPTIKKALEmGIPVVTLDTDSPDSGRYVYIGTDNYQAGYTAGLImKELLGGKGKVVIGTGSLTAmNSLQRIQGFKDAIKDSEIEIVDILNDEEDGARAVSLAEAALNAHPDLDAFFGVYAYNGPAQALVVKNAGKVGKVKIVCFDTTPDILQYVKEGVIQATmGQRPYmmGYLSVTVLYLmNKIGVQNTLmmLPKVKVDGKVDYVIDTGVDVVTPENLDEYLKKmEELGIPI 333
                                    41        51        61        71       |81        91       101       111       121       131       141    |  151       161    |  171       181       191       201       211       221       231       241       251       261  |    271       281|      291||     301       311       321    |  331  
                                                                          79-MSE                         111-MSE                            146-MSE             166-MSE                                                                                           264-MSE ||        282-MSE   292-MSE                           326-MSE   
                                                                                                                                                                                                                                                                        270-MSE                293-MSE                                    
                                                                                                                                                                                                                                                                         271-MSE                                                          

Chain D from PDB  Type:PROTEIN  Length:302
 aligned with Q9WXW9_THEMA | Q9WXW9 from UniProtKB/TrEMBL  Length:335

    Alignment length:302
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331  
         Q9WXW9_THEMA    32 LTIGVIGKSVHPYWSQVEQGVKAAGKALGVDTKFFVPQKEDINAQLQMLESFIAEGVNGIAIAPSDPTAVIPTIKKALEMGIPVVTLDTDSPDSGRYVYIGTDNYQAGYTAGLIMKELLGGKGKVVIGTGSLTAMNSLQRIQGFKDAIKDSEIEIVDILNDEEDGARAVSLAEAALNAHPDLDAFFGVYAYNGPAQALVVKNAGKVGKVKIVCFDTTPDILQYVKEGVIQATMGQRPYMMGYLSVTVLYLMNKIGVQNTLMMLPKVKVDGKVDYVIDTGVDVVTPENLDEYLKKMEELGIPI 333
               SCOP domains d2qvcd_ D: automated matches                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2qvcD01 D:32-133,D:266-310  [code=3.40.50.2300, no name defined]                                      2qvcD02 D:134-265,D:311-333  [code=3.40.50.2300, no name defined]                                                                   2qvcD01 D:32-133,D:266-310                   2qvcD02                 CATH domains
           Pfam domains (1) --Peripla_BP_4-2qvcD01 D:34-285                                                                                                                                                                                                                               ------------------------------------------------ Pfam domains (1)
           Pfam domains (2) --Peripla_BP_4-2qvcD02 D:34-285                                                                                                                                                                                                                               ------------------------------------------------ Pfam domains (2)
           Pfam domains (3) --Peripla_BP_4-2qvcD03 D:34-285                                                                                                                                                                                                                               ------------------------------------------------ Pfam domains (3)
           Pfam domains (4) --Peripla_BP_4-2qvcD04 D:34-285                                                                                                                                                                                                                               ------------------------------------------------ Pfam domains (4)
         Sec.struct. author .eeeee....hhhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhh...eeee...........eee.hhhhhhhhhhhhhhhhh..eeeeeeee....hhhhhhhhhhhhhhhh..eeeeeeeee...hhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhh......eeeee..hhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeeeeee...eee...hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qvc D  32 LTIGVIGKSVHPYWSQVEQGVKAAGKALGVDTKFFVPQKEDINAQLQmLESFIAEGVNGIAIAPSDPTAVIPTIKKALEmGIPVVTLDTDSPDSGRYVYIGTDNYQAGYTAGLImKELLGGKGKVVIGTGSLTAmNSLQRIQGFKDAIKDSEIEIVDILNDEEDGARAVSLAEAALNAHPDLDAFFGVYAYNGPAQALVVKNAGKVGKVKIVCFDTTPDILQYVKEGVIQATmGQRPYmmGYLSVTVLYLmNKIGVQNTLmmLPKVKVDGKVDYVIDTGVDVVTPENLDEYLKKmEELGIPI 333
                                    41        51        61        71       |81        91       101       111       121       131       141    |  151       161    |  171       181       191       201       211       221       231       241       251       261  |    271       281|      291||     301       311       321    |  331  
                                                                          79-MSE                         111-MSE                            146-MSE             166-MSE                                                                                           264-MSE ||        282-MSE   292-MSE                           326-MSE   
                                                                                                                                                                                                                                                                        270-MSE                293-MSE                                    
                                                                                                                                                                                                                                                                         271-MSE                                                          

   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

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
1a2qvcA01A:32-133,A:266-310
1b2qvcB01B:32-133,B:266-310
1c2qvcC01C:32-133,C:266-310
1d2qvcD01D:32-133,D:266-310
1e2qvcA02A:134-265,A:311-333
1f2qvcB02B:134-265,B:311-333
1g2qvcC02C:134-265,C:311-333
1h2qvcD02D:134-265,D:311-333

(-) Pfam Domains  (1, 4)

Asymmetric Unit

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q9WXW9_THEMA | Q9WXW9)
molecular function
    GO:0015145    monosaccharide transmembrane transporter activity    Enables the transfer of a monosaccharide from one side of a membrane to the other.
biological process
    GO:0015749    monosaccharide transport    The directed movement of monosaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monosaccharides are the simplest carbohydrates; they are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/TrEMBL
        Q9WXW9_THEMA | Q9WXW92h3h 3c6q

(-) Related Entries Specified in the PDB File

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