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(-) Description

Title :  CRYSTAL STRUCTURE OF MANNOBIOSE BOUND OLIGOPEPTIDE ABC TRANSPORTER, PERIPLASMIC OLIGOPEPTIDE-BINDING PROTEIN (TM1226) FROM THERMOTOGA MARITIMA AT 2.05 A RESOLUTION
 
Authors :  X. Lu, S. Ghimire-Rijal, M. J. Cuneo
Date :  30 Apr 14  (Deposition) - 17 Sep 14  (Release) - 05 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Oligopeptide Abc Transporter, Periplasmic Oligopeptide-Binding Protein, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ghimire-Rijal, X. Lu, D. A. Myles, M. J. Cuneo
Duplication Of Genes In An Atp-Binding Cassette Transport System Increases Dynamic Range While Maintaining Ligand Specificity.
J. Biol. Chem. V. 289 30090 2014
PubMed-ID: 25210043  |  Reference-DOI: 10.1074/JBC.M114.590992

(-) Compounds

Molecule 1 - ABC TRANSPORTER SUBSTRATE-BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: THEMA_08200, TMARI_1233
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099
    Synonym: MANNOSIDE ABC TRANSPORT SYSTEM,SUGAR-BINDING PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 24)

Asymmetric Unit (3, 24)
No.NameCountTypeFull Name
1MAB2Ligand/IonMANNOBIOSE
2MG2Ligand/IonMAGNESIUM ION
3SO420Ligand/IonSULFATE ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1MAB1Ligand/IonMANNOBIOSE
2MG-1Ligand/IonMAGNESIUM ION
3SO411Ligand/IonSULFATE ION
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1MAB1Ligand/IonMANNOBIOSE
2MG-1Ligand/IonMAGNESIUM ION
3SO49Ligand/IonSULFATE ION

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:362 , ASN A:364 , ASP A:366 , PHE A:368 , GLU A:370binding site for residue MG A 601
02AC2SOFTWAREGLY A:32 , SER A:33 , TRP A:35 , ASN A:231 , ASN A:247 , PHE A:248 , MET A:249 , TRP A:387 , ASP A:389 , TRP A:390 , TRP A:541 , HOH A:734 , HOH A:741 , HOH A:752 , HOH A:753 , HOH A:800 , HOH A:1088binding site for residue MAB A 602
03AC3SOFTWAREVAL A:216 , LYS A:551 , PHE A:554 , ASN A:555binding site for residue SO4 A 603
04AC4SOFTWAREASP A:305 , PRO A:306 , GLN A:309 , ARG A:310 , HOH A:712binding site for residue SO4 A 604
05AC5SOFTWARELYS A:318 , ALA A:319 , ASP A:320 , PRO A:321 , HOH A:933 , HOH A:981 , HOH A:997binding site for residue SO4 A 605
06AC6SOFTWARELYS A:352 , GLY A:367 , ARG A:369 , VAL A:403 , VAL A:404 , GLY A:405binding site for residue SO4 A 606
07AC7SOFTWARETYR A:150 , HOH A:1025binding site for residue SO4 A 607
08AC8SOFTWAREARG A:149 , TRP A:443 , ASN A:447 , LEU A:477 , GLU A:478 , ASN A:481 , HOH A:889 , HOH A:926 , HOH A:958binding site for residue SO4 A 608
09AC9SOFTWAREPHE A:110 , GLU A:113 , ILE A:114binding site for residue SO4 A 609
10AD1SOFTWAREGLY A:79 , GLU A:80 , TRP A:81 , HOH A:1025 , HOH A:1047binding site for residue SO4 A 610
11AD2SOFTWAREPRO A:46 , TRP A:47 , ASN A:543 , HOH A:854binding site for residue SO4 A 611
12AD3SOFTWAREGLU A:134 , SO4 A:613binding site for residue SO4 A 612
13AD4SOFTWAREARG A:109 , ILE A:133 , GLU A:134 , THR A:135 , SO4 A:612 , HOH A:985binding site for residue SO4 A 613
14AD5SOFTWAREASP B:362 , ASN B:364 , ASP B:366 , PHE B:368 , GLU B:370binding site for residue MG B 601
15AD6SOFTWAREGLY B:32 , SER B:33 , ASN B:231 , ASN B:247 , PHE B:248 , MET B:249 , TRP B:387 , ASP B:389 , TRP B:390 , HOH B:774 , HOH B:789 , HOH B:802 , HOH B:849 , HOH B:870 , HOH B:943 , HOH B:1060binding site for residue MAB B 602
16AD7SOFTWAREGLY B:79 , TYR B:87 , LEU B:157binding site for residue SO4 B 603
17AD8SOFTWAREARG B:92 , GLU B:93 , GLY B:94 , ILE B:95 , LEU B:103 , ASN B:138 , ARG B:139 , HOH B:919binding site for residue SO4 B 604
18AD9SOFTWARELYS B:318 , ALA B:319 , ASP B:320 , HOH B:913binding site for residue SO4 B 605
19AE1SOFTWAREARG B:109 , ILE B:133 , GLU B:134 , THR B:135 , HOH B:990 , HOH B:1018binding site for residue SO4 B 606
20AE2SOFTWAREPHE B:110 , GLU B:113 , ILE B:114 , HOH B:867 , HOH B:966binding site for residue SO4 B 607
21AE3SOFTWAREARG B:88 , PRO B:136 , ILE B:142 , HOH B:923 , HOH B:1033binding site for residue SO4 B 608
22AE4SOFTWARETRP B:443 , ASN B:447 , GLU B:474 , LEU B:477 , GLU B:478 , ASN B:481 , HOH B:901 , HOH B:967binding site for residue SO4 B 609
23AE5SOFTWAREVAL B:216 , LYS B:551 , PHE B:554 , ASN B:555 , HOH B:979 , HOH B:1002binding site for residue SO4 B 610
24AE6SOFTWAREPRO B:251 , THR B:388 , ASP B:389 , GLN B:392 , HOH B:707binding site for residue SO4 B 611

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Pro A:269 -Pro A:270
2Tyr A:287 -Pro A:288
3Pro B:269 -Pro B:270
4Tyr B:287 -Pro B:288

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PFU)

(-) 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:540
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhh.eeeee....................hhhhhh....eee......eee..eeeeeeee..eeeeee............hhhhhhhhhhhhhhh....hhhhhh.eeeeeeee..eeeeee...hhhhhhhhhhhh...hhhhhh..hhhhhhhh..........eeeeeee..eeeeee...hhhhhhhh......eeeee...hhhhhhhhhhh....ee.....hhhhhhhhhh...........eeeeeeeeee........hhhhhhhhhh...hhhhhhh......ee.........hhhhhhhhhhhhhhhh...hhhhhhhhhhhh....................eeee....hhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhh..............hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.eeeeeeeee..ee....ee.................hhhhhhhhhhhhhee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pfu A  21 VLERNETMYYGGSLWSPPSNWNPFTPWNAVPGTTGLVYETMFFYDPLTGNFDPWLAEKGEWLDSKTYRVVLREGIYWHDNVPLTSEDVRFTFEIAKKYKGIHYSSVWEWLDHIETPDNRTVIFVFKDPRYHEWNELLYTLPIVPKHIWEEKDETTILQSSNEYPLGSGPYVAHSWDQNKMIFERFENWWGTKVMGVKPAPKYVVIVRVLSNNVALGMLMKGELDFSNFMLPGVPILKKVYNLNTWYDEPPYHLSSTVVGLFLNARKYPLSLPEFRRAIAMSINADPIVQRVYEGAVLKADPLGFLPNSVWMKYYPKEVVEKHGFKYDPEEAKSILDKLGFRDVNGDGFRETPDGKPIKLTIECPYGWTDWMQAIQVIVDQLKVVGINAEPYFPDSSKYYENMYKGEFDIEMNANGTGISSTPWTYFNTIFYPDALESEFSYTGNYGRYQNPEVESLLEELNRTPLDNVEKVTELCGKLGEILLKDLPFIPLWYGAMAFITQDNVWTNWPNEHNPYAWPCGWANWWQTGALKILFNLKPAK 560
                                    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       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560


Chain B from PDB  Type:PROTEIN  Length:542
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhh.eeeee.....................hhhh.....eee......eee..eeeeeeee..eeeeee............hhhhhhhhhhhhhhh....hhhhhh.eeeee.....eeeeee...hhhhhhhhhhhh...hhhhhh..hhhhhhhh..........eeeeeee..eeeeee...hhhhhhhh......eeeee...hhhhhhhhhhh....ee.....hhhhhhhh.............eeeeeeeeee........hhhhhhhhhhhh.hhhhhhhh................hhhhhhhhhhhhhhhh...hhhhhhhhhhhhh..................eeeee....hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhh..............hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.eeeeeeeee..ee....ee.................hhhhhhhhhhhhhee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pfu B  20 MVLERNETMYYGGSLWSPPSNWNPFTPWNAVPGTTGLVYETMFFYDPLTGNFDPWLAEKGEWLDSKTYRVVLREGIYWHDNVPLTSEDVRFTFEIAKKYKGIHYSSVWEWLDHIETPDNRTVIFVFKDPRYHEWNELLYTLPIVPKHIWEEKDETTILQSSNEYPLGSGPYVAHSWDQNKMIFERFENWWGTKVMGVKPAPKYVVIVRVLSNNVALGMLMKGELDFSNFMLPGVPILKKVYNLNTWYDEPPYHLSSTVVGLFLNARKYPLSLPEFRRAIAMSINADPIVQRVYEGAVLKADPLGFLPNSVWMKYYPKEVVEKHGFKYDPEEAKSILDKLGFRDVNGDGFRETPDGKPIKLTIECPYGWTDWMQAIQVIVDQLKVVGINAEPYFPDSSKYYENMYKGEFDIEMNANGTGISSTPWTYFNTIFYPDALESEFSYTGNYGRYQNPEVESLLEELNRTPLDNVEKVTELCGKLGEILLKDLPFIPLWYGAMAFITQDNVWTNWPNEHNPYAWPCGWANWWQTGALKILFNLKPAKH 561
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559
   Legend:   → Mismatch (orange background)
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  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 4PFU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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(-) Related Entries Specified in the PDB File

4pft PROTEIN HOMOLOG
4pfw
4pfy