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(-) Description

Title :  MYCOPLASMA GENITALIUM MG289
 
Authors :  K. H. Sippel, S. K. Boehlein, L. Govindasamy, K. Namiki, Y. Satai, J. G. Q M. Agbandje-Mckenna, S Goodison, C. J. Rosser, B. Sankaran, R. Mcken
Date :  11 May 10  (Deposition) - 20 Oct 10  (Release) - 19 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Mycoplasma, Mycoplasma Genitalium, Mg289, P37, G37, Cypl, Extracytoplasmic, Thiamine Binding Protein, Lipoprotein, Atp Binding Cassette Transporter Binding Protein, Vib Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. H. Sippel, B. Venkatakrishnan, S. K. Boehlein, B. Sankaran, J. G. Quirit, L. Govindasamy, M. Agbandje-Mckenna, S. Goodison, C. J. Rosser, R. Mckenna
Insights Into Mycoplasma Genitalium Metabolism Revealed By The Structure Of Mg289, An Extracytoplasmic Thiamine Bindin Lipoprotein.
Proteins V. 79 528 2011
PubMed-ID: 21117240  |  Reference-DOI: 10.1002/PROT.22900
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HIGH AFFINITY TRANSPORT SYSTEM PROTEIN P37
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET31F1M1
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLAMSID
    Fragment: N-TERMINAL TRUNCATION (DELTA 1-25)
    Gene: MG289, P37
    Mutation: YES
    Organism Scientific: MYCOPLASMA GENITALIUM
    Organism Taxid: 2097
    Strain: G37

 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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2VIB2Ligand/Ion3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2VIB1Ligand/Ion3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2VIB1Ligand/Ion3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:41 , HIS A:42 , ASN A:161 , TYR A:176 , TRP A:275 , TYR A:307 , ASP A:308 , ILE A:343 , GLY A:344 , HOH A:385BINDING SITE FOR RESIDUE VIB A 500
2AC2SOFTWAREASP A:75 , ASP A:76 , THR A:79BINDING SITE FOR RESIDUE ACT A 1
3AC3SOFTWAREASN A:240 , HOH A:370 , SER B:317 , ARG B:318 , HOH B:513BINDING SITE FOR RESIDUE ACT A 2
4AC4SOFTWAREASP B:41 , HIS B:42 , ASN B:161 , TYR B:176 , ASP B:269 , TRP B:275 , TYR B:307 , ASP B:308 , PRO B:341 , ILE B:343 , GLY B:344 , HOH B:399BINDING SITE FOR RESIDUE VIB B 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MYU)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:145 -Pro A:146
2Ser B:145 -Pro B:146

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MYU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MYU)

(-) Exons   (0, 0)

(no "Exon" information available for 3MYU)

(-) 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:333
 aligned with P37_MYCGE | Q49410 from UniProtKB/Swiss-Prot  Length:368

    Alignment length:336
                                    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       341       351       361      
            P37_MYCGE    32 NTLIFNISLDHNADTSIEKFFTVFSKKLSGKLNKKINVNFNIVDDSFTKINNIQANKADFAFVNSQAIASNNWFGYTPLIQTLTTAFKEDLELDYYEDGNLQKKAEKTNLLFLSPPYKEWDDIKQKWTGNRYDFLYEPSKLVSFYRSMILITGSASEITAIKKAWNEKNWNQFMKFGIGHGQTNSASRFELPDLLFRKHFAKNYPGLQNAINSDPDKFAVVRGREIGINKNIKIVFDDANSFSWTQNIKGSKRPFYTPIDPNDRLEILTYSDPLLYDIGIVSNNLSRIYQKAIGEIFIELAQSSEDLYGPSIGYNGYKMINDFEKEVVEIIEKTYG 367
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhh....eeeehhhhh.......eeeeeeeeeeee.......hhhhhhhhhhhhhhhhhhhh.hhhhh...........hhh.eeeeeee.eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhh..eee........hhhhhhhhhhhhh....hhhhhhhhh...eee.hhhhh.......eeeee.hhhhhh....---...........eeeeeeeeeeee..eeeee...hhhhhhhhhhhhhhhhhh....hhhhhh..eeee..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3myu A  32 NTLIFNISLDHNADTSIEKFFTVFSKKLSGKLNKKINVNFNIVDDSFTKINNIQANKADFAFVNSQAIASNNWFGYTPLIQTLTTAFKEDLELDYYEDGNLQKKAEKTNLLFLSPPYKEWDDIKQKWTGNRYDFLYEPSKLVSFYRSMILITGSASEITAIKKAWNEKNWNQFMKFGIGHGQTNSASRFELPDLLFRKHFAKNYPGLQNAINSDPDKFAVVRGREIGINKNIKIVFDDANSFSWTQNIK---RPFYTPIDPNDRLEILTYSDPLLYDIGIVSNNLSRIYQKAIGEIFIELAQSSEDLYGPSIGYNGYKMINDFEKEVVEIIEKTYG 367
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271        |-  |    291       301       311       321       331       341       351       361      
                                                                                                                                                                                                                                                                                  280 284                                                                                   


Chain B from PDB  Type:PROTEIN  Length:334
 aligned with P37_MYCGE | Q49410 from UniProtKB/Swiss-Prot  Length:368

    Alignment length:336
                                    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       341       351       361      
            P37_MYCGE    32 NTLIFNISLDHNADTSIEKFFTVFSKKLSGKLNKKINVNFNIVDDSFTKINNIQANKADFAFVNSQAIASNNWFGYTPLIQTLTTAFKEDLELDYYEDGNLQKKAEKTNLLFLSPPYKEWDDIKQKWTGNRYDFLYEPSKLVSFYRSMILITGSASEITAIKKAWNEKNWNQFMKFGIGHGQTNSASRFELPDLLFRKHFAKNYPGLQNAINSDPDKFAVVRGREIGINKNIKIVFDDANSFSWTQNIKGSKRPFYTPIDPNDRLEILTYSDPLLYDIGIVSNNLSRIYQKAIGEIFIELAQSSEDLYGPSIGYNGYKMINDFEKEVVEIIEKTYG 367
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----------------Mycoplasma_p37-3myuB01 B:49-367                                                                                                                                                                                                                                                                                                 Pfam domains (1)
           Pfam domains (2) -----------------Mycoplasma_p37-3myuB02 B:49-367                                                                                                                                                                                                                                                                                                 Pfam domains (2)
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhh....eeeehhhhh.......eeeeeeeeeeee.......hhhhhhhhhhhhhhhhhhh..hhhhh...........hhh.eeeeeee.eeeeeeeeeehhhhhhhhhhhhhh.hhhhhhh..eee........hhhhhhhhhhhhhhhh.hhhhhhhhh...eee.hhhhh.......eeeee.hhhhhh....--............eeeeeeeeeeee..eeeee...hhhhhhhhhhhhhhhhhh....hhhhhh..eeee..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3myu B  32 NTLIFNISLDHNADTSIEKFFTVFSKKLSGKLNKKINVNFNIVDDSFTKINNIQANKADFAFVNSQAIASNNWFGYTPLIQTLTTAFKEDLELDYYEDGNLQKKAEKTNLLFLSPPYKEWDDIKQKWTGNRYDFLYEPSKLVSFYRSMILITGSASEITAIKKAWNEKNWNQFMKFGIGHGQTNSASRFELPDLLFRKHFAKNYPGLQNAINSDPDKFAVVRGREIGINKNIKIVFDDANSFSWTQNIK--KRPFYTPIDPNDRLEILTYSDPLLYDIGIVSNNLSRIYQKAIGEIFIELAQSSEDLYGPSIGYNGYKMINDFEKEVVEIIEKTYG 367
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271        |- |     291       301       311       321       331       341       351       361      
                                                                                                                                                                                                                                                                                  280  |                                                                                    
                                                                                                                                                                                                                                                                                     283
   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 3MYU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MYU)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (P37_MYCGE | Q49410)
molecular function
    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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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)

(no "Entries Sharing at Least One Protein Chain" available for 3MYU)

(-) Related Entries Specified in the PDB File

3e78 MYCOPLASMA HYORHINIS P37 - HOMOLOG
3e79 MYCOPLASMA HYORHINIS P37 - HOMOLOG COMPLEXED WITH I3C
3eki MYCOPLASMA HYORHINIS P37 - 1.6 ANGSTROM RESOLUTION