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MENU :
- 3D homology model 1 of Streptococcus pneumoniae TIGR4 MsmK and RafEFG raffinose transporter (TIGR4_MsmK_RafEFG_2HEU_3FH6_2R6G_2D62)
- 3D homology model 1 of Streptococcus pneumoniae TIGR4 MglA ribose transporter (TIGR4_MglA_2FQX_3B9W_3BK7)
- 3D homology model 2 of Streptococcus pneumoniae TIGR4 MglA ribose transporter (TIGR4_MglA_2R6G)
- 3D homology model 1 of Streptococcus pneumoniae TIGR4 Rbs ribose transporter (TIGR4_Rbs_3LFT_2ONK_1G6H)
- 3D homology model 2 of Streptococcus pneumoniae TIGR4 Rbs ribose transporter (TIGR4_Rbs_3LFT_2QI9_1G6H)
- 3D homology model 3 of Streptococcus pneumoniae TIGR4 Rbs ribose transporter (TIGR4_Rbs_3LFT_3D31_1G6H)
3D homology model 1 of Streptococcus pneumoniae TIGR4 MsmK and RafEFG raffinose transporter (TIGR4_MsmK_RafEFG_2HEU_3FH6_2R6G_2D62)
- RafE : Entrez Protein NP_346328 : substrate-binding. Modelled on PDBID 2HEU chain A (RafE, raffinose transporter, S.pneumoniae).
- RafF : Entrez Protein NP_346327 : 7 transmembrane helices (TMH). Modelled on PDBID 3FH6 chain F (MalF, maltose transporter, E.coli).
- RafG : Entrez Protein NP_346326 : 6 transmembrane helices (TMH). Modelled on PDBID 2R6G chain G (MalG, maltose transporter, E.coli).
- MsmK : Entrez Protein NP_346026 : ATP-binding cassette. Modelled on PDBID 2D62 chain A (multiple sugar binding transport ATP-binding protein, Pyrococcus horikoshii).
- MsmK is thought to import raffinose, and RafEFG is also thought to import raffinose, and d-galactose, melibiose, and stachyose.
- There is no experimental evidence that I know of suggesting that MsmK and RafEFG form a transporter complex together. This 3D homology model has built them together as a complex due to the following clues :
- NP_346320 : oligopeptide ABC transporter, permease protein AmiD
- NP_346321 : oligopeptide ABC transporter, permease protein AmiC
- NP_346322 : oligopeptide ABC transporter, oligopeptide-binding protein AmiA
- NP_346323 : hypothetical protein
- NP_346324 : hypothetical protein
- NP_346325 : sucrose phosphorylase
- NP_346326 : sugar ABC transporter, permease protein
- NP_346327 : sugar ABC transporter, permease protein
- NP_346328 : sugar ABC transporter, sugar-binding protein
- NP_346329 : alpha-galactosidase
- NP_346330 : msm operon regulatory protein
- PF01547 : Bacterial extracellular solute-binding, family 1
- PS01037 : Bacterial extracellular solute-binding family 1, conserved site
- G3DSA:3.40.190.10
- PS51257 : PROKAR_LIPOPROTEIN
- SSF53850 : Periplasmic binding protein-like II
- The N-terminal exhibits hydrophobicity as a helix, and is probably a signal peptide, in which case it should not be shown in the model as it would cleaved off.
- PF00528 : Binding-protein-dependent transport systems inner membrane component
- PS50928 : ABC_TM1
- 7 transmembrane helices
- PF00528 : Binding-protein-dependent transport systems inner membrane component
- PS50928 : ABC_TM1
- 6 transmembrane helices
- PF00005 : ABC transporter-like, ATP binding, ATPase activity
- SM00382 : ATPase, AAA+ type, core
- SSF50331 : Molybdate/tungstate binding, transporter activity, ATP binding, MOP-like
- PF08402 : Transport-associated OB, type 2, TOBE_2
- PS00211 : ABC transporter, conserved site
- PD000006 : Q8NZA8_STRP8_Q8NZA8
- G3DSA:2.40.50.100
- G3DSA:3.40.50.300
- PTHR19222:SF42 : SUGAR ABC TRANSPORTER
- SSF52540 : P-loop containing nucleoside triphosphate hydrolases
- MglB : Entrez Protein NP_345336 : substrate-binding. Modelled on PDBID 2FQX chain A (PnrA, guanosine-binding, Treponema pallidum).
- MglK : Entrez Protein NP_345339 : 10 transmembrane helices (TMH). Modelled on PDBID 3B9W chain A (Rhesus-homologue, ammonium transporter, Nitrosomonas europaea).
- MglC : Entrez Protein NP_345338 : 9 transmembrane helices (TMH). Modelled on PDBID 3B9W chain A (Rhesus-homologue, ammonium transporter, Nitrosomonas europaea).
- MglA : Entrez Protein NP_345337 : ATP-binding cassette. Modelled on PDBID 3BK7 chain A (ABCE1/RNAase-L Inhibitor protein, Pyrococcus abysii).
- The homologues used to build the 3D homology models for the periplasmic and membrane domains have only weak and unconvincing homology. The resulting 3D homology models for those domains are therefore probably not good models.
- This S.pneumoniae TIGR4 MglA transporter is thought to transport ribose and other sugars.
- PF02608 : Basic membrane lipoprotein, lipid binding
- PS00227 : Tubulin conserved site, GTP binding, microtubule
- PS51257 : PROKAR_LIPOPROTEIN
- SSF53822 : Periplasmic binding protein-like I
- 1 signal peptide (not included in model)
- PF02653 : Bacterial inner-membrane translocator
- 10 transmembrane helices
- PF02653 : Bacterial inner-membrane translocator
- 9 transmembrane helices
- PF00005 : ABC transporter-like, ATP binding, ATPase activity
- PS50893 : ABC_TRANSPORTER_2
- SM00382 : ATPase, AAA+ type, core
- PS00211 : ABC_TRANSPORTER_1
- PD000006 : Q97RG9_STRPN_Q97RG9
- G3DSA:3.40.50.300
- PTHR19222:SF12 : SUGAR ABC TRANSPORTER
- SSF52540 : P-loop containing nucleoside triphosphate hydrolases
- MglB : Entrez Protein NP_345336 : substrate-binding. Modelled on PDBID 2R6G chain E (MalE, maltose-binding, maltose transporter, E.coli).
- MglK : Entrez Protein NP_345339 : 10 transmembrane helices (TMH). Modelled on PDBID 2R6G chain F (MalF, transmembrane, maltose transporter, E.coli).
- MglC : Entrez Protein NP_345338 : 9 transmembrane helices (TMH). Modelled on PDBID 2R6G chain G (MalG, transmembrane, maltose transporter, E.coli).
- MglA : Entrez Protein NP_345337 : ATP-binding cassette. Modelled on PDBID 2R6G chain A (MalA, ATP-binding, maltose transporter, E.coli).
- MglA : Entrez Protein NP_345337 : ATP-binding cassette. Modelled on PDBID 2R6G chain B (MalA, ATP-binding, maltose transporter, E.coli).
- This E.coli maltose transporter that was used as a template for this S.pneumoniae 3D homology model actually does not show any significant sequence homology to the ribose transporter. It was used as a template because this S.pneumoniae is known to be a sugar transporter and there are no 3D structures in PDB that currently have sequence homology to this S.pneumoniae transporter.
- This S.pneumoniae TIGR4 MglA transporter is thought to transport ribose and other sugars.
- PF02608 : Basic membrane lipoprotein, lipid binding
- PS00227 : Tubulin conserved site, GTP binding, microtubule
- PS51257 : PROKAR_LIPOPROTEIN
- SSF53822 : Periplasmic binding protein-like I
- 1 signal peptide (not included in model)
- PF02653 : Bacterial inner-membrane translocator
- 10 transmembrane helices
- PF02653 : Bacterial inner-membrane translocator
- 9 transmembrane helices
- PF00005 : ABC transporter-like, ATP binding, ATPase activity
- PS50893 : ABC_TRANSPORTER_2
- SM00382 : ATPase, AAA+ type, core
- PS00211 : ABC_TRANSPORTER_1
- PD000006 : Q97RG9_STRPN_Q97RG9
- G3DSA:3.40.50.300
- PTHR19222:SF12 : SUGAR ABC TRANSPORTER
- SSF52540 : P-loop containing nucleoside triphosphate hydrolases
- RbsB : Entrez Protein NP_345542 : substrate-binding. Modelled on PDBID 3LFT chain A (RbsB minus N-terminal, S.pneumonia). N-terminal was modelled on PDBID 2R6G chain F (MalF periplasmic domain, maltose ABC transporter, Escherichia coli). There is no evidence that N-terminal looks like this.
- RbsC : Entrez Protein NP_345543 : 8 transmembrane helices (TMH). Modelled on PDBID 2ONK chain C (ModB, molybdate ABC transporter, 12 TMH, S.pneumonia).
- RbsA : Entrez Protein NP_345544 : ATP-binding cassette. Modelled on PDBID 1G6H chain A (MJ1267, ABC, Methanococcus jannaschii).
- The complex was assembled according to 2R6G (maltose ABC transporter, E.coli)
- The difference between models 1, 2, and 3 for Streptococcus pneumoniae TIGR4 Rbs ribose transporter is that different 3D structures were used to model the transmembrane subunit. The substrate-binding and ATP-binding subunits are the same in all 3 models.
- These S.pneumoniae TIGR4 sequences are the closest sequences that could be found to the E.coli Rbs ribose transporter sequences. However, these S.pneumoniae TIGR4 sequences are probably not a ribose transporter (perhaps they are an amino acid transporter) and S.pneumonaie probably does not actually have the Rbs ribose transporter genes.
- PF04392 : ABC transporter substrate binding protein
- SSF53822 : Periplasmic binding protein-like I
- 1 signal peptide (not included in model)
- PF02653 : Bacterial inner-membrane translocator
- 8 transmembrane helices
- PF00005 : ABC transporter-like, ATP binding, ATPase activity
- PS50893 : ABC_TRANSPORTER_2
- SM00382 : ATPase, AAA+ type, core
- PS00211 : ABC_TRANSPORTER_1
- PD000006 : Q97QX3_STRPN_Q97QX3
- G3DSA:3.40.50.300
- PTHR19222 : ATP BINDING CASSETE (ABC) TRANSPORTER
- SSF52540 : P-loop containing nucleoside triphosphate hydrolases
- RbsB : Entrez Protein NP_345542 : substrate-binding. Modelled on PDBID 3LFT chain A (RbsB minus N-terminal, S.pneumonia). N-terminal was modelled on PDBID 2R6G chain F (MalF periplasmic domain, maltose ABC transporter, E.coli). There is no evidence that N-terminal looks like this.
- RbsC : Entrez Protein NP_345543 : 8 transmembrane helices (TMH). Modelled on PDBID 2QI9 chain A (BtuCD, vitamin B12 ABC transporter, 10 TMH, E.coli).
- RbsA : Entrez Protein NP_345544 : ATP-binding cassette. Modelled on PDBID 1G6H chain A (MJ1267, ABC, Methanococcus jannaschii).
- The complex was assembled according to 2QI9 (vitamin B12 ABC transporter, E.coli)
- The difference between models 1, 2, and 3 for Streptococcus pneumoniae TIGR4 Rbs ribose transporter is that different 3D structures were used to model the transmembrane subunit. The substrate-binding and ATP-binding subunits are the same in all 3 models.
- These S.pneumoniae TIGR4 sequences are the closest sequences that could be found to the E.coli Rbs ribose transporter sequences. However, these S.pneumoniae TIGR4 sequences are probably not a ribose transporter (perhaps they are an amino acid transporter) and S.pneumonaie probably does not actually have the Rbs ribose transporter genes.
- PF04392 : ABC transporter substrate binding protein
- SSF53822 : Periplasmic binding protein-like I
- 1 signal peptide (not included in model)
- PF02653 : Bacterial inner-membrane translocator
- 8 transmembrane helices
- PF00005 : ABC transporter-like, ATP binding, ATPase activity
- PS50893 : ABC_TRANSPORTER_2
- SM00382 : ATPase, AAA+ type, core
- PS00211 : ABC_TRANSPORTER_1
- PD000006 : Q97QX3_STRPN_Q97QX3
- G3DSA:3.40.50.300
- PTHR19222 : ATP BINDING CASSETE (ABC) TRANSPORTER
- SSF52540 : P-loop containing nucleoside triphosphate hydrolases
- RbsB : Entrez Protein NP_345542 : substrate-binding. Modelled on PDBID 3LFT chain A (RbsB minus N-terminal, S.pneumonia). N-terminal was modelled on PDBID 2R6G chain F (MalF periplasmic domain, maltose ABC transporter, E.coli). There is no evidence that N-terminal looks like this.
- RbsC : Entrez Protein NP_345543 : 8 transmembrane helices (TMH). Modelled on PDBID 3D31 chain C (ModBC, molybdate/tungstate ABC transporter, 6 TMH, Methanosarcina acetivorans).
- RbsA : Entrez Protein NP_345544 : ATP-binding cassette. Modelled on PDBID 1G6H chain A (MJ1267, ABC, Methanococcus jannaschii).
- The complex was assembled according to 2R6G (maltose ABC transporter, E.coli)
- The difference between models 1, 2, and 3 for Streptococcus pneumoniae TIGR4 Rbs ribose transporter is that different 3D structures were used to model the transmembrane subunit. The substrate-binding and ATP-binding subunits are the same in all 3 models.
- These S.pneumoniae TIGR4 sequences are the closest sequences that could be found to the E.coli Rbs ribose transporter sequences. However, these S.pneumoniae TIGR4 sequences are probably not a ribose transporter (perhaps they are an amino acid transporter) and S.pneumonaie probably does not actually have the Rbs ribose transporter genes.
- PF04392 : ABC transporter substrate binding protein
- SSF53822 : Periplasmic binding protein-like I
- 1 signal peptide (not included in model)
- PF02653 : Bacterial inner-membrane translocator
- 8 transmembrane helices
- PF00005 : ABC transporter-like, ATP binding, ATPase activity
- PS50893 : ABC_TRANSPORTER_2
- SM00382 : ATPase, AAA+ type, core
- PS00211 : ABC_TRANSPORTER_1
- PD000006 : Q97QX3_STRPN_Q97QX3
- G3DSA:3.40.50.300
- PTHR19222 : ATP BINDING CASSETE (ABC) TRANSPORTER
- SSF52540 : P-loop containing nucleoside triphosphate hydrolases
- PF01547 : Bacterial extracellular solute-binding, family 1
- PR00181 : Maltose binding protein
- PS01037 : Bacterial extracellular solute-binding family 1, conserved site
- G3DSA:3.40.190.10
- SSF53850 : Periplasmic binding protein-like II
- PF00528 : Binding-protein-dependent transport systems inner membrane component
- PS50928 : Binding-protein-dependent transport systems inner membrane component
- 8 transmembrane helices
- PF00528 : Binding-protein-dependent transport systems inner membrane component
- PS50928 : Binding-protein-dependent transport systems inner membrane component
- 6 transmembrane helices
- PF00005 : ABC transporter-like
- PS50893 : ABC_TRANSPORTER_2
- SM00382 : ATPase, AAA+ type, core
- SSF50331 : Molybdate/tungstate binding (MOP-like)
- PF08402 : Transport-associated OB, type 2 (TOBE_2)
- PS51245 : ABC transporter, maltose/maltodextrin import, MalK
- PS00211 : ABC_TRANSPORTER_1
- G3DSA:2.40.50.100
- G3DSA:3.40.50.300
- PTHR19222:SF42 : SUGAR ABC TRANSPORTER
- SSF52540 : P-loop containing nucleoside triphosphate hydrolases
Here is an operon that might contain the rest of the pieces to the MsmK gene.
MsmK is the ABC-binding part of a raffinose/d-galactose/melibiose/stachyose transporter.
The following operon is for a sugar transporter and lacks an ABC-binding part.
(There is one, but it is for the preceding Ami gene, not the sugar gene here.)
It's sugar-binding protein has an RHS pattern,
and Pyrococcus horikoshii 2D62_A ABC-binding (that is similar in sequence to MsmK)
is on an operon near gene NP_142188 which has the RHS patterns
(just as the Ecoli RHS genes YP_026224/NP_415229/NP_418050 (rhsB/rhsC/rhsR) have these RHS patterns.
In addition, this operon contains "msm operon regulatory protein".
This operon also contains a gene to process alpha-galactosidase - is raffinose an alpha-galactosidase?
Could the nearby AmiD/AmiC oligopeptide ABC transporter be capable of translocating DLDH across the membrane?
PDB file of this 3D homology model
PyMOL file of this 3D homology model
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3D homology model 1 of Streptococcus pneumoniae TIGR4 MglA ribose transporter (TIGR4_MglA_2FQX_3B9W_3BK7)
PyMOL file of this 3D homology model
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3D homology model 2 of Streptococcus pneumoniae TIGR4 MglA ribose transporter (TIGR4_MglA_2R6G)
PyMOL file of this 3D homology model
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3D homology model 1 of Streptococcus pneumoniae TIGR4 Rbs ribose transporter (TIGR4_Rbs_3LFT_2ONK_1G6H)
PyMOL file (from one merged PDB file)
PyMOL file (from separate subunit PDB files)
PyMOL file (working file used to build and align model subunits)
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3D homology model 2 of Streptococcus pneumoniae TIGR4 Rbs ribose transporter (TIGR4_Rbs_3LFT_2QI9_1G6H)
PyMOL file (of the separate subunits)
PyMOL file (working file used to build and align model subunits)
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3D homology model 3 of Streptococcus pneumoniae TIGR4 Rbs ribose transporter (TIGR4_Rbs_3LFT_3D31_1G6H)
PyMOL file (of the separate subunits)
PyMOL file (working file used to build and align model subunits)
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The Crystal Structure of the E. coli Maltose Transporter (PDBID 2R6G)
Oldham ML, Khare D, Quiocho FA, Davidson AL, Chen J (2007)
Crystal structure of a catalytic intermediate of the maltose transporter.
Nature 450, 515-521. Pubmed 18033289.
 Figure 1. from Oldham et al. 2007, the xray crystal structure for PDBID 2R6G. |
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