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(-) Description

Title :  THE STRUCTURE OF BACILLUS SUBTILIS RBSD COMPLEXED WITH GLYCEROL
 
Authors :  M. -S. Kim, B. -H. Oh
Date :  30 Apr 03  (Deposition) - 01 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B,C,D,E  (2x)
Keywords :  Ribose, Transport, Sugar Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. -S. Kim, J. Shin, W. Lee, H. -S. Lee, B. -H. Oh
Crystal Structures Of Rbsd Leading To The Identification Of Cytoplasmic Sugar-Binding Proteins With A Novel Folding Architecture
J. Biol. Chem. V. 278 28173 2003
PubMed-ID: 12738765  |  Reference-DOI: 10.1074/JBC.M304523200

(-) Compounds

Molecule 1 - HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD
    Chains: A, B, C, D, E
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: CYTOPLASMIC RIBOSE-BINDING PROTEIN RBSD

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (2x): ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GOL5Ligand/IonGLYCEROL
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL10Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:2 , LYS C:2BINDING SITE FOR RESIDUE CL A1133
2AC2SOFTWARELYS D:2 , LYS E:2BINDING SITE FOR RESIDUE CL D1134
3AC3SOFTWAREASP A:28 , LEU A:31 , TYR A:120 , ASN A:122 , HIS E:20 , PHE E:131 , HOH E:2081BINDING SITE FOR RESIDUE GOL A1132
4AC4SOFTWAREHIS A:20 , VAL A:129 , ASP B:28 , GLY B:30 , LEU B:31 , PRO B:119 , TYR B:120 , ASN B:122BINDING SITE FOR RESIDUE GOL B1132
5AC5SOFTWAREHIS B:20 , HOH B:2074 , ASP C:28 , GLY C:30 , LEU C:31 , TYR C:120 , ASN C:122BINDING SITE FOR RESIDUE GOL B1133
6AC6SOFTWAREHIS C:20 , VAL C:129 , ASP D:28 , LEU D:31 , TYR D:120 , ASN D:122BINDING SITE FOR RESIDUE GOL D1132
7AC7SOFTWAREHIS D:20 , HOH D:2065 , ASP E:28 , GLY E:30 , LEU E:31 , TYR E:120 , ASN E:122BINDING SITE FOR RESIDUE GOL D1133

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OGF)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Leu A:48 -Pro A:49
2Leu B:48 -Pro B:49
3Leu C:48 -Pro C:49
4Leu D:48 -Pro D:49
5Leu E:48 -Pro E:49

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OGF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OGF)

(-) Exons   (0, 0)

(no "Exon" information available for 1OGF)

(-) 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:131
 aligned with RBSD_BACSU | P36946 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
           RBSD_BACSU     1 MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAEEMAVEKVIAAAEIKASNQENAKFLENLFSEQEIEYLSHEEFKLLTKDAKAVIRTGEFTPYANCILQAGVLF 131
               SCOP domains d1ogfa_ A: Ribose transport protein RbsD                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh....eeeee...........eee........hhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhh.eeee.........eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ogf A   1 MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAEEMAVEKVIAAAEIKASNQENAKFLENLFSEQEIEYLSHEEFKLLTKDAKAVIRTGEFTPYANCILQAGVLF 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 


Chain B from PDB  Type:PROTEIN  Length:131
 aligned with RBSD_BACSU | P36946 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
           RBSD_BACSU     1 MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAEEMAVEKVIAAAEIKASNQENAKFLENLFSEQEIEYLSHEEFKLLTKDAKAVIRTGEFTPYANCILQAGVLF 131
               SCOP domains d1ogfb_ B: Ribose transport protein RbsD                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhh.....eeeee..........eeee........hhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhh.eeee.........eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ogf B   1 MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAEEMAVEKVIAAAEIKASNQENAKFLENLFSEQEIEYLSHEEFKLLTKDAKAVIRTGEFTPYANCILQAGVLF 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 


Chain C from PDB  Type:PROTEIN  Length:131
 aligned with RBSD_BACSU | P36946 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
           RBSD_BACSU     1 MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAEEMAVEKVIAAAEIKASNQENAKFLENLFSEQEIEYLSHEEFKLLTKDAKAVIRTGEFTPYANCILQAGVLF 131
               SCOP domains d1ogfc_ C: Ribose transport protein RbsD                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh....eeeee...........eee........hhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhh.eeee.........eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ogf C   1 MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAEEMAVEKVIAAAEIKASNQENAKFLENLFSEQEIEYLSHEEFKLLTKDAKAVIRTGEFTPYANCILQAGVLF 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 


Chain D from PDB  Type:PROTEIN  Length:131
 aligned with RBSD_BACSU | P36946 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
           RBSD_BACSU     1 MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAEEMAVEKVIAAAEIKASNQENAKFLENLFSEQEIEYLSHEEFKLLTKDAKAVIRTGEFTPYANCILQAGVLF 131
               SCOP domains d1ogfd_ D: Ribose transport protein RbsD                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh....eeeee..........eeee........hhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhh.eeee.........eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ogf D   1 MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAEEMAVEKVIAAAEIKASNQENAKFLENLFSEQEIEYLSHEEFKLLTKDAKAVIRTGEFTPYANCILQAGVLF 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 


Chain E from PDB  Type:PROTEIN  Length:131
 aligned with RBSD_BACSU | P36946 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
           RBSD_BACSU     1 MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAEEMAVEKVIAAAEIKASNQENAKFLENLFSEQEIEYLSHEEFKLLTKDAKAVIRTGEFTPYANCILQAGVLF 131
               SCOP domains d1ogfe_ E: Ribose transport protein RbsD                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) RbsD_FucU-1ogfE01 E:1-131                                                                                                           Pfam domains (1)
           Pfam domains (2) RbsD_FucU-1ogfE02 E:1-131                                                                                                           Pfam domains (2)
           Pfam domains (3) RbsD_FucU-1ogfE03 E:1-131                                                                                                           Pfam domains (3)
           Pfam domains (4) RbsD_FucU-1ogfE04 E:1-131                                                                                                           Pfam domains (4)
           Pfam domains (5) RbsD_FucU-1ogfE05 E:1-131                                                                                                           Pfam domains (5)
         Sec.struct. author .......hhhhhhhhhhh....eeeee..........eeee........hhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhh.eeee.........eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ogf E   1 MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAEEMAVEKVIAAAEIKASNQENAKFLENLFSEQEIEYLSHEEFKLLTKDAKAVIRTGEFTPYANCILQAGVLF 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   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, 5)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1OGF)

(-) Pfam Domains  (1, 5)

Asymmetric Unit
(-)
Clan: no clan defined [family: RbsD_FucU] (9)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E   (RBSD_BACSU | P36946)
molecular function
    GO:0016872    intramolecular lyase activity    The catalysis of certain rearrangements of a molecule to break or form a ring.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0048029    monosaccharide binding    Interacting selectively and non-covalently with any monosaccharide. Monosaccharides are the simplest carbohydrates; they are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H[CHOH]nC(=O)[CHOH]mH with three or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
biological process
    GO:0019303    D-ribose catabolic process    The chemical reactions and pathways resulting in the breakdown of D-ribose (ribo-pentose).
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0005996    monosaccharide metabolic process    The chemical reactions and pathways involving monosaccharides, 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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RBSD_BACSU | P36946: 1ogc 1ogd 1oge

(-) Related Entries Specified in the PDB File

1ogc THE STRUCTURE OF BACILLUS SUBTILIS RBSD COMPLEXED WITH D-RIBOSE
1ogd THE STRUCTURE OF BACILLUS SUBTILIS RBSD COMPLEXED WITH D-RIBOSE
1oge THE STRUCTURE OF BACILLUS SUBTILIS RBSD COMPLEXED WITH RIBOSE 5-PHOSPHATE