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(-) Description

Title :  CRYSTAL STRUCTURE OF A DISULFIDE MUTANT GLUCOSE BINDING PROTEIN
 
Authors :  M. J. Cuneo, H. W. Hellinga
Date :  12 Oct 06  (Deposition) - 20 Mar 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.12
Chains :  Asym./Biol. Unit :  A
Keywords :  Glucose Binding Protein, Periplasmic Binding Protein, Disulfide, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Cuneo, H. W. Hellinga
The Free Energy Cost Of Domain Reorganization In E. Coli Glucose Binding Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - D-GALACTOSE-BINDING PERIPLASMIC PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET21A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: MGLB
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: GBP, D-GALACTOSE/D-GLUCOSE-BINDING PROTEIN, GGBP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2CA1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:10 , ASP A:14 , PHE A:16 , ASN A:91 , LYS A:92 , HIS A:152 , ASP A:154 , ARG A:158 , TRP A:183 , ASN A:211 , ASP A:236 , ASN A:256 , HOH A:524BINDING SITE FOR RESIDUE BGC A 501
2AC2SOFTWAREASP A:134 , ASN A:136 , ASP A:138 , GLN A:140 , GLN A:142 , GLU A:205BINDING SITE FOR RESIDUE CA A 502

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:15 -A:238

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2IPM)

(-) Sequences/Alignments

Asymmetric/Biological 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:307
 aligned with DGAL_ECOLI | P0AEE5 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:307
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       
           DGAL_ECOLI    24 ADTRIGVTIYKYDDNFMSVVRKAIEQDAKAAPDVQLLMNDSQNDQSKQNDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFNKEPSRKALDSYDKAYYVGTDSKESGIIQGDLIAKHWAANQGWDLNKDGQIQFVLLKGEPGHPDAEARTTYVIKELNDKGIKTEQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEVVIANNDAMAMGAVEALKAHNKSSIPVFGVDALPEALALVKSGALAGTVLNDANNQAKATFDLAKNLADGKGAADGTNWKIDNKVVRVPYVGVDKDNLAEFS 330
               SCOP domains d2ipma_ A: Galactose/glucose-binding protein                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2ipmA01 A:1-110,A:257-294  [code=3.40.50.2300, no name defined]                                               2ipmA02 A:111-256,A:295-307  [code=3.40.50.2300, no name defined]                                                                                 2ipmA01 A:1-110,A:257-294             2ipmA02       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh...eeee....hhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee....hhhhhhhhhhhhhhhhhh...eeeeeeee...hhhhhhhhhhhhhhh.hhhhh.eeee.hhhhhhhhhhhhhhh......ee....hhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhh...............eee...eee...hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ipm A   1 ADTRIGVTIYKYDDCFMSVVRKAIEQDAKAAPDVQLLMNDSQNDQSKQNDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFNKEPSRKALDSYDKAYYVGTDSKESGIIQGDLIAKHWAANQGWDLNKDGQIQFVLLKGEPGHPDAEARTTYVIKELNDKGIKTEQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEVVIANNDAMAMGAVEALKAHNKSSIPVFGVDACPEALALVKSGALAGTVLNDANNQAKATFDLAKNLADGKGAADGTNWKIDNKVVRVPYVGVDKDNLAEFS 307
                                    10        20        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
   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, 1)

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

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IPM)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DGAL_ECOLI | P0AEE5)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0008643    carbohydrate transport    The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are any of a group of organic compounds based of the general formula Cx(H2O)y.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    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:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        DGAL_ECOLI | P0AEE5: 1glg 2fvy 2fw0 2gbp 2hph 2ipl 2ipn 2qw1

(-) Related Entries Specified in the PDB File

2hph HIGH RESOLUTION CRYSTAL STRUCTURE OF E. COLI GLUCOSE/ GALACTOSE BINDING PROTEIN.
2ipl CRYSTAL STRUCTURE OF A DISULFIDE MUTANT GLUCOSE BINDING PROTEIN
2ipn