Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  GLUCOSE PERMEASE IIA FROM MYCOPLASMA CAPRICOLUM
 
Authors :  K. Huang, O. Herzberg
Date :  19 May 98  (Deposition) - 12 Aug 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Phosphotransferase, Glucose Permease, Enzyme Iia, Mycoplasma (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Huang, G. Kapadia, P. P. Zhu, A. Peterkofsky, O. Herzberg
A Promiscuous Binding Surface: Crystal Structure Of The Iia Domain Of The Glucose-Specific Permease From Mycoplasma Capricolum.
Structure V. 6 697 1998
PubMed-ID: 9705652  |  Reference-DOI: 10.1016/S0969-2126(98)00072-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUCOSE-PERMEASE IIA COMPONENT
    Atcc: ATCC 27343
    Cellular Location: CYTOPLASM
    Chains: A
    Collection: ATCC 27343
    EC Number: 2.7.1.69
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: DOMAIN IIA
    Organism Scientific: MYCOPLASMA CAPRICOLUM
    Organism Taxid: 2095
    Strain: KID

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2GPR)

(-) Sites  (0, 0)

(no "Site" information available for 2GPR)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GPR)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PTS_EIIA_TYPE_1PS51093 PTS_EIIA type-1 domain profile.PTGA_MYCCT26-130  1A:31-135
2PTS_EIIA_TYPE_1_HISPS00371 PTS EIIA domains phosphorylation site signature 1.PTGA_MYCCT72-84  1A:77-89

(-) Exons   (0, 0)

(no "Exon" information available for 2GPR)

(-) 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:154
 aligned with PTGA_MYCCT | P45618 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    
           PTGA_MYCCT     1 MWFFNKNLKVLAPCDGTIITLDEVEDEVFKERMLGDGFAINPKSNDFHAPVSGKLVTAFPTKHAFGIQTKSGVEILLHIGLDTVSLDGNGFESFVTQDQEVNAGDKLVTVDLKSVAKKVPSIKSPIIFTNNGGKTLEIVKMGEVKQGDVVAILK 154
               SCOP domains d2gpra_ A: Glucose permease IIa domain, IIa-glc                                                                                                            SCOP domains
               CATH domains 2gprA00 A:6-159 Glucose Permease (Domain IIA)                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee....eeee.hhh...hhhh.....eeeeeee...eee.....eeee......eeeee.....eeeee....hhhh....eee............eeeee.hhhhhhh.....eeeeeee...........eee....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------PTS_EIIA_TYPE_1  PDB: A:31-135 UniProt: 26-130                                                           ------------------------ PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------PTS_EIIA_TYPE---------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gpr A   6 MWFFNKNLKVLAPCDGTIITLDEVEDEVFKERMLGDGFAINPKSNDFHAPVSGKLVTAFPTKHAFGIQTKSGVEILLHIGLDTVSLDGNGFESFVTQDQEVNAGDKLVTVDLKSVAKKVPSIKSPIIFTNNGGKTLEIVKMGEVKQGDVVAILK 159
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155
   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: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PTGA_MYCCT | P45618)
molecular function
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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:0009401    phosphoenolpyruvate-dependent sugar phosphotransferase system    The uptake and phosphorylation of specific carbohydrates from the extracellular environment; uptake and phosphorylation are coupled, making the PTS a link between the uptake and metabolism of sugars; phosphoenolpyruvate is the original phosphate donor; phosphoenolpyruvate passes the phosphate via a signal transduction pathway, to enzyme 1 (E1), which in turn passes it on to the histidine protein, HPr; the next step in the system involves sugar-specific membrane-bound complex, enzyme 2 (EII), which transports the sugar into the cell; it includes the sugar permease, which catalyzes the transport reactions; EII is usually divided into three different domains, EIIA, EIIB, and EIIC.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2gpr)
 
  Sites
(no "Sites" information available for 2gpr)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2gpr)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2gpr
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PTGA_MYCCT | P45618
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.1.69
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PTGA_MYCCT | P45618
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2GPR)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2GPR)