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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE GAF DOMAIN FROM ACINETOBACTER PHOSPHOENOLPYRUVATE-PROTEIN PHOSPHOTRANSFERASE
 
Authors :  M. E. Cuff, G. Shackelford, Y. Kim, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  10 Mar 08  (Deposition) - 13 May 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pep-Phosphotransferase, Gaf Domain, Acinetobacter, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Kinase, Magnesium, Metal-Binding, Phosphotransferase System, Pyruvate, Sugar Transport, Transport, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Cuff, G. Shackelford, Y. Kim, A. Joachimiak
Crystal Structure Of The Gaf Domain From Acinetobacter Phosphoenolpyruvate-Protein Phosphotransferase.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHOENOLPYRUVATE-PROTEIN PHOSPHOTRANSFERASE
    Chains: A, B
    EC Number: 2.7.3.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG19B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PTSP, ACIAD0454
    Organism Scientific: ACINETOBACTER SP.
    Organism Taxid: 62977
    Strain: ADP1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 20)

Asymmetric/Biological Unit (4, 20)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE14Mod. Amino AcidSELENOMETHIONINE
3P4G2Ligand/Ion1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:5 , THR A:8 , SER A:140BINDING SITE FOR RESIDUE P4G A 169
2AC2SOFTWARELEU B:47 , ASP B:48 , LEU B:55BINDING SITE FOR RESIDUE P4G B 169
3AC3SOFTWAREGLU A:49 , GLU A:86 , ARG A:123 , LYS A:124BINDING SITE FOR RESIDUE PEG A 170
4AC4SOFTWAREGLY B:107BINDING SITE FOR RESIDUE PEG B 170
5AC5SOFTWARESER B:71 , GLN B:73 , GLU B:76BINDING SITE FOR RESIDUE GOL B 171
6AC6SOFTWAREGLU A:86 , ARG A:123 , GLU A:141 , ASP B:7BINDING SITE FOR RESIDUE GOL A 171

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CI6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CI6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CI6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CI6)

(-) Exons   (0, 0)

(no "Exon" information available for 3CI6)

(-) 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:158
 aligned with Q6FEW8_ACIAD | Q6FEW8 from UniProtKB/TrEMBL  Length:764

    Alignment length:167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       
         Q6FEW8_ACIAD     1 MSNMQLDTLRRIVQEINSSVSLHDSLDIMVNQVADAMKVDVCSIYLLDERNQRYLLMASKGLNPESVGHVSLQLSEGLVGLVGQREEIVNLENASKHERFAYLPETGEEIYNSFLGVPVMYRRKVMGVLVVQNKQPQDFSEAAESFLVTLCAQLSGVIAHAHAVGNI 167
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -3ci6A00 A:2-167  [code=3.30.450.40, no name defined]                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeeee....eeeeeeee..hhhhh...eee..hhhhhhhhhhh..eee.hhhhh...---------...eeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ci6 A   1 mSNmQLDTLRRIVQEINSSVSLHDSLDImVNQVADAmKVDVCSIYLLDERNQRYLLmASKGLNPESVGHVSLQLSEGLVGLVGQREEIVNLENASKHERF---------IYNSFLGVPVmYRRKVmGVLVVQNKQPQDFSEAAESFLVTLCAQLSGVIAHAHAVGNI 167
                            |  |    10        20        30      | 40        50      | 60        70        80        90       100       110       120     | 130       140       150       160       
                            |  |                       29-MSE  37-MSE              57-MSE                                    100       110       120-MSE |                                         
                            1-MSE                                                                                                                      126-MSE                                     
                               4-MSE                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:166
 aligned with Q6FEW8_ACIAD | Q6FEW8 from UniProtKB/TrEMBL  Length:764

    Alignment length:168
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160        
         Q6FEW8_ACIAD     1 MSNMQLDTLRRIVQEINSSVSLHDSLDIMVNQVADAMKVDVCSIYLLDERNQRYLLMASKGLNPESVGHVSLQLSEGLVGLVGQREEIVNLENASKHERFAYLPETGEEIYNSFLGVPVMYRRKVMGVLVVQNKQPQDFSEAAESFLVTLCAQLSGVIAHAHAVGNID 168
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains -3ci6B00 B:2-168  [code=3.30.450.40, no name defined]                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeeee....eeeeeeee..hhhhh...eee..hhhhhhhhhhh..eee.hhhhhh......--......eeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ci6 B   1 mSNmQLDTLRRIVQEINSSVSLHDSLDImVNQVADAmKVDVCSIYLLDERNQRYLLmASKGLNPESVGHVSLQLSEGLVGLVGQREEIVNLENASKHERFAYLP--GEEIYNSFLGVPVmYRRKVmGVLVVQNKQPQDFSEAAESFLVTLCAQLSGVIAHAHAVGNID 168
                            |  |    10        20        30      | 40        50      | 60        70        80        90       100   |  |110       120     | 130       140       150       160        
                            1-MSE                      29-MSE  37-MSE              57-MSE                                        104  |          120-MSE |                                          
                               4-MSE                                                                                                107                126-MSE
   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 3CI6)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CI6)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q6FEW8_ACIAD | Q6FEW8)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0008965    phosphoenolpyruvate-protein phosphotransferase activity    Catalysis of the reaction: phosphoenolpyruvate + protein L-histidine = pyruvate + protein N(pi)-phospho-L-histidine.
    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.
    GO:0016772    transferase activity, transferring phosphorus-containing groups    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
biological process
    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.

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    P4G  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ci6)
 

(-) 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 | Asym./Biol. Unit - sites 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
  3ci6
    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
  Q6FEW8_ACIAD | Q6FEW8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  2.7.3.9
    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
  Q6FEW8_ACIAD | Q6FEW8
    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 3CI6)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3CI6)