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 :  STRUCTURE OF GLYCOSYLATED MURINE GLUTAMINYL CYCLASE
 
Authors :  T. Dambe, D. Carrillo, C. Parthier, M. T. Stubbs
Date :  17 Jun 11  (Deposition) - 29 Jun 11  (Release) - 31 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha/Beta Hydrolase, Alzheimer'S Disease, Pyroglutamate, Pglu, Pe, Pglu-Amyloid, Glycosylation, Glycoprotein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Ruiz-Carrillo, B. Koch, C. Parthier, M. Wermann, T. Dambe, M. Buchholz, H. H. Ludwig, U. Heiser, J. U. Rahfeld, M. T. Stubbs, S. Schilling, H. U. Demuth
Structures Of Glycosylated Mammalian Glutaminyl Cyclases Reveal Conformational Variability Near The Active Center.
Biochemistry V. 50 6280 2011
PubMed-ID: 21671571  |  Reference-DOI: 10.1021/BI200249H

(-) Compounds

Molecule 1 - GLUTAMINYL-PEPTIDE CYCLOTRANSFERASE
    Chains: A
    EC Number: 2.3.2.5
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PPICZALPHAB
    Expression System Strain: X33
    Expression System Taxid: 4922
    Fragment: UNP RESIDUES 36-362
    Gene: QPCT
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: GLUTAMINYL CYCLASE, QC, GLUTAMINYL-TRNA CYCLOTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
2ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:19 , ASP A:160 , GLU A:203 , TRP A:330 , HIS A:331BINDING SITE FOR RESIDUE ZN A 601
2AC2SOFTWAREASN A:50 , SER A:52 , TYR A:118 , NAG A:702BINDING SITE FOR RESIDUE NAG A 701
3AC3SOFTWAREHOH A:365 , HOH A:366 , NAG A:701BINDING SITE FOR RESIDUE NAG A 702

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:140 -A:165

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Asp A:160 -Ser A:161
2Asp A:184 -Val A:185
3His A:229 -Pro A:230
4Pro A:231 -Gly A:232
5Ser A:324 -Pro A:325

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SI1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SI1)

(-) Exons   (0, 0)

(no "Exon" information available for 3SI1)

(-) 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:323
 aligned with QPCT_MOUSE | Q9CYK2 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:327
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       
           QPCT_MOUSE    36 AWTQEKNHHQPAHLNSSSLQQVAEGTSISEMWQNDLRPLLIERYPGSPGSYSARQHIMQRIQRLQAEWVVEVDTFLSRTPYGYRSFSNIISTLNPEAKRHLVLACHYDSKYFPRWDSRVFVGATDSAVPCAMMLELARALDKKLHSLKDVSGSKPDLSLRLIFFDGEEAFHHWSPQDSLYGSRHLAQKMASSPHPPGSRGTNQLDGMDLLVLLDLIGAANPTFPNFFPKTTRWFNRLQAIEKELYELGLLKDHSLERKYFQNFGYGNIIQDDHIPFLRKGVPVLHLIASPFPEVWHTMDDNEENLHASTIDNLNKIIQVFVLEYLHL 362
               SCOP domains d3si1a_ A: Glutaminyl-peptide cyclotransferase, QPCT                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------Peptidase_M28-3si1A01 A:134-346                                                                                                                                                                                      ---------------- Pfam domains
         Sec.struct. author hhhhhhhhh.....hhhhhhhh....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......eeeeee........eeeeee.........eeeeeee...................hhhhhhhhhhhhhh.hhhhhh....----...eeeeeee...............hhhhhhhhhhhhh.........hhhhh....eeee............hhhhhhhhhhhhhhh..................................hhhhh...eeee..................hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3si1 A  36 AWTQEKNHHQPAHLNSSSLQQVAEGTSISEMWQNDLRPLLIERYPGSPGSYSARQHIMQRIQRLQAEWVVEVDTFLSRTPYGYRSFSNIISTLNPEAKRHLVLACHYDSKYFPRWDSRVFVGATDSAVPCAMMLELARALDKKLHSLKDV----PDLSLRLIFFDGEEAFHHWSPQDSLYGSRHLAQKMASSPHPPGSRGTNQLDGMDLLVLLDLIGAANPTFPNFFPKTTRWFNRLQAIEKELYELGLLKDHSLERKYFQNFGYGNIIQDDHIPFLRKGVPVLHLIASPFPEVWHTMDDNEENLHASTIDNLNKIIQVFVLEYLHL 362
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185    |  195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       
                                                                                                                                                                               185  190
   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  (0, 0)

(no "CATH Domain" information available for 3SI1)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_MH (119)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (QPCT_MOUSE | Q9CYK2)
molecular function
    GO:0016603    glutaminyl-peptide cyclotransferase activity    Catalysis of the reaction: L-glutaminyl-peptide = 5-oxoprolyl-peptide + NH3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0017186    peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase    The chemical reactions and pathways resulting in the formation of peptidyl-pyroglutamic acid, catalyzed by glutaminyl-peptide cyclotransferase.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

 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
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:160 - Ser A:161   [ RasMol ]  
    Asp A:184 - Val A:185   [ RasMol ]  
    His A:229 - Pro A:230   [ RasMol ]  
    Pro A:231 - Gly A:232   [ RasMol ]  
    Ser A:324 - Pro A:325   [ RasMol ]  
 

(-) 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
  3si1
    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
  QPCT_MOUSE | Q9CYK2
    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)
  2.3.2.5
    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
  QPCT_MOUSE | Q9CYK2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        QPCT_MOUSE | Q9CYK2: 3si2

(-) Related Entries Specified in the PDB File

3si0 STRUCTURE OF GLYCOSYLATED HUMAN GLUTAMINYL CYCLASE
3si2 STRUCTURE OF GLYCOSYLATED MURINE GLUTAMINYL CYCLASE IN PRESENCE OF THE INHIBITOR PQ50 (PDBD150)