Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE CONSERVED HYPOTHETICAL PROTEIN APE0931 FROM AEROPYRUM PERNIX K1
 
Authors :  S. Kishishita, K. Murayama, M. Shirouzu, S. Yokoyama, Riken Structur Genomics/Proteomics Initiative (Rsgi)
Date :  13 May 04  (Deposition) - 13 Nov 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Structural Genomics, Conserved Hypothetical Protein, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kishishita, K. Shimizu, K. Murayama, T. Terada, M. Shirouzu, S. Yokoyama, N. Kunishima
Structures Of Two Archaeal Diphthine Synthases: Insights Into The Post-Translational Modification Of Elongation Factor 2.
Acta Crystallogr. , Sect. D V. 64 397 2008
PubMed-ID: 18391406  |  Reference-DOI: 10.1107/S0907444908000723

(-) Compounds

Molecule 1 - PROBABLE DIPHTHINE SYNTHASE
    Chains: A
    EC Number: 2.1.1.98
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11B
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 56636
    Synonym: DIPHTHAMIDE BIOSYNTHESIS METHYLTRANSFERASE, CONSERVED HYPOTHETICAL PROTEIN APE0931

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1WDE)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:164 -A:285

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Arg A:269 -Pro A:270
2Glu A:292 -Pro A:293

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WDE)

(-) 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:289
 aligned with DPHB_AERPE | Q9YDI2 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:289
                                    15        25        35        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         
           DPHB_AERPE     6 EAVTLLLVGWGYAPGMQTLEALDAVRRADVVYVESYTMPGSSWLYKSVVEAAGEARVVEASRRDLEERSREIVSRALDAVVAVVTAGDPMVATTHSSLAAEALEAGVAVRYIPGVSGVQAARGATMLSFYRFGGTVTLPGPWRGVTPISVARRIYLNLCAGLHTTALLDVDERGVQLSPGQGVSLLLEADREYAREAGAPALLARLPSVLVEAGAGGGHRVLYWSSLERLSTADVEGGVYSIVIPARLSGVEEWLLAAASGQRRPLEYDRSVYETVEENCKKGVYMEPV 294
               SCOP domains d1wdea_ A: Diphthine synthase, DphB                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1wdeA01 A:6-120 Cobalt-precorrin-4 Transmethylase; Domain 1                                                        1wdeA02 A:121-294 Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2                                                                                               CATH domains
               Pfam domains ---TP_methylase-1wdeA01 A:9-210                                                                                                                                                                              ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee........hhhhhhhhhhh.eeeee.......hhhhhhhhhhhh...eee.hhhhhhhhhhhhh......eeeeee........hhhhhhhhhhhh..eeeee...hhhhhhhhhhh.hhh.eeeeeee.hhhhh..hhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhhhhhhhhh...hhhhh.eeeee.hhhhh.eeeee.hhhhhhh........eeee....hhhhhhhhhhhh..........hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wde A   6 EAVTLLLVGWGYAPGmQTLEALDAVRRADVVYVESYTmPGSSWLYKSVVEAAGEARVVEASRRDLEERSREIVSRALDAVVAVVTAGDPmVATTHSSLAAEALEAGVAVRYIPGVSGVQAARGATmLSFYRFGGTVTLPGPWRGVTPISVARRIYLNLCAGLHTTALLDVDERGVQLSPGQGVSLLLEADREYAREAGAPALLARLPSVLVEAGAGGGHRVLYWSSLERLSTADVEGGVYSIVIPARLSGVEEWLLAAASGQRRPLEYDRSVYETVEENCKKGVYmEPV 294
                                    15     |  25        35       |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     |   
                                          21-MSE                43-MSE                                              95-MSE                             131-MSE                                                                                                                                                         291-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  (1, 1)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: TP_methylase] (35)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (DPHB_AERPE | Q9YDI2)
molecular function
    GO:0004164    diphthine synthase activity    Catalysis of the reaction: S-adenosyl-L-methionine + 2-(3-carboxy-3-aminopropyl)-L-histidine = S-adenosyl-L-homocysteine + 2-(3-carboxy-3-(methylammonio)propyl)-L-histidine.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor 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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0017183    peptidyl-diphthamide biosynthetic process from peptidyl-histidine    The modification of peptidyl-histidine to 2'-(3-carboxamido-3-(trimethylammonio)propyl)-L-histidine, known as diphthamide, found in translation elongation factor EF-2. The process occurs in eukaryotes and archaea but not eubacteria.

 Visualization

(-) Interactive Views

Asymmetric 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1wde)
 
  Cis Peptide Bonds
    Arg A:269 - Pro A:270   [ RasMol ]  
    Glu A:292 - Pro A:293   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 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
  1wde
    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
  DPHB_AERPE | Q9YDI2
    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)
  2.1.1.98
    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
  DPHB_AERPE | Q9YDI2
    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 1WDE)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1WDE)