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

(-) Description

Title :  TRNA-GUANINE TRANSGLYCOSYLASE Y106F, C158V, V233G MUTANT APO STRUCTURE
 
Authors :  I. Biela, N. Tidten-Luksch, A. Heine, K. Reuter, G. Klebe
Date :  19 Sep 12  (Deposition) - 07 Nov 12  (Release) - 17 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.42
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Substrate Specificity, Bacterial Tgt, Transferase, Preq1, Trna, Queuine, Guanine Exchange Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Biela, N. Tidten-Luksch, F. Immekus, S. Glinca, T. X. Nguyen, H. D. Gerber, A. Heine, G. Klebe, K. Reuter
Investigation Of Specificity Determinants In Bacterial Trna-Guanine Transglycosylase Reveals Queuine, The Substrat Of Its Eucaryotic Counterpart, As Inhibitor.
Plos One V. 8 64240 2013
PubMed-ID: 23704982  |  Reference-DOI: 10.1371/JOURNAL.PONE.0064240

(-) Compounds

Molecule 1 - QUEUINE TRNA-RIBOSYLTRANSFERASE
    Chains: A
    EC Number: 2.4.2.29
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET9D-ZM-Y106F_C158V_V233G
    Expression System Strain: BL21 DE(3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TGT, ZMO0363
    Mutation: YES
    Organism Scientific: ZYMOMONAS MOBILIS
    Organism Taxid: 264203
    Strain: ATCC 31821 / ZM4 / CP4
    Synonym: GUANINE INSERTION ENZYME, TRNA-GUANINE TRANSGLYCOSYLASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1GOL7Ligand/IonGLYCEROL
2ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 14)
No.NameCountTypeFull Name
1GOL14Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:56 , GLU A:57 , GLY A:94 , TRP A:95 , ASP A:96 , ARG A:97 , HOH A:801 , HOH A:837BINDING SITE FOR RESIDUE GOL A 401
2AC2SOFTWARECYS A:318 , CYS A:320 , CYS A:323 , HIS A:349BINDING SITE FOR RESIDUE ZN A 402
3AC3SOFTWAREGLN A:117 , ARG A:174 , PRO A:252 , ASP A:254 , LYS A:255 , HOH A:530 , HOH A:648BINDING SITE FOR RESIDUE GOL A 403
4AC4SOFTWAREGLU A:317 , LYS A:360 , PHE A:373 , ARG A:380 , HOH A:529 , HOH A:785 , HOH A:797BINDING SITE FOR RESIDUE GOL A 404
5AC5SOFTWAREALA A:20 , ARG A:21 , ARG A:82 , ALA A:305 , SER A:308 , HIS A:332 , ARG A:336 , HOH A:873BINDING SITE FOR RESIDUE GOL A 405
6AC6SOFTWAREARG A:34 , GLY A:148 , SER A:149 , ASP A:150 , ASN A:195 , HOH A:895 , HOH A:916BINDING SITE FOR RESIDUE GOL A 406
7AC7SOFTWAREPHE A:14 , SER A:15 , PHE A:16 , GLU A:119 , ARG A:174 , ARG A:177 , ASP A:254 , LYS A:255 , HOH A:552 , HOH A:631 , HOH A:736BINDING SITE FOR RESIDUE GOL A 407
8AC8SOFTWAREPHE A:106 , GLY A:229 , GLY A:230 , LEU A:231 , MET A:260 , HOH A:732 , HOH A:886 , HOH A:921BINDING SITE FOR RESIDUE GOL A 408

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H6E)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Thr A:39 -Pro A:40
2Arg A:77 -Pro A:78
3Tyr A:161 -Pro A:162
4Val A:262 -Gly A:263

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H6E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H6E)

(-) Exons   (0, 0)

(no "Exon" information available for 4H6E)

(-) 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:372
                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4h6ea_ A: Queosine tRNA-guanine transglycosylase                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeee..eeeeeeee..eeeee.eee.ee........hhhhhhhh....eeehhhhhhhh.hhhhhhhh.hhhhhhh....eee..hhhhhhhhh...ee....eeee.....eeeehhhhhhhhhhhhh..eee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeee....hhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhh.....eee....hhhhhhhhhhh...eee....hhhhhh.ee......ee..hhhhh...........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4h6e A  11 RPRFSFSIAAREGKARTGTIEMKRGVIRTPAFMPVGTAATVKALKPETVRATGADIILGNTYHLMLRPGAERIAKLGGLHSFMGWDRPILTDSGGFQVMSLSSLTKQSEEGVTFKSHDGSRHMLSPERSIEIQHLLGSDIVMAFDEVTPYPATPSRAASSMERSMRWAKRSRDAFDSRKEQAENAALFGIQQGSVFENLRQQSADALAEIGFDGYAVGGLAGGEGQDEMFRVLDFSVPMLPDDKPHYLMGVGKPDDIVGAVERGIDMFDCVLPTRSGRNGQAFTWDGPINIRNARFSEDLKPLDSECHCAVCQKWSRAYIHHLIRAGEILGAMLMTEHNIAFYQQLMQKIRDSISEGRFSQFAQDFRARYFA 383
                                    20        30        40        50        60        70        80        90       100       110       120      |131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381  
                                                                                                                                              127|                                                                                                                                                                                                                                                              
                                                                                                                                               129
   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  (0, 0)

(no "CATH Domain" information available for 4H6E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H6E)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:77 - Pro A:78   [ RasMol ]  
    Thr A:39 - Pro A:40   [ RasMol ]  
    Tyr A:161 - Pro A:162   [ RasMol ]  
    Val A:262 - Gly A:263   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  4h6e
    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
  TGT_ZYMMO | P28720
    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)
  2.4.2.29
    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
  TGT_ZYMMO | P28720
    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
        TGT_ZYMMO | P28720: 1efz 1enu 1f3e 1k4g 1k4h 1n2v 1ozm 1ozq 1p0b 1p0d 1p0e 1pud 1pxg 1q2r 1q2s 1q4w 1q63 1q65 1q66 1r5y 1s38 1s39 1wkd 1wke 1wkf 1y5v 1y5w 1y5x 2bbf 2nqz 2nso 2oko 2pot 2pwu 2pwv 2qii 2qzr 2z1v 2z1w 2z1x 2z7k 3bl3 3bld 3bll 3blo 3c2y 3eos 3eou 3gc4 3gc5 3ge7 3hfy 3rr4 3s1g 3sm0 3tll 3unt 3uvi 4dxx 4dy1 4e2v 4fps 4fr1 4fr6 4fsa 4gcx 4gd0 4gg9 4gh1 4gh3 4ghr 4gi4 4giy 4gkt 4h7z 4hqv 4hsh 4htb 4hvx 4ipp 4jbr 4kwo 4l56 4lbu 4leq 4puj 4puk 4pul 4pum 4pun 4q4m 4q4o 4q4p 4q4q 4q4r 4q4s 4q8m 4q8n 4q8o 4q8p 4q8q 4q8t 4q8u 4q8v 4q8w 5egr 5i00 5i02 5i03 5i06 5i07 5i09 5j9m 5j9n 5j9o 5jgm 5jgo 5jsv 5jsw 5jt5 5jt6 5jt7 5jxq

(-) Related Entries Specified in the PDB File

3bl3 3bld 3bll 4e2v 4gcx 4gd0