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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COVALENT THIOIMIDE INTERMEDIATE OF UNIMODULAR NITRILE REDUCTASE QUEF
 
Authors :  B. Stec, M. A. Swairjo
Date :  17 May 12  (Deposition) - 11 Jul 12  (Release) - 19 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B,C,D,E  (2x)
Keywords :  Beta Barrel, Protein Thioimide Complex, Pterin Binding Fold, Tunnel Fold, Trna Modification Enzyme, 7-Cyano-7-Deazaguanine, Nadph, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. M. Chikwana, B. Stec, B. W. Lee, V. De Crecy-Lagard, D. Iwata-Reuyl M. A. Swairjo
Structural Basis Of Biological Nitrile Reduction.
J. Biol. Chem. V. 287 30560 2012
PubMed-ID: 22787148  |  Reference-DOI: 10.1074/JBC.M112.388538

(-) Compounds

Molecule 1 - NADPH-DEPENDENT 7-CYANO-7-DEAZAGUANINE REDUCTASE
    Chains: A, B, C, D, E
    EC Number: 1.7.1.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BSU13750, QUEF, YKVM
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SUBTILIS
    Organism Taxid: 224308
    Strain: 168
    Synonym: QUEF, 7-CYANO-7-CARBAGUANINE REDUCTASE, NADPH-DEPENDENT NITRILE OXIDOREDUCTASE, PREQ(0) REDUCTASE

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (2x): ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1GD14Ligand/Ion2-AMINO-5-[(Z)-IMINOMETHYL]-3,7-DIHYDRO-4H-PYRROLO[2,3-D]PYRIMIDIN-4-ONE
2MG4Ligand/IonMAGNESIUM ION
3PE41Ligand/Ion2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
4PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1GD18Ligand/Ion2-AMINO-5-[(Z)-IMINOMETHYL]-3,7-DIHYDRO-4H-PYRROLO[2,3-D]PYRIMIDIN-4-ONE
2MG-1Ligand/IonMAGNESIUM ION
3PE42Ligand/Ion2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
4PO42Ligand/IonPHOSPHATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:33 , VAL A:77 , GLU A:78 , SER A:79 , CYS B:55 , ASP B:62 , PHE B:95 , HIS B:96 , GLU B:97 , ILE B:130BINDING SITE FOR RESIDUE GD1 B 201
02AC2SOFTWAREASP B:162 , ARG B:164 , HOH B:301 , HOH B:302 , ARG E:164 , MG E:202 , HOH E:301BINDING SITE FOR RESIDUE MG B 202
03AC3SOFTWAREASN B:39 , HOH B:337 , HOH B:340BINDING SITE FOR RESIDUE PO4 B 203
04AC4SOFTWAREVAL B:77 , GLU B:78 , SER B:79 , CYS C:55 , ASP C:62 , PHE C:95 , HIS C:96 , GLU C:97 , ILE C:130BINDING SITE FOR RESIDUE GD1 C 201
05AC5SOFTWAREASP C:162 , ARG C:164 , HOH C:301 , HOH C:302 , ARG D:164 , MG D:202 , HOH D:302BINDING SITE FOR RESIDUE MG C 202
06AC6SOFTWAREPHE C:33 , VAL C:77 , GLU C:78 , SER C:79 , CYS D:55 , PRO D:56 , ASP D:62 , PHE D:95 , HIS D:96 , GLU D:97 , ILE D:130BINDING SITE FOR RESIDUE GD1 D 201
07AC7SOFTWAREARG C:164 , MG C:202 , ASP D:162 , ARG D:164 , HOH D:301 , HOH D:302 , HOH D:303BINDING SITE FOR RESIDUE MG D 202
08AC8SOFTWARETYR B:149 , ASN B:153 , TYR B:157 , TYR C:149 , ASN C:153 , TYR C:157 , ASN D:153 , TYR D:157 , HOH D:327 , TYR E:149 , TYR E:157BINDING SITE FOR RESIDUE PE4 D 203
09AC9SOFTWAREPHE D:33 , VAL D:77 , GLU D:78 , SER D:79 , CYS E:55 , PRO E:56 , LYS E:57 , ASP E:62 , PHE E:95 , HIS E:96 , GLU E:97 , ILE E:130BINDING SITE FOR RESIDUE GD1 E 201
10BC1SOFTWAREARG B:164 , MG B:202 , ASP E:162 , ARG E:164 , HOH E:301 , HOH E:302 , HOH E:303BINDING SITE FOR RESIDUE MG E 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F8B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4F8B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F8B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F8B)

(-) Exons   (0, 0)

(no "Exon" information available for 4F8B)

(-) 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:139
                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh.eee........eeeeeeeeeeee......eeeeeeeeeee...eeehhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eeeeeeee.....ee...eeeee...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f8b A  20 NYLFEYAPDVLESFPNKHVNRDYFVKFNCPEFTSLCPKTGQPDFATIYISYIPDEKMVESKSLKLYLFSFRNHGDFHEDCMNIIMNDLIELMDPRYIEVWGKFTPRGGISIDPYTNYGKPGTKYEKMAEYRMMNHDLYP 158
                                    29        39        49        59        69        79        89        99       109       119       129       139       149         


Chain B from PDB  Type:PROTEIN  Length:145
                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh.eee.......eeeeeeeeeeeee......eeeeeeeeeee...eeehhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eeeeeeee......eeeeeeeee...hhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f8b B  20 NYLFEYAPDVLESFPNKHVNRDYFVKFNCPEFTSLCPKTGQPDFATIYISYIPDEKMVESKSLKLYLFSFRNHGDFHEDCMNIIMNDLIELMDPRYIEVWGKFTPRGGISIDPYTNYGKPGTKYEKMAEYRMMNHDLYPETIDNR 164
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159     


Chain C from PDB  Type:PROTEIN  Length:145
                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh.eee.......eeeeeeeeeeeee......eeeeeeeeeee...eeehhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eeeeeeee......eeeeeeeee...hhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f8b C  20 NYLFEYAPDVLESFPNKHVNRDYFVKFNCPEFTSLCPKTGQPDFATIYISYIPDEKMVESKSLKLYLFSFRNHGDFHEDCMNIIMNDLIELMDPRYIEVWGKFTPRGGISIDPYTNYGKPGTKYEKMAEYRMMNHDLYPETIDNR 164
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159     


Chain D from PDB  Type:PROTEIN  Length:145
                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh.eee........eeeeeeeeeeee......eeeeeeeeeee...eeehhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eeeeeeee......eeeeeeeee...hhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f8b D  20 NYLFEYAPDVLESFPNKHVNRDYFVKFNCPEFTSLCPKTGQPDFATIYISYIPDEKMVESKSLKLYLFSFRNHGDFHEDCMNIIMNDLIELMDPRYIEVWGKFTPRGGISIDPYTNYGKPGTKYEKMAEYRMMNHDLYPETIDNR 164
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159     


Chain E from PDB  Type:PROTEIN  Length:145
                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh.eee........eeeeeeeeeeee......eeeeeeeeeee...eeehhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eeeeeeee......eeeeeeeee...hhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f8b E  20 NYLFEYAPDVLESFPNKHVNRDYFVKFNCPEFTSLCPKTGQPDFATIYISYIPDEKMVESKSLKLYLFSFRNHGDFHEDCMNIIMNDLIELMDPRYIEVWGKFTPRGGISIDPYTNYGKPGTKYEKMAEYRMMNHDLYPETIDNR 164
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159
   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 4F8B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F8B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F8B)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        QUEF_BACSU | O31678: 4fgc 5udg

(-) Related Entries Specified in the PDB File

4fgc