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(-) Description

Title :  CRYSTAL STRUCTURE OF 7-CYANO-7-DEAZAGUANINE REDUCTASE, QUEF FROM VIBRIO CHOLERAE
 
Authors :  Y. Kim, M. Zhou, M. Gu, W. F. Anderson, A. Joachimiak, Center For Struc Genomics Of Infectious Diseases (Csgid)
Date :  15 Apr 11  (Deposition) - 10 Aug 11  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Tunnelling Fold, Rossman-Fold, Reductase, Cytosol, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, M. Zhou, M. Gu, W. F. Anderson, A. Joachimiak, Csgid
Crystal Structure Of 7-Cyano-7-Deazaguanine Reductase, Quef From Vibrio Cholerae
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 7-CYANO-7-DEAZAGUANINE REDUCTASE QUEF
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21 MAGIC
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: QUEF
    Mutation: YES
    Organism Scientific: VIBRIO CHOLERAE O1 BIOVAR EL TOR
    Organism Taxid: 243277
    Strain: N16961

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB
Biological Unit 2 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3MSE8Mod. Amino AcidSELENOMETHIONINE
4SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 20)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3MSE16Mod. Amino AcidSELENOMETHIONINE
4SO42Ligand/IonSULFATE ION
Biological Unit 2 (3, 10)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3MSE8Mod. Amino AcidSELENOMETHIONINE
4SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:95 , LYS A:96 , LYS A:99 , ARG A:262 , GLY A:263 , LEU A:265 , HOH A:340BINDING SITE FOR RESIDUE GOL A 291
2AC2SOFTWARETRP A:113 , HOH A:433BINDING SITE FOR RESIDUE CL A 292
3AC3SOFTWAREVAL A:148 , THR A:149 , SER B:182 , HIS B:210BINDING SITE FOR RESIDUE CL B 291
4AC4SOFTWAREARG A:262 , GLY A:263 , ARG B:262 , GLY B:263 , HOH B:344 , HOH B:428 , HOH B:445BINDING SITE FOR RESIDUE SO4 B 292

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RJ4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3RJ4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RJ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RJ4)

(-) Exons   (0, 0)

(no "Exon" information available for 3RJ4)

(-) 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:259
 aligned with QUEF_VIBCH | Q9KTK0 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:259
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272         
           QUEF_VIBCH    23 NQYDPSLLQPVPRSLNRNDLHLSATLPFQGCDIWTLYELSWLNQKGLPQVAIGEVSIPATSANLIESKSFKLYLNSYNQTRFASWDEVQTRLVHDLSACAGETVTVNVKSLNEYTAEPIVTMQGECIDDQDIEIANYEFDDALLQGAAQGEEVSEVLHSHLLKSNCLITNQPDWGSVEIAYHGAKMNREALLRYLVSFREHNEFHEQCVERIFTDIMRYCQPQSLTVYARYTRRGGLDINPFRSSHQSAPNHNQRMARQ 281
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.eeehhhhhhhhh.......eeeeeeee...eee.....eee.eeeeeee....eeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh...eeeeehhhhhh.........ee.............hhhhhh..eeeeeeeeeeeeeeee.hhhhhh...eeeeeeeeeeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rj4 A  29 NQYDPSLLQPVPRSLNRNDLHLSATLPFQGCDIWTLYELSWLNQKGLPQVAIGEVSIPATSANLIESKSFKLYLNSYNQTRFASWDEVQTRLVHDLSACAGETVTVNVKSLNEYTAEPIVTmQGECIDDQDIEIANYEFDDALLQGAAQGEEVSEVLHSHLLKSNALITNQPDWGSVEIAYHGAKmNREALLRYLVSFREHNEFHEQCVERIFTDImRYCQPQSLTVYARYTRRGGLDINPFRSSHQSAPNHNQRmARQ 287
                                    38        48        58        68        78        88        98       108       118       128       138       148 |     158       168       178       188       198       208     | 218       228       238      |248       258       268       278     |   
                                                                                                                                                   150-MSE                                                         214-MSE                        245-MSE                                284-MSE


Chain B from PDB  Type:PROTEIN  Length:255
 aligned with QUEF_VIBCH | Q9KTK0 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:259
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272         
           QUEF_VIBCH    23 NQYDPSLLQPVPRSLNRNDLHLSATLPFQGCDIWTLYELSWLNQKGLPQVAIGEVSIPATSANLIESKSFKLYLNSYNQTRFASWDEVQTRLVHDLSACAGETVTVNVKSLNEYTAEPIVTMQGECIDDQDIEIANYEFDDALLQGAAQGEEVSEVLHSHLLKSNCLITNQPDWGSVEIAYHGAKMNREALLRYLVSFREHNEFHEQCVERIFTDIMRYCQPQSLTVYARYTRRGGLDINPFRSSHQSAPNHNQRMARQ 281
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.eeehhhhhhhh........eeeeeeee...eee.....eee.eeeeeee....eeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh...eeeeehhhhhh.........ee.............hhhhhh..eeeeeeeeeeeeeeeee.----...eeeeeeeeeeeeeehhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rj4 B  29 NQYDPSLLQPVPRSLNRNDLHLSATLPFQGCDIWTLYELSWLNQKGLPQVAIGEVSIPATSANLIESKSFKLYLNSYNQTRFASWDEVQTRLVHDLSACAGETVTVNVKSLNEYTAEPIVTmQGECIDDQDIEIANYEFDDALLQGAAQGEEVSEVLHSHLLKSN----NQPDWGSVEIAYHGAKmNREALLRYLVSFREHNEFHEQCVERIFTDImRYCQPQSLTVYARYTRRGGLDINPFRSSHQSAPNHNQRmARQ 287
                                    38        48        58        68        78        88        98       108       118       128       138       148 |     158       168       178       188    |  198       208     | 218       228       238      |248       258       268       278     |   
                                                                                                                                                   150-MSE                                    193  198             214-MSE                        245-MSE                                284-MSE
   Legend:   → Mismatch (orange background)
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  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 3RJ4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RJ4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3RJ4)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (QUEF_VIBCH | Q9KTK0)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0046857    oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a nitrogenous group, excluding NH and NH2 groups, acts as a hydrogen or electron donor and reduces NAD or NADP.
    GO:0033739    preQ1 synthase activity    Catalysis of the reaction: 7-aminomethyl-7-deazaguanine + 2 NADP(+) = 7-cyano-7-deazaguanine + 3 H(+) + 2 NADPH.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0008616    queuosine biosynthetic process    The chemical reactions and pathways resulting in the formation of queuosines, any of a series of nucleosides found in tRNA and having an additional pentenyl ring added via an NH group to the methyl group of 7-methylguanosine. The pentenyl ring may carry other substituents.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        QUEF_VIBCH | Q9KTK0: 3bp1 3rzp 3s19 3uxj 3uxv 4ghm 4iqi

(-) Related Entries Specified in the PDB File

3bp1 THE SAME PROTEIN WITHOUT ANY LIGAND RELATED ID: IDP01750 RELATED DB: TARGETDB
3rjb CRYSTAL STRUCTURE OF 7-CYANO-7-DEAZAGUANINE REDUCTASE, QUEF FROM VIBRIO CHOLERAE O1 BIOVAR EL TOR COMPLEXED WITH CYTOSINE