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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C194A MUTANT OF 7-CYANO-7-DEAZAGUANINE REDUCTASE, QUEF FROM VIBRIO CHOLERAE COMPLEXED WITH PREQ1
 
Authors :  Y. Kim, M. Zhou, M. Gu, W. F. Anderson, A. Joachimiak, Center For Struc Genomics Of Infectious Diseases (Csgid)
Date :  12 May 11  (Deposition) - 29 Jun 11  (Release) - 29 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Alpha-Beta Structure, Tunneling 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 The C194A Mutant Of 7-Cyano-7-Deazaguanine Reductase, Quef From Vibrio Cholerae Complexed With Preq1
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NADPH-DEPENDENT 7-CYANO-7-DEAZAGUANINE REDUCTASE
    Chains: A, B, C, D
    EC Number: 1.7.1.13
    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, VC_0902
    Mutation: YES
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666
    Strain: N16961
    Synonym: 7-CYANO-7-CARBAGUANINE REDUCTASE, NADPH-DEPENDENT NITRILE OXIDOREDUCTASE, PREQ(0) REDUCTASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 22)

Asymmetric Unit (3, 22)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE16Mod. Amino AcidSELENOMETHIONINE
3PRF4Ligand/Ion7-DEAZA-7-AMINOMETHYL-GUANINE
Biological Unit 1 (3, 11)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE8Mod. Amino AcidSELENOMETHIONINE
3PRF2Ligand/Ion7-DEAZA-7-AMINOMETHYL-GUANINE
Biological Unit 2 (3, 11)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE8Mod. Amino AcidSELENOMETHIONINE
3PRF2Ligand/Ion7-DEAZA-7-AMINOMETHYL-GUANINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:62 , ILE A:93 , GLU A:94 , SER A:95 , ASP A:201 , PHE A:232 , HIS A:233 , GLU A:234 , ILE A:267BINDING SITE FOR RESIDUE PRF A 290
2AC2SOFTWAREARG A:262 , GLY A:263 , GLY B:263 , HOH B:344BINDING SITE FOR RESIDUE GOL A 291
3AC3SOFTWARETRP B:62 , LEU B:92 , ILE B:93 , GLU B:94 , SER B:95 , ASP B:201 , PHE B:232 , HIS B:233 , GLU B:234 , ILE B:267BINDING SITE FOR RESIDUE PRF B 290
4AC4SOFTWARETRP C:62 , LEU C:92 , ILE C:93 , GLU C:94 , SER C:95 , ASP C:201 , PHE C:232 , HIS C:233 , GLU C:234 , ILE C:267 , HOH C:293BINDING SITE FOR RESIDUE PRF C 290
5AC5SOFTWARETRP D:62 , ILE D:93 , GLU D:94 , SER D:95 , ASP D:201 , PHE D:232 , HIS D:233 , GLU D:234 , ILE D:267 , HOH D:320BINDING SITE FOR RESIDUE PRF D 290
6AC6SOFTWAREGLN C:199 , ARG C:262 , GLY C:263 , ARG D:262 , GLY D:263 , HOH D:315 , HOH D:331BINDING SITE FOR RESIDUE GOL D 291

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3RZP)

(-) 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:254
 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..eeeeeeeeeeeeeeeee.-----..eeeeeeeeeeeeeehhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rzp A  29 NQYDPSLLQPVPRSLNRNDLHLSATLPFQGCDIWTLYELSWLNQKGLPQVAIGEVSIPATSANLIESKSFKLYLNSYNQTRFASWDEVQTRLVHDLSACAGETVTVNVKSLNEYTAEPIVTmQGECIDDQDIEIANYEFDDALLQGAAQGEEVSEVLHSHLLKSN-----QPDWGSVEIAYHGAKmNREALLRYLVSFREHNEFHEQCVERIFTDImRYCQPQSLTVYARYTRRGGLDINPFRSSHQSAPNHNQRmARQ 287
                                    38        48        58        68        78        88        98       108       118       128       138       148 |     158       168       178       188    |    -|      208     | 218       228       238      |248       258       268       278     |   
                                                                                                                                                   150-MSE                                    193   199            214-MSE                        245-MSE                                284-MSE


Chain B from PDB  Type:PROTEIN  Length:258
 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.....eeeeeeeeeee....eeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh...eeeeee.hhhh.........ee.............hhhhhh......eeeeeeeeeeeee.....-..eeeeeeeeeeee..hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rzp B  29 NQYDPSLLQPVPRSLNRNDLHLSATLPFQGCDIWTLYELSWLNQKGLPQVAIGEVSIPATSANLIESKSFKLYLNSYNQTRFASWDEVQTRLVHDLSACAGETVTVNVKSLNEYTAEPIVTmQGECIDDQDIEIANYEFDDALLQGAAQGEEVSEVLHSHLLKSNALIT-QPDWGSVEIAYHGAKmNREALLRYLVSFREHNEFHEQCVERIFTDImRYCQPQSLTVYARYTRRGGLDINPFRSSHQSAPNHNQRmARQ 287
                                    38        48        58        68        78        88        98       108       118       128       138       148 |     158       168       178       188        |-|      208     | 218       228       238      |248       258       268       278     |   
                                                                                                                                                   150-MSE                                        197 |            214-MSE                        245-MSE                                284-MSE
                                                                                                                                                                                                    199                                                                                        


Chain C from PDB  Type:PROTEIN  Length:257
 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
                 3rzp C  29 NQYDPSLLQPVPRSLNRNDLHLSATLPFQGCDIWTLYELSWLNQKGLPQVAIGEVSIPATSANLIESKSFKLYLNSYNQTRFASWDEVQTRLVHDLSACAGETVTVNVKSLNEYTAEPIVTmQGECIDDQDIEIANYEFDDALLQGAAQGEEVSEVLHSHLLKSNAL--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                                      195  |             214-MSE                        245-MSE                                284-MSE
                                                                                                                                                                                                   198                                                                                         


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

    Alignment length:261
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280 
           QUEF_VIBCH    21 YANQYDPSLLQPVPRSLNRNDLHLSATLPFQGCDIWTLYELSWLNQKGLPQVAIGEVSIPATSANLIESKSFKLYLNSYNQTRFASWDEVQTRLVHDLSACAGETVTVNVKSLNEYTAEPIVTMQGECIDDQDIEIANYEFDDALLQGAAQGEEVSEVLHSHLLKSNCLITNQPDWGSVEIAYHGAKMNREALLRYLVSFREHNEFHEQCVERIFTDIMRYCQPQSLTVYARYTRRGGLDINPFRSSHQSAPNHNQRMARQ 281
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTP_cyclohydroI-3rzpD01 D:200-278                                              --------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTP_cyclohydroI-3rzpD02 D:200-278                                              --------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTP_cyclohydroI-3rzpD03 D:200-278                                              --------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTP_cyclohydroI-3rzpD04 D:200-278                                              --------- Pfam domains (4)
         Sec.struct. author .....hhhhh.eeehhhhhhhhh.......eeeeeeee...eee.....eee.eeeeeee....eeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeeeehhhhhh.........ee.............hhhhhh..eeeeeeeeeeeeeeeee------..eeeeeeeeeeeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeee............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rzp D  27 YANQYDPSLLQPVPRSLNRNDLHLSATLPFQGCDIWTLYELSWLNQKGLPQVAIGEVSIPATSANLIESKSFKLYLNSYNQTRFASWDEVQTRLVHDLSACAGETVTVNVKSLNEYTAEPIVTmQGECIDDQDIEIANYEFDDALLQGAAQGEEVSEVLHSHLLKS------QPDWGSVEIAYHGAKmNREALLRYLVSFREHNEFHEQCVERIFTDImRYCQPQSLTVYARYTRRGGLDINPFRSSHQSAPNHNQRmARQ 287
                                    36        46        56        66        76        86        96       106       116       126       136       146   |   156       166       176       186     |   -  |    206       216       226       236       246       256       266       276       286 
                                                                                                                                                     150-MSE                                   192    199            214-MSE                        245-MSE                                284-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  (0, 0)

(no "SCOP Domain" information available for 3RZP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: THBO-biosyn (64)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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 3rj4 3s19 3uxj 3uxv 4ghm 4iqi

(-) Related Entries Specified in the PDB File

3bp1 THE SAME PROTEIN BUT WILD-TYPE, COMPLEXED WITH GUANINE.
3rj4 THE SAME PROTEIN BUT WILD-TYPE.
3rjb THE SAME PROTEIN BUT WILD-TYPE, COMPLEXED WITH CYTOSINE.
3rzq THE H233A MUTANT COMPLEXED WITH PREQ0
3s19 THE R262L MUTANT COMPLEXED WITH PREQ0 RELATED ID: IDP01750 RELATED DB: TARGETDB