3S19 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE R262L MUTANT OF 7-CYANO-7-DEAZAGUANINE REDUCTASE, QUEF FROM VIBRIO CHOLERAE COMPLEXED WITH PREQ0

Authors :   Y. Kim, M. Zhou, M. Gu, W. F. Anderson, A. Joachimiak, Center For Struc Genomics Of Infectious Diseases (Csgid)

Date :   14 May 11 (Deposition) - 29 Jun 11 (Release) - 29 Jun 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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 R262L Mutant Of 7-Cyano-7-Deazaguanine Reductase, Quef From Vibrio Cholerae Complexed With Preq0
To Be Published
PubMed: search

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	:	243277
	Strain	:	N16961
	Synonym	:	7-CYANO-7-CARBAGUANINE REDUCTASE, NADPH-DEPENDENT NITRILE OXIDOREDUCTASE, PREQ(0) REDUCTASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 24)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	MSE	16	Mod. Amino Acid	SELENOMETHIONINE
3	PRF	4	Ligand/Ion	7-DEAZA-7-AMINOMETHYL-GUANINE

Biological Unit 1 (3, 12)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
3	PRF	2	Ligand/Ion	7-DEAZA-7-AMINOMETHYL-GUANINE

Biological Unit 2 (3, 12)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
3	PRF	2	Ligand/Ion	7-DEAZA-7-AMINOMETHYL-GUANINE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:62 , LEU A:92 , ILE A:93 , GLU A:94 , SER A:95 , CYS A:194 , ASP A:201 , PHE A:232 , HIS A:233 , GLU A:234 , ILE A:267	BINDING SITE FOR RESIDUE PRF A 290
2	AC2	SOFTWARE	ALA A:90 , ASN A:91 , HOH A:665 , ASN D:91 , HOH D:690 , HOH D:836	BINDING SITE FOR RESIDUE GOL A 291
3	AC3	SOFTWARE	TRP B:62 , LEU B:92 , ILE B:93 , GLU B:94 , SER B:95 , CYS B:194 , ILE B:196 , ASP B:201 , PHE B:232 , HIS B:233 , GLU B:234 , LEU B:262 , ILE B:267	BINDING SITE FOR RESIDUE PRF B 290
4	AC4	SOFTWARE	THR B:63 , TYR B:65 , GLU B:82 , TYR B:142 , ARG B:258 , ASN B:281 , ARG B:283	BINDING SITE FOR RESIDUE GOL B 291
5	AC5	SOFTWARE	TRP C:62 , LEU C:92 , ILE C:93 , GLU C:94 , SER C:95 , CYS C:194 , ILE C:196 , ASP C:201 , GLU C:231 , PHE C:232 , HIS C:233 , GLU C:234 , LEU C:262 , ILE C:267	BINDING SITE FOR RESIDUE PRF C 290
6	AC6	SOFTWARE	THR C:63 , TYR C:65 , GLU C:82 , TYR C:142 , ARG C:258 , ASN C:281 , ARG C:283 , HOH C:518 , HOH C:897	BINDING SITE FOR RESIDUE GOL C 291
7	AC7	SOFTWARE	TRP D:62 , LEU D:92 , ILE D:93 , GLU D:94 , SER D:95 , CYS D:194 , ILE D:196 , ASP D:201 , PHE D:232 , HIS D:233 , GLU D:234 , ILE D:267	BINDING SITE FOR RESIDUE PRF D 290
8	AC8	SOFTWARE	THR D:63 , TYR D:65 , GLU D:82 , TYR D:142 , ARG D:258 , ASN D:281 , ARG D:283 , HOH D:789 , HOH D:1171	BINDING SITE FOR RESIDUE GOL D 291

(no "SS Bond" information available for 3S19)

(no "Cis Peptide Bond" information available for 3S19)

(no "SAP(SNP)/Variant" information available for 3S19)

(no "PROSITE Motif" information available for 3S19)

(no "Exon" information available for 3S19)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:261
 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 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.eeehhhhhhhh........eeeeeeeeeeeeee.....eeeeeeeeeee....eeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh...eeeeehhhhhh.........ee.............hhhhhh..eeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeehhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeee............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s19 A  27 YANQYDPSLLQPVPRSLNRNDLHLSATLPFQGCDIWTLYELSWLNQKGLPQVAIGEVSIPATSANLIESKSFKLYLNSYNQTRFASWDEVQTRLVHDLSACAGETVTVNVKSLNEYTAEPIVTmQGECIDDQDIEIANYEFDDALLQGAAQGEEVSEVLHSHLLKSNCLITNQPDWGSVEIAYHGAKmNREALLRYLVSFREHNEFHEQCVERIFTDImRYCQPQSLTVYARYTRLGGLDINPFRSSHQSAPNHNQRmARQ 287
                                    36        46        56        66        76        86        96       106       116       126       136       146   |   156       166       176       186       196       206       216       226       236       246       256       266       276       286 
                                                                                                                                                     150-MSE                                                         214-MSE                        245-MSE                                284-MSE

Chain B 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.eeehhhhhhhh........eeeeeeeeeeeeee.....eeeeeeeeeee....eeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh...eeeeehhhhhh.........ee.............hhhhhh..eeeeeeeeeeeeeeeeee......eeeeeeeeeeeeeeehhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s19 B  29 NQYDPSLLQPVPRSLNRNDLHLSATLPFQGCDIWTLYELSWLNQKGLPQVAIGEVSIPATSANLIESKSFKLYLNSYNQTRFASWDEVQTRLVHDLSACAGETVTVNVKSLNEYTAEPIVTmQGECIDDQDIEIANYEFDDALLQGAAQGEEVSEVLHSHLLKSNCLITNQPDWGSVEIAYHGAKmNREALLRYLVSFREHNEFHEQCVERIFTDImRYCQPQSLTVYARYTRLGGLDINPFRSSHQSAPNHNQRmARQ 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 C 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.eeehhhhhhhh........eeeeeeeeeeeeee.....eeeeeeeeeee....eeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh...eeeeehhhhhh.........ee.............hhhhhh..eeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeehhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s19 C  29 NQYDPSLLQPVPRSLNRNDLHLSATLPFQGCDIWTLYELSWLNQKGLPQVAIGEVSIPATSANLIESKSFKLYLNSYNQTRFASWDEVQTRLVHDLSACAGETVTVNVKSLNEYTAEPIVTmQGECIDDQDIEIANYEFDDALLQGAAQGEEVSEVLHSHLLKSNCLITNQPDWGSVEIAYHGAKmNREALLRYLVSFREHNEFHEQCVERIFTDImRYCQPQSLTVYARYTRLGGLDINPFRSSHQSAPNHNQRmARQ 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 D from PDB  Type:PROTEIN  Length:261
 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-3s19D01 D:200-278                                              --------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTP_cyclohydroI-3s19D02 D:200-278                                              --------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTP_cyclohydroI-3s19D03 D:200-278                                              --------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTP_cyclohydroI-3s19D04 D:200-278                                              --------- Pfam domains (4)
         Sec.struct. author .....hhhhh.eeehhhhhhhh........eeeeeeeeeeeeee.....eeeeeeeeeee....eeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh...eeeeehhhhhh.........ee.............hhhhhh..eeeeeeeeeeeeeeeeee......eeeeeeeeeeeeeeehhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeee............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s19 D  27 YANQYDPSLLQPVPRSLNRNDLHLSATLPFQGCDIWTLYELSWLNQKGLPQVAIGEVSIPATSANLIESKSFKLYLNSYNQTRFASWDEVQTRLVHDLSACAGETVTVNVKSLNEYTAEPIVTmQGECIDDQDIEIANYEFDDALLQGAAQGEEVSEVLHSHLLKSNCLITNQPDWGSVEIAYHGAKmNREALLRYLVSFREHNEFHEQCVERIFTDImRYCQPQSLTVYARYTRLGGLDINPFRSSHQSAPNHNQRmARQ 287
                                    36        46        56        66        76        86        96       106       116       126       136       146   |   156       166       176       186       196       206       216       226       236       246       256       266       276       286 
                                                                                                                                                     150-MSE                                                         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 '\|'

(no "SCOP Domain" information available for 3S19)

(no "CATH Domain" information available for 3S19)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: THBO-biosyn (64)

Family: GTP_cyclohydroI (9)

Vibrio cholerae (2)

1a	GTP_cyclohydroI-3s19D01	D:200-278
1b	GTP_cyclohydroI-3s19D02	D:200-278
1c	GTP_cyclohydroI-3s19D03	D:200-278
1d	GTP_cyclohydroI-3s19D04	D:200-278

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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3s19)

Biological Units
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Access by PDB/NDB ID
	3s19
		Family and Domain Information	:	ProDom \| SYSTERS
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	QUEF_VIBCH \| Q9KTK0
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	1.7.1.13
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	QUEF_VIBCH \| Q9KTK0
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UniProtKB/Swiss-Prot
	QUEF_VIBCH \| Q9KTK0	:	3bp1 3rj4 3rzp 3uxj 3uxv 4ghm 4iqi

3bp1	THE SAME PROTEIN BUT WILD-TYPE, COMPLEXED WITH GUANIN
3rj4	THE SAME PROTEIN BUT WILD-TYPE
3rjb	THE SAME PROTEIN BUT WILD-TYPE, COMPLEXED WITH CYTOSINE
3rzp	THE C194A MUTANT COMPLEXED WITH PREQ1
3rzq	THE H233A MUTANT COMPLEXED WITH PREQ0 RELATED ID: IDP01750 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 24)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

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Pfam Domains (1, 4)

Gene Ontology (9, 9)

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Related Entries

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Related Entries Specified in the PDB File