4F8B - JenaLib

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

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (2x)	:	A	B	C	D	E

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (4, 10)

Asymmetric Unit (4, 10)

No.	Name	Count	Type	Full Name
1	GD1	4	Ligand/Ion	2-AMINO-5-[(Z)-IMINOMETHYL]-3,7-DIHYDRO-4H-PYRROLO[2,3-D]PYRIMIDIN-4-ONE
2	MG	4	Ligand/Ion	MAGNESIUM ION
3	PE4	1	Ligand/Ion	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 12)

No.	Name	Count	Type	Full Name
1	GD1	8	Ligand/Ion	2-AMINO-5-[(Z)-IMINOMETHYL]-3,7-DIHYDRO-4H-PYRROLO[2,3-D]PYRIMIDIN-4-ONE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	PE4	2	Ligand/Ion	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Sites (10, 10)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE 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:130	BINDING SITE FOR RESIDUE GD1 B 201
02	AC2	SOFTWARE	ASP B:162 , ARG B:164 , HOH B:301 , HOH B:302 , ARG E:164 , MG E:202 , HOH E:301	BINDING SITE FOR RESIDUE MG B 202
03	AC3	SOFTWARE	ASN B:39 , HOH B:337 , HOH B:340	BINDING SITE FOR RESIDUE PO4 B 203
04	AC4	SOFTWARE	VAL 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:130	BINDING SITE FOR RESIDUE GD1 C 201
05	AC5	SOFTWARE	ASP C:162 , ARG C:164 , HOH C:301 , HOH C:302 , ARG D:164 , MG D:202 , HOH D:302	BINDING SITE FOR RESIDUE MG C 202
06	AC6	SOFTWARE	PHE 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:130	BINDING SITE FOR RESIDUE GD1 D 201
07	AC7	SOFTWARE	ARG C:164 , MG C:202 , ASP D:162 , ARG D:164 , HOH D:301 , HOH D:302 , HOH D:303	BINDING SITE FOR RESIDUE MG D 202
08	AC8	SOFTWARE	TYR 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:157	BINDING SITE FOR RESIDUE PE4 D 203
09	AC9	SOFTWARE	PHE 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:130	BINDING SITE FOR RESIDUE GD1 E 201
10	BC1	SOFTWARE	ARG B:164 , MG B:202 , ASP E:162 , ARG E:164 , HOH E:301 , HOH E:302 , HOH E:303	BINDING SITE FOR RESIDUE MG E 202

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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)
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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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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	4f8b
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