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Title :   CRYSTAL STRUCTURE OF PTE MUTANT H254G/H257W/L303T/K185R/I274N/A80V/S61T WITH CYCLOHEXYL METHYLPHOSPHONATE INHIBITOR

Authors :   P. Tsai, N. G. Fox, Y. Li, D. P. Barondeau, F. M. Raushel

Date :   22 Nov 11 (Deposition) - 01 Aug 12 (Release) - 03 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym./Biol. Unit : A,B

Keywords :   Metalloenzyme, Tim Barrel, Nerve Agents, Phosphotriesterase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. C. Tsai, N. Fox, A. N. Bigley, S. P. Harvey, D. P. Barondeau, F. M. Raushel
Enzymes For The Homeland Defense: Optimizing Phosphotriesterase For The Hydrolysis Of Organophosphate Nerve Agents.
Biochemistry V. 51 6463 2012
PubMed-ID: 22809162 | Reference-DOI: 10.1021/BI300811T

Molecule 1 - PARATHION HYDROLASE
	Chains	:	A, B
	EC Number	:	3.1.8.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	UNP RESIDUES 35-361
	Gene	:	OPD
	Mutation	:	YES
	Organism Scientific	:	BREVUNDIMONAS DIMINUTA
	Organism Taxid	:	293
	Synonym	:	PHOSPHOTRIESTERASE, PTE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 11)

No.	Name	Count	Type	Full Name
1	CO	4	Ligand/Ion	COBALT (II) ION
2	IMD	3	Ligand/Ion	IMIDAZOLE
3	KCX	2	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
4	QMP	2	Ligand/Ion	CYCLOHEXYL METHYLPHOSPHONATE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	KCX A:169 , HIS A:201 , HIS A:230 , QMP A:902 , HOH A:1361	BINDING SITE FOR RESIDUE CO A 801
2	AC2	SOFTWARE	HIS A:55 , HIS A:57 , KCX A:169 , ASP A:301 , HOH A:1361	BINDING SITE FOR RESIDUE CO A 802
3	AC3	SOFTWARE	HIS A:57 , GLY A:60 , TRP A:131 , PHE A:132 , KCX A:169 , HIS A:201 , HIS A:230 , ASP A:301 , PHE A:306 , CO A:801	BINDING SITE FOR RESIDUE QMP A 902
4	AC4	SOFTWARE	HIS A:230 , ASP A:232 , ASP A:233 , ASP A:253 , GLY A:254 , TRP A:257 , ARG A:280 , ASP A:301	BINDING SITE FOR RESIDUE IMD A 903
5	AC5	SOFTWARE	HIS B:55 , HIS B:57 , KCX B:169 , ASP B:301 , HOH B:1368	BINDING SITE FOR RESIDUE CO B 803
6	AC6	SOFTWARE	KCX B:169 , HIS B:201 , HIS B:230 , QMP B:901 , HOH B:1368	BINDING SITE FOR RESIDUE CO B 804
7	AC7	SOFTWARE	HIS B:57 , GLY B:60 , TRP B:131 , PHE B:132 , KCX B:169 , HIS B:201 , TRP B:257 , PHE B:306 , CO B:804 , IMD B:905 , HOH B:1368	BINDING SITE FOR RESIDUE QMP B 901
8	AC8	SOFTWARE	HIS B:230 , ASP B:232 , ASP B:233 , ASP B:253 , GLY B:254 , TRP B:257 , ASP B:301	BINDING SITE FOR RESIDUE IMD B 904
9	AC9	SOFTWARE	SER B:308 , QMP B:901	BINDING SITE FOR RESIDUE IMD B 905

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

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

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

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PHOSPHOTRIESTERASE_2	PS51347	Phosphotriesterase family profile.	OPD_BREDI	35-363	2	A:35-361 B:35-361
2	PHOSPHOTRIESTERASE_1	PS01322	Phosphotriesterase family signature 1.	OPD_BREDI	50-58	2	A:50-58 B:50-58

(no "Exon" information available for 3URN)

Asymmetric/Biological 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:327
 aligned with OPD_BREDI | P0A434 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:327
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       
            OPD_BREDI    35 DRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDHIPHSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPT 361
               SCOP domains d3urna_ A: Phosphotriesterase (parathion hydrolase, PTE)                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeee.hhh..eeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhh.hhhhhhhhhhhhh.eee.eee.....hhhhhh.hhhhhhhhhhhhhhh..........eeeee.....hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhh..hhh.eee.hhhhh.hhhhhhhhhhh..eeee............hhhhhhhhh..hhhhhhhhhhhhhh..hhh.eee.............hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PHOSPHOTRIESTERASE_2  PDB: A:35-361 UniProt: 35-363                                                                                                                                                                                                                                                                                     PROSITE (1)
                PROSITE (2) ---------------PHOSPHOTR--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3urn A  35 DRINTVRGPITISEAGFTLTHEHICGTSAGFLRAWPEFFGSRKALVEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIkVATTGKATPFQELVLRAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDGIPWSAIGLEDNASASALLGNRSWQTRALLIKALIDQGYMKQILVSNDWTFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPT 361
                                    44        54        64        74        84        94       104       114       124       134       144       154       164    |  174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       
                                                                                                                                                                169-KCX

Chain B from PDB  Type:PROTEIN  Length:327
 aligned with OPD_BREDI | P0A434 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:327
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       
            OPD_BREDI    35 DRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDHIPHSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPT 361
               SCOP domains d3urnb_ B: Phosphotriesterase (parathion hydrolase, PTE)                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeehhhhh.eeeee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhh.hhhhhhhhhhhhh.eee.eee.....hhhhhh.hhhhhhhhhhhhhhh..........eeeee.....hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhh..hhh.eee.hhhhh.hhhhhhhhhhh..eeee............hhhhhhhhh..hhhhhhhhhhhhhh..hhh.eee......ee.....hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PHOSPHOTRIESTERASE_2  PDB: B:35-361 UniProt: 35-363                                                                                                                                                                                                                                                                                     PROSITE (1)
                PROSITE (2) ---------------PHOSPHOTR--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3urn B  35 DRINTVRGPITISEAGFTLTHEHICGTSAGFLRAWPEFFGSRKALVEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIkVATTGKATPFQELVLRAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDGIPWSAIGLEDNASASALLGNRSWQTRALLIKALIDQGYMKQILVSNDWTFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPT 361
                                    44        54        64        74        84        94       104       114       124       134       144       154       164    |  174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       
                                                                                                                                                                169-KCX

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Metallo-dependent hydrolases (273)

Family: Phosphotriesterase-like (43)

Protein domain: Phosphotriesterase (parathion hydrolase, PTE) (39)

Brevundimonas diminuta [TaxId: 293] (5)

1a	d3urna_	A:
1b	d3urnb_	B:

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (OPD_BREDI | P0A434)

molecular function
	GO:0004063	aryldialkylphosphatase activity	Catalysis of the reaction: aryl dialkyl phosphate + H2O = dialkyl phosphate + an aryl alcohol.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016788	hydrolase activity, acting on ester bonds	Catalysis of the hydrolysis of any ester bond.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0009056	catabolic process	The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
cellular component
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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3upm	CRYSTAL STRUCTURE OF PTE MUTANT H254Q/H257F/K185R/I274N
3ur2	CRYSTAL STRUCTURE OF PTE MUTANT H254G/H257W/L303T/K185R/ I274N/A80V
3ur3	CRYSTAL STRUCTURE OF PTE MUTANT K185R/I274N
3ura	CRYSTAL STRUCTURE OF PTE MUTANT H254G/H257W/L303T/K185R/ I274N/A80V/S61T
3urb	CRYSTAL STRUCTURE OF PTE MUTANT H254G/H257W/L303T/M317L/ I106C/F132I/L271I/K185R/I274N/A80V/R67H
3urq	CRYSTAL STRUCTURE OF PTE MUTANT H254G/H257W/L303T/M317L/ I106C/F132I/L271I/K185R/I274N/A80V/R67H WITH CYCLOHEXYL METHYLPHOSPHONATE INHIBITOR

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 11)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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