1P6C - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF PHOSPHOTRIESTERASE TRIPLE MUTANT H254G/H257W/L303T COMPLEXED WITH DIISOPROPYLMETHYLPHOSPHONATE

Authors :   C. M. Hill, W. Li, J. B. Thoden, H. M. Holden, F. M. Raushel

Date :   29 Apr 03 (Deposition) - 16 Sep 03 (Release) - 23 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Metalloenzyme, Tim Barrel, Nerve Agent, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. M. Hill, W. S. Li, J. B. Thoden, H. M. Holden, F. M. Raushel
Enhanced Degradation Of Chemical Warfare Agents Through Molecular Engineering Of The Phosphotriesterase Active Site.
J. Am. Chem. Soc. V. 125 8990 2003
PubMed-ID: 15369336 | Reference-DOI: 10.1021/JA0358798
(for further references see the PDB file header)

Molecule 1 - PARATHION HYDROLASE
	Chains	:	A, B
	EC Number	:	3.1.8.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	OPD
	Mutation	:	YES
	Organism Scientific	:	FLAVOBACTERIUM SP.
	Organism Taxid	:	239
	Synonym	:	PHOSPHOTRIESTERASE, PTE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 10)

No.	Name	Count	Type	Full Name
1	DII	2	Ligand/Ion	METHYLPHOSPHONIC ACID DIISOPROPYL ESTER
2	EBP	2	Ligand/Ion	DIETHYL 4-METHYLBENZYLPHOSPHONATE
3	KCX	2	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
4	ZN	4	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	DII A:7 , HIS A:55 , HIS A:57 , KCX A:169 , ASP A:301 , ZN A:402 , HOH A:456	BINDING SITE FOR RESIDUE ZN A 401
2	AC2	SOFTWARE	DII A:7 , KCX A:169 , HIS A:201 , HIS A:230 , ZN A:401 , HOH A:456	BINDING SITE FOR RESIDUE ZN A 402
3	AC3	SOFTWARE	HOH B:16 , HIS B:55 , HIS B:57 , KCX B:169 , ASP B:301 , ZN B:404	BINDING SITE FOR RESIDUE ZN B 403
4	AC4	SOFTWARE	DII B:8 , HOH B:16 , KCX B:169 , HIS B:201 , HIS B:230 , ZN B:403	BINDING SITE FOR RESIDUE ZN B 404
5	AC5	SOFTWARE	GLN A:155 , TYR A:156 , PHE B:51	BINDING SITE FOR RESIDUE EBP A 5
6	AC6	SOFTWARE	PHE A:51 , GLU A:71 , GLN B:155 , TYR B:156	BINDING SITE FOR RESIDUE EBP B 6
7	AC7	SOFTWARE	HIS A:57 , TRP A:131 , KCX A:169 , HIS A:201 , ASP A:301 , ZN A:401 , ZN A:402 , HOH A:456	BINDING SITE FOR RESIDUE DII A 7
8	AC8	SOFTWARE	TRP B:131 , HIS B:201 , ZN B:404	BINDING SITE FOR RESIDUE DII B 8

(no "SS Bond" information available for 1P6C)

(no "Cis Peptide Bond" information available for 1P6C)

(no "SAP(SNP)/Variant" information available for 1P6C)

Asymmetric/Biological Unit (2, 4)

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

(no "Exon" information available for 1P6C)

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:331
 aligned with OPD_SPHSA | P0A433 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:331
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363 
            OPD_SPHSA    34 GDRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDHIPHSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLRA 364
               SCOP domains d1p6ca_ A: Phosphotriesterase (parathion hydrolase, PTE)                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1p6cA00 A:34-364 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee.hhh..eeeee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhh.hhhhhhhhhhhhh.eee.eee.....hhhhhh.hhhhhhhhhhhhhhh..........eeeee.....hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhh...hhh.eee.hhhhh.hhhhhhhhhhh..eeee............hhhhhhhhh..hhhhhhhhhhhhhhh.hhh.eee......ee.....hhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -PHOSPHOTRIESTERASE_2  PDB: A:35-363 UniProt: 35-363                                                                                                                                                                                                                                                                                      - PROSITE (1)
                PROSITE (2) ----------------PHOSPHOTR------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p6c A  34 GDRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIkVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDGIPWSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWTFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLRA 364
                                    43        53        63        73        83        93       103       113       123       133       143       153       163     | 173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363 
                                                                                                                                                                 169-KCX

Chain B from PDB  Type:PROTEIN  Length:330
 aligned with OPD_SPHSA | P0A433 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:330
                                    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       364
            OPD_SPHSA    35 DRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDHIPHSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLRA 364
               SCOP domains d1p6cb_ B: Phosphotriesterase (parathion hydrolase, PTE)                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1p6cB00 B:35-364 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eeeehhhhh.eeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhh.hhhhhhhhhhhhh.eee.eee.....hhhhhh.hhhhhhhhhhhhhhh..........eeeee.....hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhh..hhh.eee.hhhhh.hhhhhhhhhhhh.eeee............hhhhhhhhh..hhhhhhhhhhhhhhh.hhh.eee.............hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) PHOSPHOTRIESTERASE_2  PDB: B:35-363 UniProt: 35-363                                                                                                                                                                                                                                                                                      - PROSITE (1)
                PROSITE (2) ---------------PHOSPHOTR------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1p6c B  35 DRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIkVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDGIPWSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWTFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLRA 364
                                    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       364
                                                                                                                                                                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( (-)

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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)

Flavobacterium sp. atcc 27551 [TaxId: 74567] (2)

1a	d1p6ca_	A:
1b	d1p6cb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Metal-dependent hydrolases (190)

Flavobacterium sp.. Organism_taxid: 239. (2)

1a	1p6cB00	B:35-364
1b	1p6cA00	A:34-364

(no "Pfam Domain" information available for 1P6C)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (OPD_SPHSA | P0A433)

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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	1p6c
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	OPD_SPHSA \| P0A433	:	1p6b

1p6b	SAME PROTEIN IN "APO" FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 10)

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)

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