2OB3 - JenaLib

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Title :   STRUCTURE OF PHOSPHOTRIESTERASE MUTANT H257Y/L303T

Authors :   J. Kim, U. A. Ramagopal, P. Tsai, F. M. Raushel, S. C. Almo

Date :   18 Dec 06 (Deposition) - 30 Jan 07 (Release) - 07 Jul 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.04

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

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

Reference :   J. Kim, U. A. Ramagopal, P. Tsai, F. M. Raushel, S. C. Almo
Structure Of Phosphotriesterase Mutant H257Y/L303T
To Be Published
PubMed: search
(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 BL21(DE3)
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	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 (3, 8)

No.	Name	Count	Type	Full Name
1	BTB	2	Ligand/Ion	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	KCX	2	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
3	ZN	4	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:55 , HIS A:57 , KCX A:169 , ASP A:301 , HOH A:1143	BINDING SITE FOR RESIDUE ZN A 901
2	AC2	SOFTWARE	KCX A:169 , HIS A:201 , HIS A:230 , HOH A:973 , HOH A:1028 , HOH A:1143	BINDING SITE FOR RESIDUE ZN A 902
3	AC3	SOFTWARE	HIS B:55 , HIS B:57 , KCX B:169 , ASP B:301 , HOH B:1332	BINDING SITE FOR RESIDUE ZN B 903
4	AC4	SOFTWARE	KCX B:169 , HIS B:201 , HIS B:230 , HOH B:1332 , HOH B:1333 , HOH B:1337	BINDING SITE FOR RESIDUE ZN B 904
5	AC5	SOFTWARE	PHE B:72 , PHE B:73 , THR B:311 , ASP B:315 , HOH B:927 , HOH B:976 , HOH B:1117 , HOH B:1193 , HOH B:1244 , HOH B:1335	BINDING SITE FOR RESIDUE BTB B 905
6	AC6	SOFTWARE	PHE A:72 , PHE A:73 , THR A:311 , ASP A:315 , HOH A:918 , HOH A:942 , HOH A:1068 , HOH A:1094 , HOH A:1109 , HOH A:1306	BINDING SITE FOR RESIDUE BTB A 906

(no "SS Bond" information available for 2OB3)

(no "Cis Peptide Bond" information available for 2OB3)

(no "SAP(SNP)/Variant" information available for 2OB3)

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:35-363 B:35-363
2	PHOSPHOTRIESTERASE_1	PS01322	Phosphotriesterase family signature 1.	OPD_BREDI	50-58	2	A:50-58 B:50-58

(no "Exon" information available for 2OB3)

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:330
 aligned with OPD_BREDI | P0A434 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_BREDI    35 DRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDHIPHSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLRA 364
               SCOP domains d2ob3a_ A: Phosphotriesterase (parathion hydrolase, PTE)                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2ob3A00 A:35-364 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee..eeehhhhhh.eeeee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhh.hhhhhhhhhhhhh.eee.eee.....hhhhhh.hhhhhhhhhhhhhhh..........eeeee.....hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhh..hhh.eee.hhhhh.hhhhhhhhhhh..eeee............hhhhhhhhh..hhhhhhhhhhhhhhh.hhh.eee......ee.....hhhhhhhhhh.hhhhhhhhhhhhhhhhh..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
                 2ob3 A  35 DRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIkVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDHIPYSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWTFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLRA 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

Chain B from PDB  Type:PROTEIN  Length:330
 aligned with OPD_BREDI | P0A434 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_BREDI    35 DRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDHIPHSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLRA 364
               SCOP domains d2ob3b_ B: Phosphotriesterase (parathion hydrolase, PTE)                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2ob3B00 B:35-364 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                CATH domains
           Pfam domains (1) ---------PTE-2ob3B01 B:44-359                                                                                                                                                                                                                                                                                                        ----- Pfam domains (1)
           Pfam domains (2) ---------PTE-2ob3B02 B:44-359                                                                                                                                                                                                                                                                                                        ----- Pfam domains (2)
         Sec.struct. author ..eee..eeehhhhhh.eeeee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhh.hhhhhhhhhhhhh.eee.eee.....hhhhhh.hhhhhhhhhhhhhhh..........eeeee.....hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhh..hhh.eee.hhhhh.hhhhhhhhhhh..eeee............hhhhhhhhh..hhhhhhhhhhhhhhhhhhh.eee......ee.....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
                 2ob3 B  35 DRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIkVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDHIPYSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWTFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLRA 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( (-)

)

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)

Pseudomonas diminuta [TaxId: 293] (19)

1a	d2ob3a_	A:
1b	d2ob3b_	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)

Brevundimonas diminuta. Organism_taxid: 293. (7)

1a	2ob3A00	A:35-364
1b	2ob3B00	B:35-364

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Amidohydrolase (126)

Family: PTE (19)

Brevundimonas diminuta (Pseudomonas diminuta) (8)

1a	PTE-2ob3B01	B:44-359
1b	PTE-2ob3B02	B:44-359

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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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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