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Title :   THREE-DIMENSIONAL STRUCTURE OF THE ZINC-CONTAINING PHOSPHOTRIESTERASE WITH BOUND SUBSTRATE ANALOG DIETHYL 4-METHYLBENZYLPHOSPHONATE

Authors :   J. L. Vanhooke, M. M. Benning, F. M. Raushel, H. M. Holden

Date :   13 Feb 96 (Deposition) - 20 Aug 97 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Hydrolase, Membrane, Plasmid, Signal, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. L. Vanhooke, M. M. Benning, F. M. Raushel, H. M. Holden
Three-Dimensional Structure Of The Zinc-Containing Phosphotriesterase With The Bound Substrate Analog Diethyl 4-Methylbenzylphosphonate.
Biochemistry V. 35 6020 1996
PubMed-ID: 8634243 | Reference-DOI: 10.1021/BI960325L
(for further references see the PDB file header)

Molecule 1 - PHOSPHOTRIESTERASE
	Chains	:	A, B
	Organism Scientific	:	BREVUNDIMONAS DIMINUTA
	Organism Taxid	:	293

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 10)

No.	Name	Count	Type	Full Name
1	EBP	4	Ligand/Ion	DIETHYL 4-METHYLBENZYLPHOSPHONATE
2	FMT	2	Ligand/Ion	FORMIC ACID
3	ZN	4	Ligand/Ion	ZINC ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:55 , HIS A:57 , ASP A:301 , ZN A:801 , FMT A:902 , HOH A:909	BINDING SITE FOR RESIDUE ZN A 800
02	AC2	SOFTWARE	HIS A:55 , HIS A:201 , HIS A:230 , ZN A:800 , EBP A:900 , FMT A:902 , HOH A:909	BINDING SITE FOR RESIDUE ZN A 801
03	AC3	SOFTWARE	HIS B:55 , HIS B:57 , ASP B:301 , ZN B:803 , FMT B:904 , HOH B:924	BINDING SITE FOR RESIDUE ZN B 802
04	AC4	SOFTWARE	HIS B:201 , HIS B:230 , ZN B:802 , EBP B:902 , FMT B:904 , HOH B:924	BINDING SITE FOR RESIDUE ZN B 803
05	AC5	SOFTWARE	TRP A:131 , HIS A:201 , HIS A:257 , LEU A:271 , ASP A:301 , MET A:317 , ZN A:801	BINDING SITE FOR RESIDUE EBP A 900
06	AC6	SOFTWARE	ARG A:152 , GLN A:155 , TYR A:156 , PHE B:51	BINDING SITE FOR RESIDUE EBP A 901
07	AC7	SOFTWARE	TRP B:131 , HIS B:201 , HIS B:257 , LEU B:271 , ASP B:301 , MET B:317 , ZN B:803 , HOH B:924	BINDING SITE FOR RESIDUE EBP B 902
08	AC8	SOFTWARE	GLU A:71 , GLN B:155 , TYR B:156 , ARG B:164	BINDING SITE FOR RESIDUE EBP B 903
09	AC9	SOFTWARE	HIS A:55 , HIS A:57 , LYS A:169 , HIS A:201 , HIS A:230 , ZN A:800 , ZN A:801 , HOH A:909	BINDING SITE FOR RESIDUE FMT A 902
10	BC1	SOFTWARE	HIS B:55 , HIS B:57 , LYS B:169 , HIS B:201 , HIS B:230 , ZN B:802 , ZN B:803 , HOH B:924	BINDING SITE FOR RESIDUE FMT B 904

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

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

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

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:36-363 B:36-363
2	PHOSPHOTRIESTERASE_1	PS01322	Phosphotriesterase family signature 1.	OPD_BREDI	50-58	2	A:50-58 B:50-58

(no "Exon" information available for 1DPM)

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:329
 aligned with OPD_BREDI | P0A434 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:329
                                    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 DRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDHIPHSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLR 363
               SCOP domains d1dpma_ A: Phosphotriesterase (parathion hydrolase, PTE)                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1dpmA00 A:35-363 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeehhhh...............hhhh.hhhh..hhhhhhhhhhhhhhhhh....eee....hhh...hhhhhhhhhhh..eee.eee......hhhh...hhhhhhhhhhhhh...........eeeee......hhhhhhhhhhhhhhhhh..eeeee..hhh.hhhhhhhhhhhh...hhheee..hhh...hhhhhhhhh....eee.............hhhhhhh....hhhhhhhhhhhhh...hhheee..............hhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhh.hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PHOSPHOTRIESTERASE_2  PDB: A:36-363 UniProt: 35-363                                                                                                                                                                                                                                                                                       PROSITE (1)
                PROSITE (2) ---------------PHOSPHOTR----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dpm A  35 ARINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDHIPHSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLR 363
                                    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

Chain B from PDB  Type:PROTEIN  Length:329
 aligned with OPD_BREDI | P0A434 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:329
                                    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 DRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDHIPHSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLR 363
               SCOP domains d1dpmb_ B: Phosphotriesterase (parathion hydrolase, PTE)                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1dpmB00 B:35-363 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeehhhh...............hhhh.hhhh..hhhhhhhhhhhhhhhhhh...eee....hhh...hhhhhhhhhhh..eee.eee......hhhh...hhhhhhhhhhhhh...........eeeee......hhhhhhhhhhhhhhhhh...eeee..hhh.hhhhhhhhhhh....hhheee..hhh...hhhhhhhhhh...eee.............hhhhhhh....hhhhhhhhhhhhh...hhheee..............hhhhhhhh...hhhhhhh.hhhhhhh....hhhhhhhh.hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PHOSPHOTRIESTERASE_2  PDB: B:36-363 UniProt: 35-363                                                                                                                                                                                                                                                                                       PROSITE (1)
                PROSITE (2) ---------------PHOSPHOTR----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dpm B  35 ARINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDHIPHSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLR 363
                                    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

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	d1dpma_	A:
1b	d1dpmb_	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 (2)

1a	1dpmA00	A:35-363
1b	1dpmB00	B:35-363

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

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

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Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (0, 0)

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