2DFP - JenaLib

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Title :   X-RAY STRUCTURE OF AGED DI-ISOPROPYL-PHOSPHORO-FLUORIDATE (DFP) BOUND TO ACETYLCHOLINESTERASE

Authors :   G. Kryger, C. B. Millard, I. Silman, J. L. Sussman

Date :   07 Dec 98 (Deposition) - 28 Jun 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Aged Organophosphate, Dfp, Serine Hydrolase, Neurotransmitter Cleavage, Catalytic Triad, Alpha/Beta Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. B. Millard, G. Kryger, A. Ordentlich, H. M. Greenblatt, M. Harel, M. L. Raves, Y. Segall, D. Barak, A. Shafferman, I. Silman, J. L. Sussma
Crystal Structures Of Aged Phosphonylated Acetylcholinesterase: Nerve Agent Reaction Products At The Atomic Level.
Biochemistry V. 38 7032 1999
PubMed-ID: 10353814 | Reference-DOI: 10.1021/BI982678L
(for further references see the PDB file header)

Molecule 1 - PROTEIN (ACETYLCHOLINESTERASE)
	Chains	:	A
	EC Number	:	3.1.1.7
	Organ	:	ELECTRIC ORGAN
	Organism Common	:	PACIFIC ELECTRIC RAY
	Organism Scientific	:	TORPEDO CALIFORNICA
	Organism Taxid	:	7787
	Other Details	:	THE PROTEIN, ACETYLCHOLINESTERASE, WAS TREATED WITH THE ORGANOPHOSPHATE, DFP, PRIOR TO CRYSTALLIZATION.
	Tissue	:	ELECTROPLAQUE
	Variant	:	G2 FORM

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2	MIS	1	Mod. Amino Acid	MONOISOPROPYLPHOSPHORYLSERINE
3	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (3, 14)

No.	Name	Count	Type	Full Name
1	MES	2	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2	MIS	2	Mod. Amino Acid	MONOISOPROPYLPHOSPHORYLSERINE
3	NAG	10	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:416 , HOH A:2286 , HOH A:2287 , NAG A:3003	BINDING SITE FOR RESIDUE NAG A 3002
2	AC2	SOFTWARE	NAG A:3002	BINDING SITE FOR RESIDUE NAG A 3003
3	AC3	SOFTWARE	ASN A:457 , HOH A:2340 , HOH A:2372 , HOH A:2373 , NAG A:3005	BINDING SITE FOR RESIDUE NAG A 3004
4	AC4	SOFTWARE	NAG A:3004	BINDING SITE FOR RESIDUE NAG A 3005
5	AC5	SOFTWARE	ASN A:59 , SER A:61 , HOH A:2365 , HOH A:2366 , HOH A:2367 , HOH A:2368	BINDING SITE FOR RESIDUE NAG A 3001
6	AC6	SOFTWARE	MET A:405 , HIS A:406 , ASN A:409 , GLN A:500 , CYS A:521 , VAL A:522 , ASN A:525 , HOH A:2296 , HOH A:2297 , HOH A:2299	BINDING SITE FOR RESIDUE MES A 4001
7	CAT	AUTHOR	MIS A:200 , GLU A:327 , HIS A:440	TRIAD
8	OPB	AUTHOR	MIS A:200	ORGANOPHOSPHATE SITE

Asymmetric Unit

No.	Residues
1	A:67	-	A:94
2	A:254	-	A:265
3	A:402	-	A:521

Asymmetric Unit

No.	Residues
1	Ser A:103	-	Pro A:104

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

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CARBOXYLESTERASE_B_2	PS00941	Carboxylesterases type-B signature 2.	ACES_TETCF	113-123	1	A:92-102
2	CARBOXYLESTERASE_B_1	PS00122	Carboxylesterases type-B serine active site.	ACES_TETCF	208-223	1	A:187-202

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CARBOXYLESTERASE_B_2	PS00941	Carboxylesterases type-B signature 2.	ACES_TETCF	113-123	2	A:92-102
2	CARBOXYLESTERASE_B_1	PS00122	Carboxylesterases type-B serine active site.	ACES_TETCF	208-223	2	A:187-202

(no "Exon" information available for 2DFP)

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
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Chain A from PDB  Type:PROTEIN  Length:534
 aligned with ACES_TETCF | P04058 from UniProtKB/Swiss-Prot  Length:586

    Alignment length:534
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552    
           ACES_TETCF    23 DHSELLVNTKSGKVMGTRVPVLSSHISAFLGIPFAEPPVGNMRFRRPEPKKPWSGVWNASTYPNNCQQYVDEQFPGFSGSEMWNPNREMSEDCLYLNIWVPSPRPKSTTVMVWIYGGGFYSGSSTLDVYNGKYLAYTEEVVLVSLSYRVGAFGFLALHGSQEAPGNVGLLDQRMALQWVHDNIQFFGGDPKTVTIFGESAGGASVGMHILSPGSRDLFRRAILQSGSPNCPWASVSVAEGRRRAVELGRNLNCNLNSDEELIHCLREKKPQELIDVEWNVLPFDSIFRFSFVPVIDGEFFPTSLESMLNSGNFKKTQILLGVNKDEGSFFLLYGAPGFSKDSESKISREDFMSGVKLSVPHANDLGLDAVTLQYTDWMDDNNGIKNRDGLDDIVGDHNVICPLMHFVNKYTKFGNGTYLYFFNHRASNLVWPEWMGVIHGYEIEFVFGLPLVKELNYTAEEEALSRRIMHYWATFAKTGNPNEPHSQESKWPLFTTKEQKFIDLNTEPMKVHQRLRVQMCVFWNQFLPKLLNAT 556
               SCOP domains d2dfpa_ A: Acetylcholinesterase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2dfpA00 A:2-535  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee..eeeeeeeee....eeeeeeeee......hhh.............eeee..................hhhh.............eeeeeee.......eeeeeee...........hhh..hhhhhhh..eeeeee...hhhhh............hhhhhhhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhh.hhhh....eeeeee...........hhhhhhhhhhhhhh.......hhhhhhhhhh..hhhhhhhhhh........................hhhhhhh......eeeeeee....hhhhhhh.............hhhhhhhhhhh.....hhhhhhhhhhh........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..eeeeeee..........hhh.......hhhh..hhh.hhh...hhhhhhhhhhhhhhhhhhhh......................eeee....eeeee...hhhhhhhh.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------CARBOXYLEST------------------------------------------------------------------------------------CARBOXYLESTERASE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dfp A   2 DHSELLVNTKSGKVMGTRVPVLSSHISAFLGIPFAEPPVGNMRFRRPEPKKPWSGVWNASTYPNNCQQYVDEQFPGFSGSEMWNPNREMSEDCLYLNIWVPSPRPKSTTVMVWIYGGGFYSGSSTLDVYNGKYLAYTEEVVLVSLSYRVGAFGFLALHGSQEAPGNVGLLDQRMALQWVHDNIQFFGGDPKTVTIFGEsAGGASVGMHILSPGSRDLFRRAILQSGSPNCPWASVSVAEGRRRAVELGRNLNCNLNSDEELIHCLREKKPQELIDVEWNVLPFDSIFRFSFVPVIDGEFFPTSLESMLNSGNFKKTQILLGVNKDEGSFFLLYGAPGFSKDSESKISREDFMSGVKLSVPHANDLGLDAVTLQYTDWMDDNNGIKNRDGLDDIVGDHNVICPLMHFVNKYTKFGNGTYLYFFNHRASNLVWPEWMGVIHGYEIEFVFGLPLVKELNYTAEEEALSRRIMHYWATFAKTGNPNEPHSQESKWPLFTTKEQKFIDLNTEPMKVHQRLRVQMCVFWNQFLPKLLNAT 535
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531    
                                                                                                                                                                                                                                200-MIS

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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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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

Fold: alpha/beta-Hydrolases (971)

Superfamily: alpha/beta-Hydrolases (971)

Family: Acetylcholinesterase-like (219)

Protein domain: Acetylcholinesterase (107)

Pacific electric ray (Torpedo californica) [TaxId: 7787] (75)

d2dfpa_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1820, no name defined] (692)

Pacific electric ray (Torpedo californica) (75)

2dfpA00

A:2-535

(no "Pfam Domain" information available for 2DFP)

Asymmetric Unit(hide GO term definitions)

Chain A (ACES_TETCF | P04058)

molecular function
	GO:0003990	acetylcholinesterase activity	Catalysis of the reaction: acetylcholine + H2O = choline + acetate.
	GO:0052689	carboxylic ester hydrolase activity	Catalysis of the hydrolysis of a carboxylic ester bond.
	GO:0004104	cholinesterase activity	Catalysis of the reaction: an acylcholine + H2O = choline + a carboxylic acid anion.
	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.
biological process
	GO:0001507	acetylcholine catabolic process in synaptic cleft	The chemical reactions and pathways resulting in the breakdown of acetylcholine that occurs in the synaptic cleft during synaptic transmission.
	GO:0042135	neurotransmitter catabolic process	The chemical reactions and pathways resulting in the breakdown of any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell.
cellular component
	GO:0031225	anchored component of membrane	The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	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.
	GO:0045202	synapse	The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
	GO:0043083	synaptic cleft	The narrow gap that separates the presynaptic and postsynaptic membranes, into which neurotransmitter is released.

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(no "Related Entries Specified in the PDB File" available for 2DFP)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (8, 8)

SS Bonds (3, 3)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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