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(-) Description

Title :  DFPASE AT 0.85 ANGSTROM RESOLUTION (H ATOMS INCLUDED)
 
Authors :  D. Liebschner, M. Elias, J. Koepke, C. Lecomte, B. Guillot, C. Jelsch, E. Chabriere
Date :  27 Jul 10  (Deposition) - 17 Aug 11  (Release) - 14 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Propeller, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Elias, D. Liebschner, J. Koepke, C. Lecomte, B. Guillot, C. Jelsch, E. Chabriere
Hydrogen Atoms In Protein Structures: High-Resolution X-Ray Diffraction Structure Of The Dfpase.
Bmc Res Notes V. 6 308 2013
PubMed-ID: 23915572  |  Reference-DOI: 10.1186/1756-0500-6-308

(-) Compounds

Molecule 1 - DIISOPROPYL-FLUOROPHOSPHATASE
    Chains: A
    EC Number: 3.1.8.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: COMMON EUROPEAN SQUID
    Organism Scientific: LOLIGO VULGARIS
    Organism Taxid: 6622
    Synonym: DFPASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 23)

Asymmetric/Biological Unit (9, 23)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2DXE2Ligand/Ion1,2-DIMETHOXYETHANE
3EDO8Ligand/Ion1,2-ETHANEDIOL
4GOL2Ligand/IonGLYCEROL
5ME21Ligand/Ion1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE
6MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
7MXE2Ligand/Ion2-METHOXYETHANOL
8PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
9PGE2Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:37 , GLY A:312 , ILE A:313 , PHE A:314 , DXE A:442 , HOH A:619BINDING SITE FOR RESIDUE GOL A 401
02AC2SOFTWAREPRO A:8 , LEU A:9 , PHE A:10 , ASP A:143 , LYS A:310 , HOH A:559 , HOH A:716 , HOH A:728BINDING SITE FOR RESIDUE GOL A 403
03AC3SOFTWAREGLU A:7 , LYS A:43 , PRO A:44 , ASN A:67 , GLY A:68 , TYR A:69 , ARG A:91 , ARG A:264 , PHE A:311 , ME2 A:471 , HOH A:508 , HOH A:628 , HOH A:728BINDING SITE FOR RESIDUE MES A 411
04AC4SOFTWAREGLU A:65 , THR A:102 , PHE A:103 , GLN A:258 , HOH A:598 , HOH A:687 , HOH A:830 , HOH A:1129BINDING SITE FOR RESIDUE MES A 412
05AC5SOFTWARELYS A:57 , VAL A:167 , ASP A:168 , ILE A:211 , MXE A:451 , HOH A:859BINDING SITE FOR RESIDUE EDO A 421
06AC6SOFTWAREPHE A:86 , PHE A:124 , PHE A:158 , THR A:159 , THR A:160 , PEG A:461 , HOH A:517 , HOH A:692 , HOH A:702 , HOH A:858 , HOH A:979BINDING SITE FOR RESIDUE EDO A 422
07AC7SOFTWAREARG A:115 , GLU A:138 , ASN A:289 , TRP A:293 , HOH A:516 , HOH A:617 , HOH A:959BINDING SITE FOR RESIDUE EDO A 423
08AC8SOFTWAREPRO A:196 , LYS A:198 , THR A:223 , HIS A:224 , PGE A:433 , HOH A:647 , HOH A:970BINDING SITE FOR RESIDUE EDO A 424
09AC9SOFTWAREHIS A:219 , ILE A:220 , PRO A:221 , GLN A:258 , HOH A:876BINDING SITE FOR RESIDUE EDO A 425
10BC1SOFTWAREMET A:148 , ASP A:184 , GLU A:225 , PHE A:314 , PGE A:433 , HOH A:581 , HOH A:906 , HOH A:1001BINDING SITE FOR RESIDUE EDO A 426
11BC2SOFTWAREGLY A:256 , GLY A:257 , GLN A:258 , LYS A:260 , PEG A:462 , HOH A:877BINDING SITE FOR RESIDUE EDO A 427
12BC3SOFTWAREGLU A:37 , HOH A:1082 , HOH A:1125BINDING SITE FOR RESIDUE EDO A 428
13BC4SOFTWAREMET A:148 , GLN A:172 , ASP A:184 , PRO A:196 , THR A:197 , EDO A:424 , EDO A:426 , HOH A:644 , HOH A:826 , HOH A:970 , HOH A:1102 , HOH A:1103BINDING SITE FOR RESIDUE PGE A 433
14BC5SOFTWAREILE A:106 , PHE A:158 , GLY A:162 , GLN A:163 , THR A:279 , LYS A:280 , THR A:281 , GLU A:296 , HOH A:521 , HOH A:544 , HOH A:685 , HOH A:735BINDING SITE FOR RESIDUE PGE A 434
15BC6SOFTWARETRP A:244 , LYS A:269 , HIS A:287 , GOL A:401 , HOH A:734BINDING SITE FOR RESIDUE DXE A 442
16BC7SOFTWAREPRO A:8 , LYS A:280 , GLU A:296 , TRP A:297 , PEG A:461 , HOH A:532 , HOH A:770 , HOH A:893BINDING SITE FOR RESIDUE DXE A 443
17BC8SOFTWARELYS A:58 , THR A:59 , ASN A:213 , LYS A:214 , EDO A:421 , HOH A:569 , HOH A:768 , HOH A:859 , HOH A:923BINDING SITE FOR RESIDUE MXE A 451
18BC9SOFTWARELYS A:151 , THR A:169 , ALA A:170 , PHE A:171 , GLU A:194 , LYS A:214 , HOH A:531BINDING SITE FOR RESIDUE MXE A 452
19CC1SOFTWAREGLN A:84 , ILE A:106 , LYS A:280 , EDO A:422 , DXE A:443 , HOH A:639 , HOH A:702 , HOH A:832 , HOH A:858BINDING SITE FOR RESIDUE PEG A 461
20CC2SOFTWARELYS A:63 , GLU A:65 , ASP A:255 , GLY A:256 , GLY A:257 , EDO A:427 , HOH A:573 , HOH A:629 , HOH A:844BINDING SITE FOR RESIDUE PEG A 462
21CC3SOFTWAREVAL A:5 , GLU A:7 , HIS A:248 , ARG A:264 , MES A:411 , HOH A:976BINDING SITE FOR RESIDUE ME2 A 471
22CC4SOFTWAREGLU A:21 , ASN A:120 , ASN A:175 , ASP A:229 , HOH A:502 , HOH A:524 , HOH A:604BINDING SITE FOR RESIDUE CA A 491
23CC5SOFTWAREASP A:232 , LEU A:273 , HIS A:274 , HOH A:509 , HOH A:615 , HOH A:623BINDING SITE FOR RESIDUE CA A 492

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O4P)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Met A:1 -Glu A:2
2Glu A:2 -Ile A:3
3Ala A:140 -Pro A:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O4P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3O4P)

(-) Exons   (0, 0)

(no "Exon" information available for 3O4P)

(-) Sequences/Alignments

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:314
 aligned with DFPA_LOLVU | Q7SIG4 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:314
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310    
           DFPA_LOLVU     1 MEIPVIEPLFTKVTEDIPGAEGPVFDKNGDFYIVAPEVEVNGKPAGEILRIDLKTGKKTVICKPEVNGYGGIPAGCQCDRDANQLFVADMRLGLLVVQTDGTFEEIAKKDSEGRRMQGCNDCAFDYEGNLWITAPAGEVAPADYTRSMQEKFGSIYCFTTDGQMIQVDTAFQFPNGIAVRHMNDGRPYQLIVAETPTKKLWSYDIKGPAKIENKKVWGHIPGTHEGGADGMDFDEDNNLLVANWGSSHIEVFGPDGGQPKMRIRCPFEKPSNLHFKPQTKTIFVTEHENNAVWKFEWQRNGKKQYCETLKFGIF 314
               SCOP domains d3o4pa_ A: Diisopropylfluorophosphatase (phosphotriesterase, DFP)                                                                                                                                                                                                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....eeee......eeeee.....eeeee...ee..ee..eeeee......eeeee..ee..ee..eeeeee.....eeeeee...eeeeee....eee...............eeee.....eeeee..................eeeeee.....eeeeeeee..eeeeeeee.....eeeeeeee....eeeeeeeee..eeeeeeeeee.......eeeeeee.....eeeeee...eeeee........eeee.....eeeeee.....eeeeee....eeeeee.......hhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o4p A   1 MEIPVIEPLFTKVTEDIPGAEGPVFDKNGDFYIVAPEVEVNGKPAGEILRIDLKTGKKTVICKPEVNGYGGIPAGCQCDRDANQLFVADMRLGLLVVQTDGTFEEIAKKDSEGRRMQGCNDCAFDYEGNLWITAPAGEVAPADYTRSMQEKFGSIYCFTTDGQMIQVDTAFQFPNGIAVRHMNDGRPYQLIVAETPTKKLWSYDIKGPAKIENKKVWGHIPGTHEGGADGMDFDEDNNLLVANWGSSHIEVFGPDGGQPKMRIRCPFEKPSNLHFKPQTKTIFVTEHENNAVWKFEWQRNGKKQYCETLKFGIF 314
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O4P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3O4P)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DFPA_LOLVU | Q7SIG4)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0047862    diisopropyl-fluorophosphatase activity    Catalysis of the reaction: diisopropyl fluorophosphate + H(2)O = diisopropyl phosphate + 2 H(+) + hydrogen fluoride.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DFPA_LOLVU | Q7SIG4: 1e1a 1pjx 2gvu 2gvv 2gvw 2gvx 2iao 2iap 2iaq 2iar 2ias 2iat 2iau 2iav 2iaw 2iax 3byc 3hlh 3hli 3i1c 3kgg 3li3 3li4 3li5 3u0s 4o5s 4o5t

(-) Related Entries Specified in the PDB File

1pjx DFPASE AT 0.85 A RESOLUTION (NO H ATOMS)