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(-) Description

Title :  ENGINEERING OF ORGANOPHOSPHATE HYDROLASE BY COMPUTATIONAL DESIGN AND DIRECTED EVOLUTION
 
Authors :  R. Takeuchi, B. L. Stoddard
Date :  21 Jul 11  (Deposition) - 08 Feb 12  (Release) - 29 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A
Keywords :  Computational Design, Directed Evolution, Tim Beta/Alpha-Barrel, Metallo-Dependent Hydrolase, Organophosphate Binding, Hydrolysis, Artificial Enzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. D. Khare, Y. Kipnis, P. J. Greisen, R. Takeuchi, Y. Ashani, M. Goldsmith, Y. Song, J. L. Gallaher, I. Silman, H. Leader, J. L. Sussman, B. L. Stoddard, D. S. Tawfik, D. Baker
Computational Redesign Of A Mononuclear Zinc Metalloenzyme For Organophosphate Hydrolysis.
Nat. Chem. Biol. V. 8 294 2012
PubMed-ID: 22306579  |  Reference-DOI: 10.1038/NCHEMBIO.777

(-) Compounds

Molecule 1 - ORGANOPHOSPHATE HYDROLASE
    ChainsA
    EC Number3.-.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28B
    Expression System StrainBL21(DE3)-RIL
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneADENOSINE DEAMINASE, ADA
    MutationYES
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2ZN4Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:15 , HIS A:17 , HIS A:214 , HIS A:238 , ASP A:295 , HOH A:398BINDING SITE FOR RESIDUE ZN A 353
2AC2SOFTWAREASP A:41 , GLU A:45 , GLU A:189 , ZN A:356BINDING SITE FOR RESIDUE ZN A 354
3AC3SOFTWAREASP A:123 , ASP A:128 , HOH A:446 , HOH A:448 , HOH A:466 , HOH A:469BINDING SITE FOR RESIDUE ZN A 355
4AC4SOFTWAREASP A:41 , GLU A:45 , ZN A:354BINDING SITE FOR RESIDUE ZN A 356
5AC5SOFTWAREGLU A:186 , GLU A:217 , PHE A:218 , GLY A:219 , HOH A:477BINDING SITE FOR RESIDUE CA A 357

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3T1G)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:113 -Pro A:114

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3T1G)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1A_DEAMINASEPS00485 Adenosine and AMP deaminase signature.ADA_MOUSE291-297  1A:291-297

(-) Exons   (0, 0)

(no "Exon" information available for 3T1G)

(-) 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:349
 aligned with ADA_MOUSE | P03958 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:349
                                    13        23        33        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         
            ADA_MOUSE     4 TPAFNKPKVELHVHLDGAIKPETILYFGKKRGIALPADTVEELRNIIGMDKPLSLPGFLAKFDYYMPVIAGCREAIKRIAYEFVEMKAKEGVVYVEVRYSPHLLANSKVDPMPWNQTEGDVTPDDVVDLVNQGLQEGEQAFGIKVRSILCCMRHQPSWSLEVLELCKKYNQKTVVAMDLAGDETIEGSSLFPGHVEAYEGAVKNGIHRTVHAGEVGSPEVVREAVDILKTERVGHGYHTIEDEALYNRLLKENMHFEVCPWSSYLTGAWDPKTTHAVVRFKNDKANYSLNTDDPLIFKSTLDTDYQMTKKDMGFTEEEFKRLNINAAKSSFLPEEEKKELLERLYREYQ 352
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee...hhhhh.hhhhhhhhhhhhh......hhhhhhhhhh.....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeeeeeehhhhhh......hhhhh.....hhhhhhhhhhhhhhhhhhhhh.eeeeeeeee..hhhhhhhhhhhhhhh....eeeeeee......hhhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh..eeeehhhhhhhh........hhhhhhhhh..eeee...hhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A_DEAMI------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t1g A   4 TPAFNKPKVELHVHLSGAIKPETILYFGKKRGIALPADTVEELRNIIGMDKPLSQPGTLAKWDYYMPVIAGCREAIKRIAYEFVEMKAKEGVVYVEVRYSPHLLANSKVDPMPWNQTEGDVTPDDVVDLVNQGLHEGEQAFGIKVRSILCCMRHQPSWSLEVLELCKKYNQKTVVAMDLIGDETIEGSSLFPGHVEAYEGAVKNGIHRTVHAGEFGSPEVVREAVDILKTERVGHGYHTIEDEALYNRLLKENMHFEVCPWSSYLTGAWDPKTTHAVVRFKNDKANYSLNTDAPLEFKSTLDTDYQMTKKDMGFTEEEFKRLNINAAKSSFLPEEEKKELLERLYREYQ 352
                                    13        23        33        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         

   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  (0, 0)

(no "SCOP Domain" information available for 3T1G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3T1G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T1G)

(-) Gene Ontology  (70, 70)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ADA_MOUSE | P03958)
molecular function
    GO:0004000    adenosine deaminase activity    Catalysis of the reaction: adenosine + H2O = inosine + NH3.
    GO:0019239    deaminase activity    Catalysis of the removal of an amino group from a substrate, producing ammonia (NH3).
    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.
    GO:0001883    purine nucleoside binding    Interacting selectively and non-covalently with a purine nucleoside, a compound consisting of a purine base linked either to ribose or deoxyribose.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0048541    Peyer's patch development    The process whose specific outcome is the progression of Peyer's patches over time, from their formation to the mature structure. Peyer's patches are typically found as nodules associated with gut epithelium with distinct internal structures including B- and T-zones for the activation of lymphocytes.
    GO:0042110    T cell activation    The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
    GO:0006154    adenosine catabolic process    The chemical reactions and pathways resulting in the breakdown of adenosine, adenine riboside, a ribonucleoside found widely distributed in cells of every type as the free nucleoside and in combination in nucleic acids and various nucleoside coenzymes.
    GO:0046085    adenosine metabolic process    The chemical reactions and pathways involving adenosine, adenine riboside, a ribonucleoside found widely distributed in cells of every type as the free nucleoside and in combination in nucleic acids and various nucleoside coenzymes.
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0046061    dATP catabolic process    The chemical reactions and pathways resulting in the breakdown of dATP, deoxyadenosine triphosphate (2'-deoxyadenosine 5'-triphosphate).
    GO:0006157    deoxyadenosine catabolic process    The chemical reactions and pathways resulting in the breakdown of deoxyadenosine, 2-deoxyribosyladenine, one of the four major nucleosides of DNA.
    GO:0048566    embryonic digestive tract development    The process whose specific outcome is the progression of the gut over time, from its formation to the mature structure during embryonic development. The gut is the region of the digestive tract extending from the beginning of the intestines to the anus.
    GO:0002314    germinal center B cell differentiation    The process in which a B cell in the spleen acquires the specialized features of a germinal center B cell. Germinal center B cells are rapidly cycling B cells which have downregulated IgD expression and exhibit high levels of binding by peanut agglutinin (PNA).
    GO:0001821    histamine secretion    The regulated release of histamine by a cell or tissue. It is formed by decarboxylation of histidine and it acts through receptors in smooth muscle and in secretory systems.
    GO:0046101    hypoxanthine biosynthetic process    The chemical reactions and pathways resulting in the formation of hypoxanthine, 6-hydroxy purine, an intermediate in the degradation of adenylate. Its ribonucleoside is known as inosine and its ribonucleotide as inosinate.
    GO:0043103    hypoxanthine salvage    Any process that generates hypoxanthine, 6-hydroxy purine, from derivatives of it without de novo synthesis.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0046103    inosine biosynthetic process    The chemical reactions and pathways resulting in the formation of inosine, hypoxanthine riboside, a nucleoside found free but not in combination in nucleic acids except in the anticodons of some tRNAs.
    GO:0001889    liver development    The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
    GO:0048286    lung alveolus development    The process whose specific outcome is the progression of the alveolus over time, from its formation to the mature structure. The alveolus is a sac for holding air in the lungs; formed by the terminal dilation of air passageways.
    GO:0030324    lung development    The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
    GO:0060169    negative regulation of adenosine receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the adenosine receptor signaling pathway. The adenosine receptor pathway is the series of molecular signals generated as a consequence of an adenosine receptor binding to one of its physiological ligands.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0042323    negative regulation of circadian sleep/wake cycle, non-REM sleep    Any process that stops, prevents or reduces the duration or quality of non-rapid eye movement (NREM) sleep.
    GO:0050728    negative regulation of inflammatory response    Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
    GO:0002686    negative regulation of leukocyte migration    Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte migration.
    GO:0002906    negative regulation of mature B cell apoptotic process    Any process that stops, prevents, or reduces the frequency, rate, or extent of mature B cell apoptotic process.
    GO:0070256    negative regulation of mucus secretion    Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of mucus from a cell or a tissue.
    GO:0060407    negative regulation of penile erection    Any process that stops, prevents, or reduces the rate, frequency or extent of penile erection. Penile erection is the hardening, enlarging and rising of the penis which often occurs in the sexually aroused male and enables sexual intercourse. Achieved by increased inflow of blood into the vessels of erectile tissue, and decreased outflow.
    GO:0070244    negative regulation of thymocyte apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of thymocyte death by apoptotic process.
    GO:0009117    nucleotide metabolic process    The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
    GO:0001890    placenta development    The process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
    GO:0030890    positive regulation of B cell proliferation    Any process that activates or increases the rate or extent of B cell proliferation.
    GO:0050870    positive regulation of T cell activation    Any process that activates or increases the frequency, rate or extent of T cell activation.
    GO:0045582    positive regulation of T cell differentiation    Any process that activates or increases the frequency, rate or extent of T cell differentiation.
    GO:0033089    positive regulation of T cell differentiation in thymus    Any process that activates or increases the frequency, rate or extent of T cell differentiation in the thymus.
    GO:0050862    positive regulation of T cell receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0046638    positive regulation of alpha-beta T cell differentiation    Any process that activates or increases the frequency, rate or extent of alpha-beta T cell differentiation.
    GO:0050850    positive regulation of calcium-mediated signaling    Any process that activates or increases the frequency, rate or extent of calcium-mediated signaling.
    GO:0002636    positive regulation of germinal center formation    Any process that activates or increases the frequency, rate, or extent of germinal center formation.
    GO:0010460    positive regulation of heart rate    Any process that activates or increases the frequency or rate of heart contraction.
    GO:0045987    positive regulation of smooth muscle contraction    Any process that activates or increases the frequency, rate or extent of smooth muscle contraction.
    GO:0032261    purine nucleotide salvage    Any process which produces a purine nucleotide from derivatives of it, without de novo synthesis.
    GO:0009168    purine ribonucleoside monophosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of purine ribonucleoside monophosphate, a compound consisting of a purine base linked to a ribose sugar esterified with phosphate on the sugar.
    GO:0045580    regulation of T cell differentiation    Any process that modulates the frequency, rate or extent of T cell differentiation.
    GO:0033632    regulation of cell-cell adhesion mediated by integrin    Any process that modulates the frequency, rate, or extent of cell-cell adhesion mediated by integrin.
    GO:0045187    regulation of circadian sleep/wake cycle, sleep    Any process that modulates the frequency, rate or extent of sleep; a readily reversible state of reduced awareness and metabolic activity that occurs periodically in many animals.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0042542    response to hydrogen peroxide    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydrogen peroxide (H2O2) stimulus.
    GO:0001666    response to hypoxia    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0043278    response to morphine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a morphine stimulus. Morphine is an opioid alkaloid, isolated from opium, with a complex ring structure.
    GO:0033197    response to vitamin E    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vitamin E stimulus.
    GO:0001829    trophectodermal cell differentiation    The process in which a relatively unspecialized cell acquires the specialized features of a trophectoderm cell.
    GO:0046111    xanthine biosynthetic process    The chemical reactions and pathways resulting in the formation of xanthine, 2,6-dihydroxypurine, a purine formed in the metabolic breakdown of guanine but not present in nucleic acids.
cellular component
    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:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0060205    cytoplasmic vesicle lumen    The volume enclosed by a cytoplasmic vesicle.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0032839    dendrite cytoplasm    All of the contents of a dendrite, excluding the surrounding plasma membrane.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ADA_MOUSE | P039581a4l 1a4m 1add 1fkw 1fkx 1uio 1uip 2ada 3km8 3mvi 3mvt

(-) Related Entries Specified in the PDB File

1a4l THE PARENTAL ENZYME