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(-) Description

Title :  CATALYTIC DOMAIN OF MOUSE 2',3'-CYCLIC NUCLEOTIDE 3'-PHOSPHODIESTERASE, WITH MUTATION V321A, CRYSTALLIZED WITH 2'-AMPS
 
Authors :  M. Myllykoski, A. Raasakka, M. Lehtimaki, H. Han, P. Kursula
Date :  13 Nov 12  (Deposition) - 10 Jul 13  (Release) - 13 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Myelin, Nervous System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Myllykoski, A. Raasakka, M. Lehtimaki, H. Han, I. Kursula, P. Kursula
Crystallographic Analysis Of The Reaction Cycle Of 2', 3'-Cyclic Nucleotide 3'-Phosphodiesterase, A Unique Member Of The 2H Phosphoesterase Family
J. Mol. Biol. V. 425 4307 2013
PubMed-ID: 23831225  |  Reference-DOI: 10.1016/J.JMB.2013.06.012

(-) Compounds

Molecule 1 - 2', 3'-CYCLIC NUCLEOTIDE 3'-PHOSPHODIESTERASE
    ChainsA
    EC Number3.1.4.37
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTH 27
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantROSETTA
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL CATALYTIC DOMAIN, RESIDUES 159-378
    MutationYES
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymCNP, CNPASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2OVE1Ligand/Ion2'-O-(SULFIDOPHOSPHINATO)ADENOSINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:305 , SER A:306 , ARG A:307BINDING SITE FOR RESIDUE CL A1379
2AC2SOFTWARETYR A:168 , HIS A:230 , THR A:232 , PHE A:235 , HIS A:309 , THR A:311 , PRO A:320 , ALA A:321 , THR A:323 , HOH A:2068BINDING SITE FOR RESIDUE OVE A1380

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ZBS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ZBS)

(-) 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:209
 aligned with CN37_MOUSE | P16330 from UniProtKB/Swiss-Prot  Length:420

    Alignment length:216
                                   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392      
           CN37_MOUSE   183 DFLPLYFGWFLTKKSSETLRKAGQVFLEELGNHKAFKKELRHFISGDEPKEKLELVSYFGKRPPGVLHCTTKFCDYGKAAGAEEYAQQEVVKRSYGKAFKLSISALFVTPKTAGAQVVLTDQELQLWPSDLDKPSASEGLPPGSRAHVTLGCAADVQPVQTGLDLLDILQQVKGGSQGEAVGELPRGKLYSLGKGRWMLSLTKKMEVKAIFTGYYG 398
               SCOP domains d3zbsa_ A: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...----...hhhhhh........eeeeee.hhhh..hhhhhhhhhhhhhhh..eeeeeeeeeee...eeeeee..hhhhhh.....---hhhhh........eeeeee......hhhhhhhhhhhhhhhh.......eee..eeeeeee..eeeeeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3zbs A 163 DFLPLYFGWFLTKKSSETLRKAGQVFLEELGNHKAFKKELRHFISG----EKLELVSYFGKRPPGVLHCTTKFCDYGKAAGAEEYAQQEVVKRSYGKAFKLSISALFVTPKTAGAQVVLTDQELQLWPSD---PSASEGLPPGSRAHVTLGCAADVQPAQTGLDLLDILQQVKGGSQGEAVGELPRGKLYSLGKGRWMLSLTKKMEVKAIFTGYYG 378
                                   172       182       192       202     |   -|      222       232       242       252       262       272       282       292   |   302       312       322       332       342       352       362       372      
                                                                       208  213                                                                            292 296                                                                                  

   Legend:   → Mismatch (orange background)
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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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CN37_MOUSE | P16330)
molecular function
    GO:0004113    2',3'-cyclic-nucleotide 3'-phosphodiesterase activity    Catalysis of the reaction: nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 2'-phosphate.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0030551    cyclic nucleotide binding    Interacting selectively and non-covalently with a cyclic nucleotide, a nucleotide in which the phosphate group is in diester linkage to two positions on the sugar residue.
    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:0008344    adult locomotory behavior    Locomotory behavior in a fully developed and mature organism.
    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:0007409    axonogenesis    De novo generation of a long process of a neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells. Refers to the morphogenesis or creation of shape or form of the developing axon.
    GO:0009214    cyclic nucleotide catabolic process    The chemical reactions and pathways resulting in the breakdown of a cyclic nucleotide, a nucleotide in which the phosphate group is in diester linkage to two positions on the sugar residue.
    GO:0030900    forebrain development    The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions).
    GO:0000226    microtubule cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins.
    GO:0048709    oligodendrocyte differentiation    The process in which a relatively unspecialized cell acquires the specialized features of an oligodendrocyte. An oligodendrocyte is a type of glial cell involved in myelinating the axons of neurons in the central nervous system.
    GO:0046902    regulation of mitochondrial membrane permeability    Any process that modulates the frequency, rate or extent of the passage or uptake of molecules by the mitochondrial membrane.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0009636    response to toxic substance    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 toxic stimulus.
    GO:0021762    substantia nigra development    The progression of the substantia nigra over time from its initial formation until its mature state. The substantia nigra is the layer of gray substance that separates the posterior parts of the cerebral peduncles (tegmentum mesencephali) from the anterior parts; it normally includes a posterior compact part with many pigmented cells (pars compacta) and an anterior reticular part whose cells contain little pigment (pars reticularis).
cellular component
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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:0042470    melanosome    A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    GO:0005902    microvillus    Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005741    mitochondrial outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
    GO:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
    GO:0035748    myelin sheath abaxonal region    The region of the myelin sheath furthest from the axon.
    GO:0035749    myelin sheath adaxonal region    The region of the myelin sheath nearest to the axon.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    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:0031143    pseudopodium    A temporary protrusion or retractile process of a cell, associated with flowing movements of the protoplasm, and serving for locomotion and feeding.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CN37_MOUSE | P163302xmi 2y1p 2y3x 2ydb 2ydc 2ydd 2yoz 2yp0 2ypc 2ype 2yph 2yq9 3zbr 3zbz 4wbi 4wbl 4wc9 4wca 4wcb 4wcc 4wda 4wdb 4wdd 4wde 4wdf 4wdg 4wdh 4wex 4wfr 5ae0

(-) Related Entries Specified in the PDB File

2xmi CATALYTIC DOMAIN OF MOUSE 2',3'-CYCLIC NUCLEOTIDE 3'- PHOSPHODIESTERASE, COMPLEXED WITH CITRATE
2y1p CATALYTIC DOMAIN OF MOUSE 2',3'-CYCLIC NUCLEOTIDE 3'- PHOSPHODIESTERASE, COMPLEXED WITH CITRATE
2y3x CATALYTIC DOMAIN OF MOUSE 2',3'-CYCLIC NUCLEOTIDE 3'- PHOSPHODIESTERASE, COMPLEXED WITH SULFATE
2ydb CATALYTIC DOMAIN OF MOUSE 2',3'-CYCLIC NUCLEOTIDE 3'- PHOSPHODIESTERASE, SOAKED WITH 2',3'-CYCLIC NADP
2ydc CATALYTIC DOMAIN OF MOUSE 2',3'-CYCLIC NUCLEOTIDE 3'- PHOSPHODIESTERASE, SOAKED WITH GTP
2ydd CATALYTIC DOMAIN OF MOUSE 2',3'-CYCLIC NUCLEOTIDE 3'- PHOSPHODIESTERASE, SOAKED WITH 2',3'-CYCLIC AMP
2yoz CATALYTIC DOMAIN OF MOUSE 2',3'-CYCLIC NUCLEOTIDE 3 '- PHOSPHODIESTERASE, CRYSTALLIZED WITH 2'-AMPS
2yp0 CATALYTIC DOMAIN OF MOUSE 2',3'-CYCLIC NUCLEOTIDE 3 '- PHOSPHODIESTERASE, CRYSTALLIZED WITH 2'-AMPS
2ypc CATALYTIC DOMAIN OF MOUSE 2',3'-CYCLIC NUCLEOTIDE 3 '- PHOSPHODIESTERASE, CRYSTALLIZED WITH 2'-AMPS
2ype CATALYTIC DOMAIN OF MOUSE 2',3'-CYCLIC NUCLEOTIDE 3 '- PHOSPHODIESTERASE, WITH MUTATION H309S, CRYSTALLIZED WITH 2',3'-CYCLIC AMP
2yph CATALYTIC DOMAIN OF MOUSE 2',3'-CYCLIC NUCLEOTIDE 3 '- PHOSPHODIESTERASE, WITH MUTATION H230S, CRYSTALLIZED WITH 2',3-(RP)-CYCLIC-AMPS
2yq9 CATALYTIC DOMAIN OF MOUSE 2',3'-CYCLIC NUCLEOTIDE 3 '- PHOSPHODIESTERASE, WITH MUTATION V321A, CRYSTALLIZED WITH 2'-AMP
3zbr CATALYTIC DOMAIN OF MOUSE 2',3'-CYCLIC NUCLEOTIDE 3 '- PHOSPHODIESTERASE, WITH MUTATION H230S, CRYSTALLIZED WITH NADP
3zbz CATALYTIC DOMAIN OF MOUSE 2',3'-CYCLIC NUCLEOTIDE 3 '- PHOSPHODIESTERASE, WITH MUTATION V321A, CRYSTALLIZED WITH 2'-AMPS