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(-) Description

Title :  S28N - ANGIOGENIN MUTANTS AND AMYOTROPHIC LATERAL SCLEROSIS - A BIOCHEMICAL AND BIOLOGICAL ANALYSIS
 
Authors :  N. Thiyagarajan, R. Ferguson, S. Saha, T. Pham, V. Subramanian, K. R. A
Date :  06 Feb 12  (Deposition) - 10 Oct 12  (Release) - 24 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Amyotrophic, Lateral Sclerosis, Neovascularisation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Thiyagarajan, R. Ferguson, V. Subramanian, K. R. Acharya
Structural And Molecular Insights Into The Mechanism Of Action Of Human Angiogenin-Als Variants In Neurons.
Nat. Commun. V. 3 1121 2012
PubMed-ID: 23047679  |  Reference-DOI: 10.1038/NCOMMS2126

(-) Compounds

Molecule 1 - ANGIOGENIN
    ChainsA
    EC Number3.1.27.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B(PLUS)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantCODON PLUS - RIPL
    Expression System Vector TypePLASMID
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRIBONUCLEASE 5, RNASE 5

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1TAR1Ligand/IonD(-)-TARTARIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:24 , HIS A:65 , PHE A:100 , ARG A:101BINDING SITE FOR RESIDUE TAR A1123

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:26 -A:81
2A:39 -A:92
3A:57 -A:107

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:37 -Pro A:38
2Pro A:90 -Pro A:91

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (14, 14)

Asymmetric/Biological Unit (14, 14)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_044147Q36LANGI_HUMANDisease (ALS9)121909535AQ12L
02UniProtVAR_073021Y38HANGI_HUMANDisease (ALS9)  ---AY14H
03UniProtVAR_044148K41EANGI_HUMANDisease (ALS9)121909537AK17E
04UniProtVAR_044149K41IANGI_HUMANDisease (ALS9)121909536AK17I
05UniProtVAR_073022D46GANGI_HUMANDisease (ALS9)  ---AD22G
06UniProtVAR_044150S52NANGI_HUMANDisease (ALS9)121909542AN28N
07UniProtVAR_044151R55KANGI_HUMANDisease (ALS9)121909538AR31K
08UniProtVAR_044152C63WANGI_HUMANDisease (ALS9)121909539AC39W
09UniProtVAR_044153K64IANGI_HUMANDisease (ALS9)121909540AK40I
10UniProtVAR_044154I70VANGI_HUMANPolymorphism121909541AI46V
11UniProtVAR_013148K84EANGI_HUMANPolymorphism17560AK60E
12UniProtVAR_044155P136LANGI_HUMANDisease (ALS9)121909543AP112L
13UniProtVAR_044156V137IANGI_HUMANDisease (ALS9)121909544AV113I
14UniProtVAR_044157H138RANGI_HUMANDisease (ALS9)  ---AH114R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNASE_PANCREATICPS00127 Pancreatic ribonuclease family signature.ANGI_HUMAN63-69  1A:39-45

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003979902aENSE00002201651chr14:21156932-21157033102ANGI_HUMAN-00--
1.3cENST000003979903cENSE00001758396chr14:21161706-21162338633ANGI_HUMAN1-1531531A:2-122 (gaps)121

(-) 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:120
 aligned with ANGI_HUMAN | P03950 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:121
                                    35        45        55        65        75        85        95       105       115       125       135       145 
           ANGI_HUMAN    26 DNSRYTHFLTQHYDAKPQGRDDRYCESIMRRRGLTSPCKDINTFIHGNKRSIKAICENKNGNPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGFRNVVVACENGLPVHLDQSIFRR 146
               SCOP domains d4ahga_ A: Angiogenin                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..........-..hhhhhh........eeeee..hhhhhhhhhh...eeee...eeee...eeeeeeee..........eeeeeeee..eeeee..eeeee.hhhhhh Sec.struct. author
             SAPs(SNPs) (1) ----------L-H--E----G-----N--K-------WI-----V-------------E---------------------------------------------------LIR-------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------I--------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -------------------------------------RNASE_P----------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3c  PDB: A:2-122 (gaps) UniProt: 1-153 [INCOMPLETE]                                                                Transcript 1
                 4ahg A   2 DNSRYTHFLTQHYDAKPQGRDDR-CENIMRRRGLTSPCKDINTFIHGNKRSIKAICENKNGNPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGFRNVVVACENGLPVHLDQSIFRR 122
                                    11        21  | |   31        41        51        61        71        81        91       101       111       121 
                                                 24 |                                                                                                
                                                   26                                                                                                

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AHG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AHG)

(-) Gene Ontology  (54, 54)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ANGI_HUMAN | P03950)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0042277    peptide binding    Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0019843    rRNA binding    Interacting selectively and non-covalently with ribosomal RNA.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0030041    actin filament polymerization    Assembly of actin filaments by the addition of actin monomers to a filament.
    GO:0032431    activation of phospholipase A2 activity    Any process that initiates the activity of the inactive enzyme phospholipase A2.
    GO:0007202    activation of phospholipase C activity    The initiation of the activity of the inactive enzyme phospolipase C as the result of a series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand.
    GO:0032148    activation of protein kinase B activity    Any process that initiates the activity of the inactive enzyme protein kinase B.
    GO:0034332    adherens junction organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an adherens junction. An adherens junction is a cell junction at which the cytoplasmic face of the plasma membrane is attached to actin filaments.
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0019731    antibacterial humoral response    An immune response against bacteria mediated through a body fluid. Examples of this process are the antibacterial humoral responses in Mus musculus and Drosophila melanogaster.
    GO:0019732    antifungal humoral response    An immune response against a fungus mediated through a body fluid. An example of this process is the antifungal humoral response in Drosophila melanogaster.
    GO:0007154    cell communication    Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0050830    defense response to Gram-positive bacterium    Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
    GO:0006651    diacylglycerol biosynthetic process    The chemical reactions and pathways resulting in the formation of diacylglycerol, a glyceride in which any two of the R groups (positions not specified) are acyl groups while the remaining R group can be either H or an alkyl group.
    GO:0042592    homeostatic process    Any biological process involved in the maintenance of an internal steady state.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0048662    negative regulation of smooth muscle cell proliferation    Any process that stops, prevents or reduces the rate or extent of smooth muscle cell proliferation.
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0001556    oocyte maturation    A developmental process, independent of morphogenetic (shape) change, that is required for an oocyte to attain its fully functional state. Oocyte maturation commences after reinitiation of meiosis commonly starting with germinal vesicle breakdown, and continues up to the second meiotic arrest prior to fertilization.
    GO:0001541    ovarian follicle development    The process whose specific outcome is the progression of the ovarian follicle over time, from its formation to the mature structure.
    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:0001938    positive regulation of endothelial cell proliferation    Any process that activates or increases the rate or extent of endothelial cell proliferation.
    GO:0042327    positive regulation of phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule.
    GO:0050714    positive regulation of protein secretion    Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell.
    GO:0009303    rRNA transcription    The synthesis of ribosomal RNA (rRNA), any RNA that forms part of the ribosomal structure, from a DNA template.
    GO:0009725    response to hormone    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 hormone 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:0001878    response to yeast    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 from a yeast species.
cellular component
    GO:0032311    angiogenin-PRI complex    A stable heterodimer of angiogenin and placental ribonuclease inhibitor; interaction between angiogenin and PRI prevents angiogenin binding to its receptor to stimulate angiogenesis.
    GO:0005605    basal lamina    A thin sheet of proteoglycans and glycoproteins, especially laminin, secreted by cells as an extracellular matrix.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ANGI_HUMAN | P039501a4y 1ang 1awz 1b1e 1b1i 1b1j 1gv7 1h0d 1h52 1h53 1hby 1k58 1k59 1k5a 1k5b 1un3 1un4 1un5 2ang 4ahd 4ahe 4ahf 4ahh 4ahi 4ahj 4ahk 4ahl 4ahm 4ahn 4aoh 4b36 5eop 5epz 5eqo 5m9a 5m9c 5m9g 5m9j 5m9m 5m9p 5m9q 5m9r 5m9s 5m9t 5m9v

(-) Related Entries Specified in the PDB File

1a4y RIBONUCLEASE INHIBITOR-ANGIOGENIN COMPLEX
1ang ANGIOGENIN
1awz 3D SOLUTION STRUCTURE OF HUMAN ANGIOGENIN DETERMINED BY 1H, 15N NMR SPECTROSCOPY, 30 STRUCTURES
1b1e CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT K40Q
1b1i CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN
1b1j CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT H13A.
1h0d CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN IN COMPLEX WITH FAB FRAGMENT OF ITS MONOCLONAL ANTIBODY MAB 26-2F
1h52 BINDING OF PHOSPHATE AND PYROPHOSPHATE IONS AT THE ACTIVE SITE OF HUMAN ANGIOGENIN AS REVEALED BY X-RAY CRYSTALLOGRAPHY
1h53 BINDING OF PHOSPHATE AND PYROPHOSPHATE IONS AT THE ACTIVE SITE OF HUMAN ANGIOGENIN AS REVEALED BY X-RAY CRYSTALLOGRAPHY
1hby BINDING OF PHOSPHATE AND PYROPHOSPHATE IONS AT THE ACTIVE SITE OF HUMAN ANGIOGENIN AS REVEALED BY X-RAY CRYSTALLOGRAPHY
1k58 CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT D116H
1k59 CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT Q117G
1k5a CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN DOUBLE VARIANTI119A /F120A
1k5b CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT DES(121- 123)
1un3 CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT T44D
1un4 CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT T80A
1un5 ARH-II, AN ANGIOGENIN/RNASE A CHIMERA
2ang CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN OF THE MET(-1) FORM
4ahd Q12L - ANGIOGENIN MUTANTS AND AMYOTROPHIC LATERAL SCLEROSIS - A BIOCHEMICAL AND BIOLOGICAL ANALYSIS
4ahe K17I - ANGIOGENIN MUTANTS AND AMYOTROPHIC LATERAL SCLEROSIS - A BIOCHEMICAL AND BIOLOGICAL ANALYSIS
4ahf K17E - ANGIOGENIN MUTANTS AND AMYOTROPHIC LATERAL SCLEROSIS - A BIOCHEMICAL AND BIOLOGICAL ANALYSIS
4ahh R31K - ANGIOGENIN MUTANTS AND AMYOTROPHIC LATERAL SCLEROSIS - A BIOCHEMICAL AND BIOLOGICAL ANALYSIS
4ahi K40I - ANGIOGENIN MUTANTS AND AMYOTROPHIC LATERAL SCLEROSIS - A BIOCHEMICAL AND BIOLOGICAL ANALYSIS
4ahj I46V - ANGIOGENIN MUTANTS AND AMYOTROPHIC LATERAL SCLEROSIS - A BIOCHEMICAL AND BIOLOGICAL ANALYSIS
4ahk K54E - ANGIOGENIN MUTANTS AND AMYOTROPHIC LATERAL SCLEROSIS - A BIOCHEMICAL AND BIOLOGICAL ANALYSIS
4ahl P112L - ANGIOGENIN MUTANTS AND AMYOTROPHIC LATERAL SCLEROSIS - A BIOCHEMICAL AND BIOLOGICAL ANALYSIS
4ahm V113I - ANGIOGENIN MUTANTS AND AMYOTROPHIC LATERAL SCLEROSIS - A BIOCHEMICAL AND BIOLOGICAL ANALYSIS