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(-) Description

Title :  BIOLOGICAL AND STRUCTURAL FEATURES OF MURINE ANGIOGENIN-4, AN ANGIOGENIC PROTEIN
 
Authors :  B. Crabtree, D. E. Holloway, M. D. Baker, K. R. Acharya, V. Subramanian
Date :  05 Sep 06  (Deposition) - 20 Feb 07  (Release) - 21 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.02
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Angiogenesis, Endonuclease, Differentiation, Cancer, Nuclease, Hydrolase, Ribonuclease, Developmental Protein, Protein Synthesis Inhibitor, Pyrrolidone Carboxylic Acid (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Crabtree, D. E. Holloway, M. D. Baker, K. R. Acharya, V. Subramanian
Biological And Structural Features Of Murine Angiogenin-4, An Angiogenic Protein
Biochemistry V. 46 2431 2007
PubMed-ID: 17279775  |  Reference-DOI: 10.1021/BI062158N

(-) Compounds

Molecule 1 - ANGIOGENIN-4
    ChainsA, B
    EC Number3.1.27.5
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymMOUSE ANGIOGENIN-4

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2J4T)

(-) Sites  (0, 0)

(no "Site" information available for 2J4T)

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:25 -A:79
2A:38 -A:90
3A:56 -A:105
4B:25 -B:79
5B:38 -B:90
6B:56 -B:105

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:36 -Pro A:37
2Ser B:36 -Pro B:37

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J4T)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNASE_PANCREATICPS00127 Pancreatic ribonuclease family signature.ANG4_MOUSE62-68
 
  2A:38-44
B:38-44
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNASE_PANCREATICPS00127 Pancreatic ribonuclease family signature.ANG4_MOUSE62-68
 
  1A:38-44
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNASE_PANCREATICPS00127 Pancreatic ribonuclease family signature.ANG4_MOUSE62-68
 
  1-
B:38-44

(-) Exons   (0, 0)

(no "Exon" information available for 2J4T)

(-) Sequences/Alignments

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
(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:119
 aligned with ANG4_MOUSE | Q3TMQ6 from UniProtKB/Swiss-Prot  Length:144

    Alignment length:119
                                    35        45        55        65        75        85        95       105       115       125       135         
           ANG4_MOUSE    26 NERYEKFLRQHYDAKPNGRDDRYCESMMKERKLTSPCKDVNTFIHGTKKNIRAICGKKGSPYGENFRISNSPFQITTCTHSGASPRPPCGYRAFKDFRYIVIACEDGWPVHFDESFISP 144
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2j4tA00 A:2-120 P-30 Protein                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.......hhhhhhhhhhhh........eeeee...hhhhhhhhh..eee....eeee...eeeeeeee..........eeeeeeee..eeeee..eeeee.hhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------RNASE_P---------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 2j4t A   2 NERYEKFLRQHYDAKPQGRDDRYCESMMKERKLTSPCKDVNTFIHGTKKNIRAICGKKGSPYGENFRISNSPFQITTCTHSRGSPWPPCGYRAFKDFRYIVIACEDGWPVHFDESFISP 120
                                    11        21        31        41        51        61        71        81        91       101       111         

Chain B from PDB  Type:PROTEIN  Length:119
 aligned with ANG4_MOUSE | Q3TMQ6 from UniProtKB/Swiss-Prot  Length:144

    Alignment length:119
                                    35        45        55        65        75        85        95       105       115       125       135         
           ANG4_MOUSE    26 NERYEKFLRQHYDAKPNGRDDRYCESMMKERKLTSPCKDVNTFIHGTKKNIRAICGKKGSPYGENFRISNSPFQITTCTHSGASPRPPCGYRAFKDFRYIVIACEDGWPVHFDESFISP 144
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2j4tB00 B:2-120 P-30 Protein                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.......hhhhhhhhhhhh........eeeeee.hhhhhhhhhh..eee.....eee...eeeeeeee..........eeeeeeee..eeeee..eeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------RNASE_P---------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 2j4t B   2 NERYEKFLRQHYDAKPQGRDDRYCESMMKERKLTSPCKDVNTFIHGTKKNIRAICGKKGSPYGENFRISNSPFQITTCTHSRGSPWPPCGYRAFKDFRYIVIACEDGWPVHFDESFISP 120
                                    11        21        31        41        51        61        71        81        91       101       111         

   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 2J4T)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J4T)

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ANG4_MOUSE | Q3TMQ6)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    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:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0006401    RNA catabolic process    The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    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:0071222    cellular response to lipopolysaccharide    Any process that results in a change in state or activity of a cell (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:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
cellular component
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    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: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.
    GO:0030141    secretory granule    A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.

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