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(-) Description

Title :  INVESTIGATION OF GLOBAL AND LOCAL EFFECTS OF RADIATION DAMAGE ON PORCINE PANCREATIC ELASTASE. SEVENTH STAGE OF RADIATION DAMAGE
 
Authors :  T. Petrova, S. Ginell, Y. Kim, G. Joachimiak, A. Joachimiak
Date :  22 Apr 10  (Deposition) - 05 May 10  (Release) - 03 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Radiation Damage, Disulfide Bridge, Atomic Resolution, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Petrova, S. Ginell, A. Mitschler, Y. Kim, V. Y. Lunin, G. Joachimiak A. Cousido-Siah, I. Hazemann, A. Podjarny, K. Lazarski, A. Joachimia
X-Ray-Induced Deterioration Of Disulfide Bridges At Atomic Resolution.
Acta Crystallogr. , Sect. D V. 66 1075 2010
PubMed-ID: 20944241  |  Reference-DOI: 10.1107/S0907444910033986

(-) Compounds

Molecule 1 - CHYMOTRYPSIN-LIKE ELASTASE FAMILY MEMBER 1
    ChainsA
    EC Number3.4.21.36
    Organism CommonPIGS,SWINE,WILD BOAR
    Organism ScientificSUS SCROFA
    Organism Taxid9823
    SynonymELASTASE-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:70 , ASN A:72 , GLN A:75 , ASN A:77 , GLU A:80 , HOH A:518 , HOH A:560BINDING SITE FOR RESIDUE NA A 280
2AC2SOFTWAREGLY A:127 , ARG A:145 , ARG A:230 , SER A:232 , ALA A:233 , HOH A:456 , HOH A:552 , HOH A:619BINDING SITE FOR RESIDUE SO4 A 290
3AC3SOFTWAREHIS A:57 , GLN A:192 , GLY A:193 , SER A:195 , HOH A:298 , HOH A:303 , HOH A:588 , HOH A:674 , HOH A:684 , HOH A:719BINDING SITE FOR RESIDUE SO4 A 295

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MO9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MO9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MO9)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.CELA1_PIG27-264  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.CELA1_PIG67-72  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.CELA1_PIG208-219  1A:189-200

(-) Exons   (0, 0)

(no "Exon" information available for 3MO9)

(-) 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:240
 aligned with CELA1_PIG | P00772 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:240
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266
           CELA1_PIG     27 VVGGTEAQRNSWPSQISLQYRSGSSWAHTCGGTLIRQNWVMTAAHCVDRELTFRVVVGEHNLNQNDGTEQYVGVQKIVVHPYWNTDDVAAGYDIALLRLAQSVTLNSYVQLGVLPRAGTILANNSPCYITGWGLTRTNGQLAQTLQQAYLPTVDYAICSSSSYWGSTVKNSMVCAGGDGVRSGCQGDSGGPLHCLVNGQYAVHGVTSFVSRLGCNVTRKPTVFTRVSAYISWINNVIASN  266
               SCOP domains d3mo9a_ A: Elastase                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains Trypsin-3mo9A01 A:16-238                                                                                                                                                                                                                 ------- Pfam domains
         Sec.struct. author ....ee........eeeeeeee..eeeeeeeeeeee..eeeehhhhhh....eeeee............eeeeeeeeee.......hhhhh...eeeee...........................eeeee..............eeee..eehhhhhh....hhhhh...eeee...............eeeeee..eeeeeeeeee............eeeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 27-264                                                                                                                                                                                                    -- PROSITE (1)
                PROSITE (2) ----------------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3mo9 A   16 VVGGTEAQRNSWPSQISLQYRSGSSWAHTCGGTLIRQNWVMTAAHCVDRELTFRVVVGEHNLNQNNGTEQYVGVQKIVVHPYWNTDDVAAGYDIALLRLAQSVTLNSYVQLGVLPRAGTILANNSPCYITGWGLTRTNGQLAQTLQQAYLPTVDYAICSSSSYWGSTVKNSMVCAGGDGVRSGCQGDSGGPLHCLVNGQYAVHGVTSFVSRLGCNVTRKPTVFTRVSAYISWINNVIASN  245
                                    25        35 |||    42        52        62   |    71        81        91       99B       109       119       129       139     ||150       160       170||     178       188|      197       207       217|    | 225       235       245
                                               36A||                           65A                                99A|                                           145|                    170A|               188A                          217A 221A                        
                                                36B|                                                               99B                                            147                     170B                                                                              
                                                 36C                                                                                                                                                                                                                        

   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 3MO9)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CELA1_PIG | P00772)
molecular function
    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:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    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:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    GO:0055123    digestive system development    The process whose specific outcome is the progression of the digestive system over time, from its formation to the mature structure. The digestive system is the entire structure in which digestion takes place. Digestion is all of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
    GO:0060309    elastin catabolic process    The chemical reactions and pathways resulting in the breakdown of elastin. Elastin is a glycoprotein which is randomly coiled and crosslinked to form elastic fibers that are found in connective tissue.
    GO:0031017    exocrine pancreas development    The process whose specific outcome is the progression of the exocrine pancreas over time, from its formation to the mature structure. The exocrine pancreas produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0035264    multicellular organism growth    The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0061113    pancreas morphogenesis    Morphogenesis of the pancreas. Morphogenesis is the process in which anatomical structures are generated and organized.
    GO:0045766    positive regulation of angiogenesis    Any process that activates or increases angiogenesis.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0009791    post-embryonic development    The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0045595    regulation of cell differentiation    Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0048771    tissue remodeling    The reorganization or renovation of existing tissues. This process can either change the characteristics of a tissue such as in blood vessel remodeling, or result in the dynamic equilibrium of a tissue such as in bone remodeling.
cellular component
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CELA1_PIG | P007721b0e 1bma 1btu 1c1m 1e34 1e35 1e36 1e37 1e38 1eai 1eas 1eat 1eau 1ela 1elb 1elc 1eld 1ele 1elf 1elg 1esa 1esb 1est 1fle 1fzz 1gvk 1gwa 1h9l 1hax 1hay 1haz 1hb0 1hv7 1inc 1jim 1l0z 1l1g 1lka 1lkb 1lvy 1mcv 1mmj 1nes 1okx 1qgf 1qix 1qnj 1qr3 1uo6 1uvo 1uvp 2a7c 2a7j 2bb4 2bd2 2bd3 2bd4 2bd5 2bd7 2bd8 2bd9 2bda 2bdb 2bdc 2blo 2blq 2cv3 2d26 2de8 2de9 2est 2fo9 2foa 2fob 2foc 2fod 2foe 2fof 2fog 2foh 2g4t 2g4u 2h1u 2iot 2oqu 2v0b 2v35 3e3t 3est 3hgn 3hgp 3mnb 3mnc 3mns 3mnx 3mo3 3mo6 3moc 3mty 3mu0 3mu1 3mu4 3mu5 3mu8 3odd 3odf 3uou 4est 4gvu 4ym9 5avd 5est 6est 7est 8est 9est

(-) Related Entries Specified in the PDB File

1gvk PORCINE PANCREATIC ELASTASE ACYL ENZYME AT 0.95 A RESOLUTION
3mnb INVESTIGATION OF GLOBAL AND LOCAL EFFECTS OF RADIATION DAMAGE ON PORCINE PANCREATIC ELASTASE. FIRST STAGE OF RADIATION DAMAGE
3mnc INVESTIGATION OF GLOBAL AND LOCAL EFFECTS OF RADIATION DAMAGE ON PORCINE PANCREATIC ELASTASE. SECOND STAGE OF RADIATION DAMAGE
3mns INVESTIGATION OF GLOBAL AND LOCAL EFFECTS OF RADIATION DAMAGE ON PORCINE PANCREATIC ELASTASE. THIRD STAGE OF RADIATION DAMAGE
3mnx INVESTIGATION OF GLOBAL AND LOCAL EFFECTS OF RADIATION DAMAGE ON PORCINE PANCREATIC ELASTASE. FOURTH STAGE OF RADIATION DAMAGE
3mo3 INVESTIGATION OF GLOBAL AND LOCAL EFFECTS OF RADIATION DAMAGE ON PORCINE PANCREATIC ELASTASE. FIFTH STAGE OF RADIATION DAMAGE
3mo6 INVESTIGATION OF GLOBAL AND LOCAL EFFECTS OF RADIATION DAMAGE ON PORCINE PANCREATIC ELASTASE. SIXTH STAGE OF RADIATION DAMAGE
3moc