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(-) Description

Title :  STRUCTURE OF ARABIDOPSIS ATSERPIN1. NATIVE STRESSED CONFORMATION
 
Authors :  S. J. Harrop, T. V. Joss, P. M. G. Cumi, T. H. Roberts
Date :  14 Jan 10  (Deposition) - 23 Feb 10  (Release) - 12 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Plant Serpin Serpin-Zx Arathzx Serpin-1 Atserpin1, Apoplast, Glycoprotein, Protease Inhibitor, Secreted, Serine Protease Inhibitor, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Lampl, O. Budai-Hadrian, O. Davydov, T. V. Joss, S. J. Harrop, P. M. Curmi, T. H. Roberts, R. Fluhr
Arabidopsis Atserpin1, Crystal Structure And In Vivo Interaction With Its Target Protease Responsive To Desiccation-21 (Rd21).
J. Biol. Chem. V. 285 13550 2010
PubMed-ID: 20181955  |  Reference-DOI: 10.1074/JBC.M109.095075

(-) Compounds

Molecule 1 - SERPIN-ZX
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: AT1G47710, F16N3.3, SERPIN-ZX, T2E6.22
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: ARATHZX, SERPIN-1, ATSERPIN1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:213 , TYR A:215 , ASP A:216 , HOH A:405 , HOH A:420 , HOH A:447 , HOH A:452 , HOH A:594 , HOH A:636BINDING SITE FOR RESIDUE SO4 A 392
2AC2SOFTWARESER A:235 , TYR A:237 , PRO A:266 , HOH A:563 , HOH A:650BINDING SITE FOR RESIDUE ACT A 393
3AC3SOFTWAREGLY A:89 , PRO A:90 , LYS A:174 , GLY A:175 , THR A:176 , HOH A:633BINDING SITE FOR RESIDUE ACT A 394
4AC4SOFTWARESER A:344 , GLY A:346 , VAL A:347 , ILE A:348 , LYS A:349BINDING SITE FOR RESIDUE GOL A 395

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LE2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LE2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LE2)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SERPINPS00284 Serpins signature.SPZX_ARATH362-372  1A:362-372
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SERPINPS00284 Serpins signature.SPZX_ARATH362-372  1A:362-372
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SERPINPS00284 Serpins signature.SPZX_ARATH362-372  2A:362-372

(-) Exons   (0, 0)

(no "Exon" information available for 3LE2)

(-) 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:393
 aligned with SPZX_ARATH | Q9S7T8 from UniProtKB/Swiss-Prot  Length:391

    Alignment length:393
                              1                                                                                                                                                                                                                                                                                                                                                                                                      
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388   
           SPZX_ARATH     - --MDVRESISLQNQVSMNLAKHVITTVSQNSNVIFSPASINVVLSIIAAGSAGATKDQILSFLKFSSTDQLNSFSSEIVSAVLADGSANGGPKLSVANGAWIDKSLSFKPSFKQLLEDSYKAASNQADFQSKAVEVIAEVNSWAEKETNGLITEVLPEGSADSMTKLIFANALYFKGTWNEKFDESLTQEGEFHLLDGNKVTAPFMTSKKKQYVSAYDGFKVLGLPYLQGQDKRQFSMYFYLPDANNGLSDLLDKIVSTPGFLDNHIPRRQVKVREFKIPKFKFSFGFDASNVLKGLGLTSPFSGEEGLTEMVESPEMGKNLCVSNIFHKACIEVNEEGTEAAAASAGVIKLRGLLMEEDEIDFVADHPFLLVVTENITGVVLFIGQVVDPLH 391
               SCOP domains d3le2a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------Serpin-3le2A01 A:8-389                                                                                                                                                                                                                                                                                                                                                                        -- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhh......eeehhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhh..eeeeeeeeeee.....hhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhh..................eeeeeeeeee.......hhhhheeeeee.....eeeeeeee....eeeeee..eeeeeee.........eeeeeeee....hhhhhhhhhhhh..hhhhh....eeeeeeeeee.eeeeeeeehhhhhhhh..hhhhh..........hhhhhh.....eeeeeeeeee............hhhhhhh......eeeee....eeeeeee.....eeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SERPIN     ------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3le2 A  -1 AGMDVRESISLQNQVSMNLAKHVITTVSQNSNVIFSPASINVVLSIIAAGSAGATKDQILSFLKFSSTDQLNSFSSEIVSAVLADGSANGGPKLSVANGAWIDKSLSFKPSFKQLLEDSYKAASNQADFQSKAVEVIAEVNSWAEKETNGLITEVLPEGSADSMTKLIFANALYFKGTWNEKFDESLTQEGEFHLLDGNKVTAPFMTSKKKQYVSAYDGFKVLGLPYLQGQDKRQFSMYFYLPDANNGLSDLLDKIVSTPGFLDNHIPRRQVKVREFKIPKFKFSFGFDASNVLKGLGLTSPFSGEEGLTEMVESPEMGKNLCVSNIFHKACIEVNEEGTEAAAASAGVIKLRGLLMEEDEIDFVADHPFLLVVTENITGVVLFIGQVVDPLH 391
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388
   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 Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LE2)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: Serpin] (63)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (SPZX_ARATH | Q9S7T8)
molecular function
    GO:0004869    cysteine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of a cysteine-type endopeptidase, any enzyme that hydrolyzes peptide bonds in polypeptides by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    GO:0004867    serine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
cellular component
    GO:0048046    apoplast    The cell membranes and intracellular regions in a plant are connected through plasmodesmata, and plants may be described as having two major compartments: the living symplast and the non-living apoplast. The apoplast is external to the plasma membrane and includes cell walls, intercellular spaces and the lumen of dead structures such as xylem vessels. Water and solutes pass freely through it.
    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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  3le2
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  SPZX_ARATH | Q9S7T8
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