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(-) Description

Title :  CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 3 (UCHL3)
 
Authors :  W. A. Weihofen, K. Artavanis-Tsakonas, R. Gaudet, H. L. Ploegh
Date :  27 Mar 09  (Deposition) - 29 Dec 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.42
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cystein Proteinase, Deneddylating Enzyme, Ubiquitin Isopeptidase, Deubiquitinating Enzyme, Hydrolase, Peptidase_c12, Uch-L Superfamily (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Artavanis-Tsakonas, W. A. Weihofen, J. M. Antos, B. I. Coleman, C. A. Comeaux, M. T. Duraisingh, R. Gaudet, H. L. Ploegh
Characterization And Structural Studies Of The Plasmodium Falciparum Ubiquitin And Nedd8 Hydrolase Uchl3.
J. Biol. Chem. V. 285 6857 2010
PubMed-ID: 20042598  |  Reference-DOI: 10.1074/JBC.M109.072405

(-) Compounds

Molecule 1 - UBIQUITIN CARBOXYL-TERMINAL HYDROLASE L3
    Chains: A, B
    EC Number: 3.4.19.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: MALARIA PARASITE
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 5833
    Strain: CLONE 3D7
    Synonym: UCHL3, UCH-L3, UBIQUITIN THIOLESTERASE

 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 2WE6)

(-) Sites  (0, 0)

(no "Site" information available for 2WE6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WE6)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gln A:47 -Pro A:48
2Gln B:47 -Pro B:48

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WE6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WE6)

(-) Exons   (0, 0)

(no "Exon" information available for 2WE6)

(-) 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:208
 aligned with Q8IKM8_PLAF7 | Q8IKM8 from UniProtKB/TrEMBL  Length:232

    Alignment length:224
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224    
         Q8IKM8_PLAF7     5 DIWTPLESNPDSLYLYSCKLGQSKLKFVDIYGFNNDLLDMIPQPVQAVIFLYPVNDNIVSENNTNDKHNLKENFDNVWFIKQYIPNSCGTIALLHLYGNLRNKFELDKDSVLDDFFNKVNEMSAEKRGQELKNNKSIENLHHEFCGQVENRDDILDVDTHFIVFVQIEGKIIELDGRKDHPTVHCFTNGDNFLYDTGKIIQDKFIEKCKDDLRFSALAVIPNDN 228
               SCOP domains d2we6a_ A: automated matches                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhh...eeeeee...hhhhhh.......eeeeeee.----------------................hhhhhhhhhhhhhhh........hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.......hhhhh....eeeeeeeee..eeeee.......eeeee....hhhhhhhhhhhhhh..........eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2we6 A   5 DIWTPLESNPDSLYLYSCKLGQSKLKFVDIYGFNNDLLDMIPQPVQAVIFLYPV----------------KENFDNVWFIKQYIPNSCGTIALLHLYGNLRNKFELDKDSVLDDFFNKVNEMSAEKRGQELKNNKSIENLHHEFCGQVENRDDILDVDTHFIVFVQIEGKIIELDGRKDHPTVHCFTNGDNFLYDTGKIIQDKFIEKCKDDLRFSALAVIPNDN 228
                                    14        24        34        44        54   |     -         -|       84        94       104       114       124       134       144       154       164       174       184       194       204       214       224    
                                                                                58               75                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:207
 aligned with Q8IKM8_PLAF7 | Q8IKM8 from UniProtKB/TrEMBL  Length:232

    Alignment length:224
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223    
         Q8IKM8_PLAF7     4 NDIWTPLESNPDSLYLYSCKLGQSKLKFVDIYGFNNDLLDMIPQPVQAVIFLYPVNDNIVSENNTNDKHNLKENFDNVWFIKQYIPNSCGTIALLHLYGNLRNKFELDKDSVLDDFFNKVNEMSAEKRGQELKNNKSIENLHHEFCGQVENRDDILDVDTHFIVFVQIEGKIIELDGRKDHPTVHCFTNGDNFLYDTGKIIQDKFIEKCKDDLRFSALAVIPND 227
               SCOP domains d2we6b_ B: automated matches                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Peptidase_C12-2we6B01 B:6-212                                                                                                                                                                                  --------------- Pfam domains (1)
           Pfam domains (2) --Peptidase_C12-2we6B02 B:6-212                                                                                                                                                                                  --------------- Pfam domains (2)
         Sec.struct. author .........hhhhhhhhhhhhh...eeeee....hhhhhh.......eeeeeee.-----------------...............hhhhhhhhhhhhhh.........hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh........hhhhhh..eeeeeeeee..eeeee.......eeeee....hhhhhhhhhhhhhh..........eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2we6 B   4 NDIWTPLESNPDSLYLYSCKLGQSKLKFVDIYGFNNDLLDMIPQPVQAVIFLYPV-----------------ENFDNVWFIKQYIPNSCGTIALLHLYGNLRNKFELDKDSVLDDFFNKVNEMSAEKRGQELKNNKSIENLHHEFCGQVENRDDILDVDTHFIVFVQIEGKIIELDGRKDHPTVHCFTNGDNFLYDTGKIIQDKFIEKCKDDLRFSALAVIPND 227
                                    13        23        33        43        53    |    -         -  |     83        93       103       113       123       133       143       153       163       173       183       193       203       213       223    
                                                                                 58                76
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WE6)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Peptidase_CA (169)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8IKM8_PLAF7 | Q8IKM8)
molecular function
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    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: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:0004843    thiol-dependent ubiquitin-specific protease activity    Catalysis of the thiol-dependent hydrolysis of a peptide bond formed by the C-terminal glycine of ubiquitin and another protein.
    GO:0036459    thiol-dependent ubiquitinyl hydrolase activity    Catalysis of the thiol-dependent hydrolysis of an ester, thioester, amide, peptide or isopeptide bond formed by the C-terminal glycine of ubiquitin.
    GO:0043130    ubiquitin binding    Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
biological process
    GO:0000338    protein deneddylation    The removal of a ubiquitin-like protein of the NEDD8 type from a protein.
    GO:0016579    protein deubiquitination    The removal of one or more ubiquitin groups from a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006511    ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0000151    ubiquitin ligase complex    A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex.

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(-) Related Entries Specified in the PDB File

2wdt CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM UCHL3 IN COMPLEX WITH THE SUICIDE INHIBITOR UBVME