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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DUB DOMAIN OF HUMAN AMSH-LP
 
Authors :  Y. Sato, Y. Azusa, A. Yamagata, H. Mimura, X. Wang, M. Yamashita, K. Ookata, O. Nureki, K. Iwai, M. Komada, S. Fukai
Date :  01 May 08  (Deposition) - 02 Sep 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Metal Binding Protein, Alternative Splicing, Hydrolase, Metal-Binding, Metalloprotease, Protease, Ubl Conjugation Pathway, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Sato, A. Yoshikawa, A. Yamagata, H. Mimura, M. Yamashita, K. Ookata, O. Nureki, K. Iwai, M. Komada, S. Fukai
Structural Basis For Specific Cleavage Of Lys 63-Linked Polyubiquitin Chains
Nature V. 455 358 2008
PubMed-ID: 18758443  |  Reference-DOI: 10.1038/NATURE07254
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AMSH-LIKE PROTEASE
    Chains: A
    EC Number: 3.1.2.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCOLD GST
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: MPN DOMAIN, DUB DOMAIN, UNP RESIDUES 264-436
    Gene: STAMBPL1, AMSHLP, KIAA1373
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: AMSH-LP, STAM-BINDING PROTEIN-LIKE 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2PR1Ligand/IonPRASEODYMIUM ION
3ZN2Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:362 , CYS A:402 , HIS A:408 , HIS A:410BINDING SITE FOR RESIDUE ZN A 1
02AC2SOFTWAREHIS A:347 , HIS A:349 , ASP A:360 , HOH A:517BINDING SITE FOR RESIDUE ZN A 2
03AC3SOFTWAREASP A:274 , ASP A:427 , HOH A:705 , HOH A:706 , HOH A:707 , HOH A:708BINDING SITE FOR RESIDUE PR A 437
04AC4SOFTWARETYR A:322 , ASP A:324 , LYS A:429 , HOH A:454 , HOH A:538 , HOH A:630BINDING SITE FOR RESIDUE EDO A 438
05AC5SOFTWARELEU A:271 , PRO A:272 , GLU A:273 , LEU A:275 , CYS A:276BINDING SITE FOR RESIDUE EDO A 439
06AC6SOFTWARECYS A:420 , VAL A:423 , HOH A:469 , HOH A:470 , HOH A:557BINDING SITE FOR RESIDUE EDO A 3
07AC7SOFTWAREHIS A:262 , GLU A:264 , THR A:307 , HOH A:458 , HOH A:490 , HOH A:536BINDING SITE FOR RESIDUE EDO A 4
08AC8SOFTWAREARG A:267 , ASN A:304 , LEU A:369 , HOH A:477 , HOH A:656BINDING SITE FOR RESIDUE EDO A 5
09AC9SOFTWAREGLU A:284 , GLU A:305 , HOH A:606 , HOH A:655BINDING SITE FOR RESIDUE EDO A 6
10BC1SOFTWARELYS A:315 , PRO A:409 , ARG A:436 , HOH A:519BINDING SITE FOR RESIDUE EDO A 7

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:413 -Pro A:414

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ZNR)

(-) 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:178
 aligned with STALP_HUMAN | Q96FJ0 from UniProtKB/Swiss-Prot  Length:436

    Alignment length:247
                                   199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       
          STALP_HUMAN   190 ARGQMRSQQTSGLSEQIDGSALSCFSTHQNNSLLNVFADQPNKSDATNYASHSPPVNRALTPAATLSAVQNLVVEGLRCVVLPEDLCHKFLQLAESNTVRGIETCGILCGKLTHNEFTITHVIVPKQSAGPDYCDMENVEELFNVQDQHDLLTLGWIHTHPTQTAFLSSVDLHTHCSYQLMLPEAIAIVCSPKHKDTGIFRLTNAGMLEVSACKKKGFHPHTKEPRLFSICKHVLVKDIKIIVLDLR 436
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------JAB-2znrA01 A:264-373                                                                                         --------------------------------------------------------------- Pfam domains
         Sec.struct. author .....---------------------------------------------------------------------.....eeee.hhhhhhhhhhhhhhh.....eeeeeeeee..eeeeeeeee..eeee..eeee.hhhhhhhhhhhhh.eeeeeeee........hhhhhhhhhhhhhhh...eeeeeehhhheeeeeeehhhhhhhhhhh..............eee...eeee....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2znr A 259 GPGHM---------------------------------------------------------------------EGLRCVVLPEDLCHKFLQLAESNTVRGIETCGILCGKLTHNEFTITHVIVPKQSAGPDYCDMENVEELFNVQDQHDLLTLGWIHTHPTQTAFLSSVDLHTHCSYQLMLPEAIAIVCSPKHKDTGIFRLTNAGMLEVSACKKKGFHPHTKEPRLFSICKHVLVKDIKIIVLDLR 436
                                |    -         -         -         -         -         -         -    |  269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       
                              263                                                                   264
   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  (0, 0)

(no "SCOP Domain" information available for 2ZNR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: JAB (8)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (STALP_HUMAN | Q96FJ0)
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:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    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).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  Cis Peptide Bonds
    Glu A:413 - Pro A:414   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        STALP_HUMAN | Q96FJ0: 2znv

(-) Related Entries Specified in the PDB File

2znv THE SAME PROTEIN IN COMPLEX WITH UBIQUITIN