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(-) Description

Title :  DISTAL C2-LIKE DOMAIN OF HUMAN CALPAIN-7
 
Authors :  J. R. Walker, D. Cuerrier, R. Ravulapalli, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon
Date :  27 Jun 07  (Deposition) - 10 Jul 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A
Keywords :  C2-Like Domain, Hydrolase; Nuclear Protein; Protease; Thiol Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. R. Walker, D. Cuerrier, R. Ravulapalli, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon
Structure Of The C2 Domain Of Human Calpain-7
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CALPAIN-7
    ChainsA
    EC Number3.4.22.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28A-LIC
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentDISTAL C2-LIKE DOMAIN
    GeneCAPN7, PALBH
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPALB HOMOLOG, PALBH

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 18)

Asymmetric/Biological Unit (1, 18)
No.NameCountTypeFull Name
1BR18Ligand/IonBROMIDE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:736 , ASN A:783BINDING SITE FOR RESIDUE BR A 1
02AC2SOFTWAREHOH A:56 , ARG A:732BINDING SITE FOR RESIDUE BR A 3
03AC3SOFTWAREARG A:691 , ARG A:732 , PHE A:798BINDING SITE FOR RESIDUE BR A 4
04AC4SOFTWARESER A:676BINDING SITE FOR RESIDUE BR A 5
05AC5SOFTWARELYS A:690 , ILE A:809BINDING SITE FOR RESIDUE BR A 7
06AC6SOFTWAREHOH A:93BINDING SITE FOR RESIDUE BR A 8
07AC7SOFTWAREHOH A:37 , HOH A:161 , ASN A:776BINDING SITE FOR RESIDUE BR A 9
08AC8SOFTWAREARG A:759BINDING SITE FOR RESIDUE BR A 10
09AC9SOFTWAREHOH A:34 , SER A:762 , ASP A:764 , ARG A:766BINDING SITE FOR RESIDUE BR A 11
10BC1SOFTWARETYR A:765BINDING SITE FOR RESIDUE BR A 12
11BC2SOFTWAREPHE A:707 , GLN A:708 , GLU A:709BINDING SITE FOR RESIDUE BR A 13
12BC3SOFTWAREGLN A:708 , LYS A:712 , GLU A:773BINDING SITE FOR RESIDUE BR A 14
13BC4SOFTWAREGLN A:811BINDING SITE FOR RESIDUE BR A 15
14BC5SOFTWAREHOH A:64 , HOH A:98 , HOH A:124 , CYS A:767BINDING SITE FOR RESIDUE BR A 16
15BC6SOFTWAREGLN A:699BINDING SITE FOR RESIDUE BR A 17
16BC7SOFTWARELYS A:760 , SER A:761BINDING SITE FOR RESIDUE BR A 18

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2QFE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000002536931cENSE00000901305chr3:15247750-15248104355CAN7_HUMAN1-34340--
1.3ENST000002536933ENSE00001772143chr3:15253611-15253719109CAN7_HUMAN35-71370--
1.4bENST000002536934bENSE00001772477chr3:15258932-15259089158CAN7_HUMAN71-123530--
1.5ENST000002536935ENSE00001641121chr3:15259980-1526004768CAN7_HUMAN124-146230--
1.6aENST000002536936aENSE00001149507chr3:15262288-15262488201CAN7_HUMAN146-213680--
1.7ENST000002536937ENSE00001713631chr3:15264982-1526506887CAN7_HUMAN213-242300--
1.8aENST000002536938aENSE00001700421chr3:15269346-15269472127CAN7_HUMAN242-284430--
1.9ENST000002536939ENSE00001803695chr3:15270481-1527056686CAN7_HUMAN285-313290--
1.10ENST0000025369310ENSE00001665389chr3:15271949-1527204294CAN7_HUMAN313-344320--
1.12ENST0000025369312ENSE00001653102chr3:15274026-15274172147CAN7_HUMAN345-393490--
1.13ENST0000025369313ENSE00001776600chr3:15275374-15275480107CAN7_HUMAN394-429360--
1.14ENST0000025369314ENSE00001731020chr3:15276532-15276652121CAN7_HUMAN429-469410--
1.15bENST0000025369315bENSE00001780897chr3:15281980-15282124145CAN7_HUMAN470-518490--
1.16ENST0000025369316ENSE00001640361chr3:15282261-15282360100CAN7_HUMAN518-551340--
1.17ENST0000025369317ENSE00000901319chr3:15282960-15283095136CAN7_HUMAN551-596460--
1.18ENST0000025369318ENSE00001605792chr3:15283685-1528376076CAN7_HUMAN597-622260--
1.19ENST0000025369319ENSE00001796602chr3:15287033-15287178146CAN7_HUMAN622-670491A:675-6839
1.20bENST0000025369320bENSE00001772398chr3:15288239-1528830163CAN7_HUMAN671-691211A:684-6918
1.21bENST0000025369321bENSE00001628583chr3:15288834-15288964131CAN7_HUMAN692-735441A:692-73544
1.22aENST0000025369322aENSE00000901324chr3:15292438-1529253093CAN7_HUMAN735-766321A:735-76632
1.23dENST0000025369323dENSE00001241433chr3:15292623-152944251803CAN7_HUMAN766-813481A:766-81348

(-) 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:139
 aligned with CAN7_HUMAN | Q9Y6W3 from UniProtKB/Swiss-Prot  Length:813

    Alignment length:164
                                   659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809    
           CAN7_HUMAN   650 HTFTLVVSQYEKQNTIHYTVRVYSACSFTFSKIPSPYTLSKRINGKWSGQSAGGCGNFQETHKNNPIYQFHIEKTGPLLIELRGPRQYSVGFEVVTVSTLGDPGPHGFLRKSSGDYRCGFCYLELENIPSGIFNIIPSTFLPKQEGPFFLDFNSIIPIKITQLQ 813
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------Calpain_III-2qfeA01 A:687-810                                                                                               --- Pfam domains
         Sec.struct. author .........-------------------------....eeeeeeeeehhhhh........hhhhh..eeeee...eeeeeeee.....eeeeeeeeee...........eee....ee.eeeeeeeee..eeeeeeeee......eeeeeeeee....eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.19            Exon 1.20b           Exon 1.21b  PDB: A:692-735 UniProt: 692-735 ------------------------------Exon 1.23d  PDB: A:766-813 UniProt: 766-813      Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------Exon 1.22a  PDB: A:735-766      ----------------------------------------------- Transcript 1 (2)
                 2qfe A 675 HSSGLVPRG-------------------------SPYTLSKRINGKWSGQSAGGCGNFQETHKNNPIYQFHIEKTGPLLIELRGPRQYSVGFEVVTVSTLGDPGPHGFLRKSSGDYRCGFCYLELENIPSGIFNIIPSTFLPKQEGPFFLDFNSIIPIKITQLQ 813
                                    |-         -         -    |  689       699       709       719       729       739       749       759       769       779       789       799       809    
                                  683                       684                                                                                                                                 

   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 2QFE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CAN7_HUMAN | Q9Y6W3)
molecular function
    GO:0090541    MIT domain binding    Interacting selectively and non-covalently with the MIT domain of a protein. The MIT domain is found in vacuolar sorting proteins, spastin (probable ATPase involved in the assembly or function of nuclear protein complexes), and a sorting nexin, which may play a role in intracellular trafficking.
    GO:0004198    calcium-dependent cysteine-type endopeptidase activity    Catalysis of the hydrolysis of nonterminal peptide bonds in a polypeptide chain by a mechanism using a cysteine residue at the enzyme active center, and requiring the presence of calcium.
    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:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    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: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:0010634    positive regulation of epithelial cell migration    Any process that activates or increases the frequency, rate or extent of epithelial cell migration.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0097264    self proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their own peptide bonds.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

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