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(-) Description

Title :  CATALYTIC DOMAIN OF HUMAN CALPAIN-9
 
Authors :  J. R. Walker, T. Davis, E. M. Newman, F. Mackenzie, A. Dong, J. Choe, C. Arrowsmith, M. Sundstrom, A. Edwards, A. Bochkarev, S. Dhe- Paganon, Structural Genomics Consortium (Sgc)
Date :  27 Apr 05  (Deposition) - 05 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym./Biol. Unit :  A
Keywords :  Cysteine Protease, Papain, Calcium-Dependent, Thiol Protease, Structural Genomics Consortium, Sgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. L. Davis, J. R. Walker, P. J. Finerty, F. Mackenzie, E. M. Newman, S. Dhe-Paganon
The Crystal Structures Of Human Calpains 1 And 9 Imply Diverse Mechanisms Of Action And Auto-Inhibition.
J. Mol. Biol. V. 366 216 2007
PubMed-ID: 17157313  |  Reference-DOI: 10.1016/J.JMB.2006.11.037
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CALPAIN 9
    ChainsA
    EC Number3.4.22.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET28-LIC
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentCALPAIN CATALYTIC DOMAIN
    GeneCAPN9, NCL4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDIGESTIVE TRACT-SPECIFIC CALPAIN, NCL-4, CG36 PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1BME2Ligand/IonBETA-MERCAPTOETHANOL
2CA2Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:284 , ASP A:291 , LEU A:312 , ASP A:314 , GLU A:316BINDING SITE FOR RESIDUE CA A 1
2AC2SOFTWARELEU A:81 , GLY A:83 , ASP A:88 , GLU A:167 , HOH A:389BINDING SITE FOR RESIDUE CA A 2
3AC3SOFTWAREGLY A:95 , CYS A:97 , LEU A:100 , GLU A:174 , HOH A:376BINDING SITE FOR RESIDUE BME A 3
4AC4SOFTWAREGLU A:197 , THR A:200 , GLY A:202 , VAL A:203 , CYS A:334 , ASN A:335BINDING SITE FOR RESIDUE BME A 4

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZIV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ZIV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 8)

Asymmetric/Biological Unit (8, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_022188A102VCAN9_HUMANPolymorphism12562749AA102V
2UniProtVAR_022189S122RCAN9_HUMANPolymorphism28359608AS122R
3UniProtVAR_022190D164NCAN9_HUMANPolymorphism28359632AD164N
4UniProtVAR_022191I234TCAN9_HUMANPolymorphism28359644AI234T
5UniProtVAR_022192A239TCAN9_HUMANPolymorphism28359647AA239T
6UniProtVAR_022193R277WCAN9_HUMANPolymorphism28359655AR277W
7UniProtVAR_022194K322QCAN9_HUMANPolymorphism1933631AK322Q
8UniProtVAR_022195H327QCAN9_HUMANPolymorphism28359684AH327Q

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CALPAIN_CATPS50203 Cysteine proteinase, calpain-type, catalytic domain profile.CAN9_HUMAN42-337  1A:42-337
2THIOL_PROTEASE_CYSPS00139 Eukaryotic thiol (cysteine) proteases cysteine active site.CAN9_HUMAN91-102  1A:91-102

(-) Exons   (9, 9)

Asymmetric/Biological Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002719711aENSE00001070036chr1:230883130-230883455326CAN9_HUMAN1-71711A:28-71 (gaps)44
1.2ENST000002719712ENSE00000921431chr1:230891083-23089115270CAN9_HUMAN72-95241A:72-9524
1.3ENST000002719713ENSE00000961374chr1:230895258-230895376119CAN9_HUMAN95-134401A:95-13440
1.4ENST000002719714ENSE00000961375chr1:230898399-230898532134CAN9_HUMAN135-179451A:135-17945
1.5ENST000002719715ENSE00000961376chr1:230903287-230903455169CAN9_HUMAN179-235571A:179-23557
1.6ENST000002719716ENSE00000961377chr1:230904926-23090500984CAN9_HUMAN236-263281A:236-26328
1.7ENST000002719717ENSE00000961378chr1:230907760-23090784586CAN9_HUMAN264-292291A:264-29229
1.8ENST000002719718ENSE00000961379chr1:230910300-23091037778CAN9_HUMAN292-318271A:292-31827
1.9ENST000002719719ENSE00000961380chr1:230914719-230914879161CAN9_HUMAN318-372551A:318-33720
1.10ENST0000027197110ENSE00000961381chr1:230915925-230916082158CAN9_HUMAN372-424530--
1.11ENST0000027197111ENSE00000961382chr1:230916246-230916454209CAN9_HUMAN425-494700--
1.12ENST0000027197112ENSE00000961383chr1:230921727-23092176337CAN9_HUMAN494-506130--
1.13ENST0000027197113ENSE00000961384chr1:230923268-23092334881CAN9_HUMAN507-533270--
1.14ENST0000027197114ENSE00000961385chr1:230925878-23092593558CAN9_HUMAN534-553200--
1.15aENST0000027197115aENSE00000961386chr1:230927610-23092767465CAN9_HUMAN553-574220--
1.16ENST0000027197116ENSE00000961387chr1:230928172-23092824069CAN9_HUMAN575-597230--
1.17ENST0000027197117ENSE00000961388chr1:230928596-23092867479CAN9_HUMAN598-624270--
1.18ENST0000027197118ENSE00000961389chr1:230930909-230931025117CAN9_HUMAN624-663400--
1.19ENST0000027197119ENSE00001416134chr1:230933908-23093396659CAN9_HUMAN663-682200--
1.20bENST0000027197120bENSE00001414530chr1:230937316-230937518203CAN9_HUMAN683-69080--

(-) 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:308
 aligned with CAN9_HUMAN | O14815 from UniProtKB/Swiss-Prot  Length:690

    Alignment length:310
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337
           CAN9_HUMAN    28 SFEQMRQECLQRGTLFEDADFPASNSSLFYSERPQIPFVWKRPGEIVKNPEFILGGATRTDICQGELGDCWLLAAIASLTLNQKALARVIPQDQSFGPGYAGIFHFQFWQHSEWLDVVIDDRLPTFRDRLVFLHSADHNEFWSALLEKAYAKLNGSYEALKGGSAIEAMEDFTGGVAETFQTKEAPENFYEILEKALKRGSLLGCFIDTRSAAESEARTPFGLIKGHAYSVTGIDQVSFRGQRIELIRIRNPWGQVEWNGSWSDSSPEWRSVGPAEQKRLCHTALDDGEFWMAFKDFKAHFDKVEICNLT 337
               SCOP domains d1ziva1 A:28-337 Calpain large   subunit, catalytic domain (domain II)                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------Peptidase_C2-1ziv  A01 A:42-337                                                                                                                                                                                                                                                                          Pfam domains
         Sec.struct. author hhhhhhhhhhhh...........hhhhh...--.....eeehhhhh...........hhhhh........hhhhhhhhhhhhhhhhhhhh............eeeeeee....eeeeeee..eee...............hhhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhh...eeee.hhh..hhhhhhhhhhhhh.eeeee....hhhhh.............eeeeeeeeeee..eeeeeeeee...............hhhhhhhhhhhhhhh........eeeeehhhhhhhh.eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------V-------------------R-----------------------------------------N---------------------------------------------------------------------T----T-------------------------------------W--------------------------------------------Q----Q---------- SAPs(SNPs)
                PROSITE (1) --------------CALPAIN_CAT  PDB: A:42-337 UniProt: 42-337                                                                                                                                                                                                                                                               PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1a  PDB: A:28-71 (gaps) UniProt: 1-71Exon 1.2  PDB: A:72-95  ---------------------------------------Exon 1.4  PDB: A:135-179 UniProt: 135-179    --------------------------------------------------------Exon 1.6  PDB: A:236-263    Exon 1.7  PDB: A:264-292     -------------------------Exon 1.9             Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------Exon 1.3  PDB: A:95-134 UniProt: 95-134 --------------------------------------------Exon 1.5  PDB: A:179-235 UniProt: 179-235                --------------------------------------------------------Exon 1.8  PDB: A:292-318   ------------------- Transcript 1 (2)
                 1ziv A  28 SFEQMRQECLQRGTLFEDADFPASNSSLFYS--PQIPFVWKRPGEIVKNPEFILGGATRTDICQGELGDCWLLAAIASLTLNQKALARVIPQDQSFGPGYAGIFHFQFWQHSEWLDVVIDDRLPTFRDRLVFLHSADHNEFWSALLEKAYAKLNGSYEALKGGSAIEAMEDFTGGVAETFQTKEAPENFYEILEKALKRGSLLGCFIDTRSAAESEARTPFGLIKGHAYSVTGIDQVSFRGQRIELIRIRNPWGQVEWNGSWSDSSPEWRSVGPAEQKRLCHTALDDGEFWMAFKDFKAHFDKVEICNLT 337
                                    37        47        57|  |    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337
                                                         58 61                                                                                                                                                                                                                                                                                    

   Legend:   → Mismatch (orange background)
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    → 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/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ZIV)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CAN9_HUMAN | O14815)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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: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.
biological process
    GO:0007586    digestion    The whole 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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CAN9_HUMAN | O148152p0r

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