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(-) Description

Title :  CRYSTAL STRUCTURE OF ACTIVE LEGUMAIN IN COMPLEX WITH YVAD-CMK AT PH 5.0
 
Authors :  E. Dall, H. Brandstetter
Date :  01 Jun 12  (Deposition) - 26 Jun 13  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,I
Keywords :  Hydrolase-Hydrolase Inhibitor Complex, Cysteine Protease, Lysosomal, Aep, Substrate Specificity, Mhcii, Antigen Processing, Cancer (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Dall, H. Brandstetter
Mechanistic And Structural Studies On Legumain Explain Its Zymogenicity, Distinct Activation Pathways, And Regulation
Proc. Natl. Acad. Sci. Usa V. 110 10940 2013
PubMed-ID: 23776206  |  Reference-DOI: 10.1073/PNAS.1300686110

(-) Compounds

Molecule 1 - LEGUMAIN
    ChainsA
    EC Number3.4.22.34
    EngineeredYES
    Expression SystemLEISHMANIA TARENTOLAE
    Expression System StrainP10
    Expression System Taxid5689
    FragmentCATALYTIC DOMAIN, RESIDUES 26-309
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymASPARAGINYL ENDOPEPTIDASE, PROTEASE, CYSTEINE 1
 
Molecule 2 - YVAD-CMK
    ChainsI
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
10QE1Mod. Amino AcidCHLOROMETHANE
2ACE1Mod. Amino AcidACETYL GROUP
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:252 , HIS A:256 , GLN A:269BINDING SITE FOR RESIDUE SO4 A 312
2AC2SOFTWAREARG A:58 , LYS A:224 , ARG A:225 , NAG A:407 , HOH A:2035 , HOH A:2111BINDING SITE FOR RESIDUE SO4 A 313
3AC3SOFTWAREASN A:91 , ASP A:222 , VAL A:243 , ASP A:245 , SO4 A:313 , HOH A:2036BINDING SITE FOR MONO-SACCHARIDE NAG A 407 BOUND TO ASN A 91
4AC4SOFTWAREASN A:167 , HIS A:197 , PRO A:199 , HOH A:2084 , HOH A:2108BINDING SITE FOR MONO-SACCHARIDE NAG A 405 BOUND TO ASN A 167
5AC5SOFTWARELYS A:181 , ASP A:200 , ASN A:201 , ASN A:272 , HOH A:2109 , HOH A:2110BINDING SITE FOR MONO-SACCHARIDE NAG A 406 BOUND TO ASN A 272
6AC6SOFTWAREARG A:44 , HIS A:45 , GLU A:122 , ALA A:123 , LYS A:125 , ASP A:147 , HIS A:148 , GLY A:149 , SER A:150 , THR A:151 , GLU A:187 , CYS A:189 , GLU A:190 , ARG A:213 , SER A:216 , TYR A:217 , ALA A:218 , TYR A:228 , ASP A:231 , TRP A:232 , HOH A:2066 , HOH I:2001BINDING SITE FOR CHAIN I OF YVAD-CMK

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AWA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AWA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AWA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AWA)

(-) Exons   (0, 0)

(no "Exon" information available for 4AWA)

(-) 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:263
 aligned with LGMN_HUMAN | Q99538 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:263
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285   
           LGMN_HUMAN    26 GGKHWVVIVAGSNGWYNYRHQADACHAYQIIHRNGIPDEQIVVMMYDDIAYSEDNPTPGIVINRPNGTDVYQGVPKDYTGEDVTPQNFLAVLRGDAEAVKGIGSGKVLKSGPQDHVFIYFTDHGSTGILVFPNEDLHVKDLNETIHYMYKHKMYRKMVFYIEACESGSMMNHLPDNINVYATTAANPRESSYACYYDEKRSTYLGDWYSVNWMEDSDVEDLTKETLHKQYHLVKSHTNTSHVMQYGNKTISTMKVMQFQGMKR 288
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee......hhhhhhhhhhhhhhhhhh..hhh.eeee.......................................hhhhhhhhhhh....................eeeeeee..ee..eee....eeehhhhhhhhhhhhhh....eeeeeee..hhhhhh........eeeee.........eeeee....eeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhh.....eeee.hhhhhh.hhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4awa A  26 GGKHWVVIVAGSNGWYNYRHQADACHAYQIIHRNGIPDEQIVVMMYDDIAYSEDNPTPGIVINRPNGTDVYQGVPKDYTGEDVTPQNFLAVLRGDAEAVKGIGSGKVLKSGPQDHVFIYFTDHGSTGILVFPNEDLHVKDLNETIHYMYKHKMYRKMVFYIEACESGSMMNHLPDNINVYATTAANPRESSYACYYDEKRSTYLGDWYSVNWMEDSDVEDLTKETLHKQYHLVKSHTQTSHVMQYGNKTISTMKVMQFQGMKR 288
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285   

Chain I from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 4awa I 300 xYVADx 305
                            |    |
                          300-ACE|
                               305-0QE

   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 4AWA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AWA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AWA)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LGMN_HUMAN | Q99538)
molecular function
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-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: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.
biological process
    GO:0019886    antigen processing and presentation of exogenous peptide antigen via MHC class II    The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.
    GO:1901185    negative regulation of ERBB signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of ERBB signaling pathway.
    GO:0040015    negative regulation of multicellular organism growth    Any process that stops, prevents, or reduces the frequency, rate or extent of growth of an organism to reach its usual body size.
    GO:0043524    negative regulation of neuron apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0051603    proteolysis involved in cellular protein catabolic process    The hydrolysis of a peptide bond or bonds within a protein as part of the chemical reactions and pathways resulting in the breakdown of a protein by individual cells.
    GO:0032801    receptor catabolic process    The chemical reactions and pathways resulting in the breakdown of a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0003014    renal system process    A organ system process carried out by any of the organs or tissues of the renal system. The renal system maintains fluid balance, and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels; in other species, the renal system may comprise related structures (e.g., nephrocytes and malpighian tubules in Drosophila).
    GO:0010447    response to acidic pH    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus with pH < 7. pH is a measure of the acidity or basicity of an aqueous solution.
    GO:0002224    toll-like receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a toll-like receptor. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.
    GO:0006624    vacuolar protein processing    Protein processing that takes place in the vacuole. Most protein processing in the vacuole represents proteolytic cleavage of precursors to form active enzymes.
    GO:0042359    vitamin D metabolic process    The chemical reactions and pathways involving vitamin D, any of a group of related, fat-soluble compounds that are derived from delta-5,7 steroids and play a central role in calcium metabolism. Specific forms of vitamin D include calciferol (ergocalciferol; vitamin D2) and cholecalciferol (calciol; vitamin D3).
cellular component
    GO:0045177    apical part of cell    The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue.
    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:0005770    late endosome    A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
    GO:0043202    lysosomal lumen    The volume enclosed within the lysosomal membrane.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LGMN_HUMAN | Q995384aw9 4awb 4fgu 4n6n 4n6o 5lu8 5lu9 5lua 5lub

(-) Related Entries Specified in the PDB File

4aw9 CRYSTAL STRUCTURE OF ACTIVE LEGUMAIN IN COMPLEX WITH YVAD-CMK
4awb CRYSTAL STRUCTURE OF ACTIVE LEGUMAIN IN COMPLEX WITH AAN-CMK
4fgu CRYSTAL STRUCTURE OF PROLEGUMAIN