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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LYSOSOMAL 66.3 KDA PROTEIN FROM MOUSE SOLVED BY S-SAD
 
Authors :  K. Lakomek, A. Dickmanns, U. Mueller, R. Ficner
Date :  20 Nov 08  (Deposition) - 03 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Alpha Beta, Glycosylated, Disulphide Bonds, Oxidized Cysteine, Glycoprotein, Hydrolase, Lipid Degradation, Lysosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Lakomek, A. Dickmanns, U. Mueller, K. Kollmann, F. Deuschl, A. Berndt, T. Lubke, R. Ficner
De Novo Sulfur Sad Phasing Of The Lysosomal 66. 3 Kda Protei From Mouse
Acta Crystallogr. , Sect. D V. 65 220 2009
PubMed-ID: 19237744  |  Reference-DOI: 10.1107/S0907444908041814

(-) Compounds

Molecule 1 - PUTATIVE PHOSPHOLIPASE B-LIKE 2
    Chains: A
    EC Number: 3.1.1.-
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell: FIBROSARCOMA CELL
    Expression System Cell Line: HT1080
    Expression System Common: HUMAN
    Expression System Plasmid: PCDNA3.1/HYGRO(+)
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: AAG44101
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: C3H/RV
    Synonym: 66.3 KDA PROTEIN, LAMINA ANCESTOR HOMOLOG 2, LAMA-LIKE PROTEIN 2, 76 KDA PROTEIN, P76, PUTATIVE PHOSPHOLIPASE B-LIKE 2 28 KDA FORM, PUTATIVE PHOSPHOLIPASE B-LIKE 2 40 KDA FORM, PUTATIVE PHOSPHOLIPASE B-LIKE 2 15 KDA FORM

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 15)

Asymmetric Unit (8, 15)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL3Ligand/IonGLYCEROL
3NA1Ligand/IonSODIUM ION
4NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
5OCS1Mod. Amino AcidCYSTEINESULFONIC ACID
6PG42Ligand/IonTETRAETHYLENE GLYCOL
7PGE1Ligand/IonTRIETHYLENE GLYCOL
8XE1Ligand/IonXENON
Biological Unit 1 (6, 26)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL6Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE
5OCS2Mod. Amino AcidCYSTEINESULFONIC ACID
6PG44Ligand/IonTETRAETHYLENE GLYCOL
7PGE2Ligand/IonTRIETHYLENE GLYCOL
8XE-1Ligand/IonXENON

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARENAG A:12 , ASN A:115 , PHE A:207 , HOH A:641 , HOH A:729BINDING SITE FOR RESIDUE NAG A 11
02AC2SOFTWARENAG A:11 , LEU A:71 , GLY A:76 , PHE A:207 , THR A:209BINDING SITE FOR RESIDUE NAG A 12
03AC3SOFTWARELYS A:159 , ASN A:236 , PG4 A:606BINDING SITE FOR RESIDUE NAG A 21
04AC4SOFTWAREASN A:441 , GLN A:446 , HOH A:862BINDING SITE FOR RESIDUE NAG A 31
05AC5SOFTWAREASN A:520BINDING SITE FOR RESIDUE NAG A 41
06AC6SOFTWARENAG A:21 , LYS A:159 , PHE A:163 , ALA A:234 , TRP A:339 , VAL A:342 , PRO A:344 , HOH A:800BINDING SITE FOR RESIDUE PG4 A 606
07AC7SOFTWAREASP A:363 , GLY A:364 , ALA A:365 , ASP A:369 , LYS A:372 , THR A:404 , VAL A:415 , ASP A:417 , HOH A:879BINDING SITE FOR RESIDUE PG4 A 23
08AC8SOFTWAREASN A:167 , CYS A:347 , LEU A:349BINDING SITE FOR RESIDUE XE A 607
09AC9SOFTWAREASP A:369 , VAL A:370 , ARG A:373 , HOH A:618BINDING SITE FOR RESIDUE GOL A 1
10BC1SOFTWAREGLY A:148 , GLU A:151 , VAL A:154BINDING SITE FOR RESIDUE ACT A 608
11BC2SOFTWAREHIS A:138 , LEU A:222 , SER A:225 , ASN A:270 , ASN A:274 , TYR A:307 , THR A:310 , HOH A:830BINDING SITE FOR RESIDUE GOL A 2
12BC3SOFTWAREARG A:373 , ASP A:470 , ALA A:479 , ARG A:482 , LEU A:483BINDING SITE FOR RESIDUE GOL A 3
13BC4SOFTWAREGLN A:193 , TYR A:282 , LEU A:284 , GLY A:299 , LEU A:302 , TYR A:318 , VAL A:355 , ASN A:358 , ARG A:359 , HOH A:687BINDING SITE FOR RESIDUE PGE A 22
14BC5SOFTWAREOCS A:249 , ASP A:315 , GLU A:328 , THR A:330 , TYR A:379BINDING SITE FOR RESIDUE NA A 609

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:147 -A:157
2A:497 -A:500

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:75 -Gly A:76
2Asp A:315 -Asp A:316
3Asn A:501 -Pro A:502
4Val A:591 -Pro A:592

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FBX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FBX)

(-) Exons   (0, 0)

(no "Exon" information available for 3FBX)

(-) 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:520
 aligned with PLBL2_MOUSE | Q3TCN2 from UniProtKB/Swiss-Prot  Length:594

    Alignment length:530
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592
          PLBL2_MOUSE    63 VSRTRSLLLDAASGQLRLEDGFHPDAVAWANLTNAIRETGWAYLDLSTNGRYNDSLQAYAAGVVEASVSEELIYMHWMNTVVNYCGPFEYEVGYCEKLKNFLEANLEWMQREMELNPDSPYWHQVRLTLLQLKGLEDSYEGRLTFPTGRFTIKPLGFLLLQISGDLEDLEPALNKTNTKPSLGSGSCSALIKLLPGGHDLLVAHNTWNSYQNMLRIIKKYRLQFREGPQEEYPLVAGNNLVFSSYPGTIFSGDDFYILGSGLVTLETTIGNKNPALWKYVQPQGCVLEWIRNVVANRLALDGATWADVFKRFNSGTYNNQWMIVDYKAFLPNGPSPGSRVLTILEQIPGMVVVADKTAELYKTTYWASYNIPYFETVFNASGLQALVAQYGDWFSYTKNPRAKIFQRDQSLVEDMDAMVRLMRYNDFLHDPLSLCEACNPKPNAENAISARSDLNPANGSYPFQALHQRAHGGIDVKVTSFTLAKYMSMLAASGPTWDQCPPFQWSKSPFHSMLHMGQPDLWMFSPIRVP 592
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee......eeeee.......eeeeeeehhhhhh.eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhh...----------.eeeeee.hhhh.eeeeee.eee.hhh..eeeeee.................eeeeee..........eeee...eeeeeee....hhhhhhhh......hhhhhhhhhhhhh.hhhhhhhhhh........eeeeeee.hhh...........eeeeeee..eeeeeehhhhhhhhheeee.....hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhh......hhhhh................hhhhh.......hhhhh...eee.eeeeehhhhhhh..eeeee.........ee.hhh............ee....eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fbx A  63 VSRTRSLLLDAASGQLRLEDGFHPDAVAWANLTNAIRETGWAYLDLSTNGRYNDSLQAYAAGVVEASVSEELIYMHWMNTVVNYCGPFEYEVGYCEKLKNFLEANLEWMQREMELNPDSPYWHQVRLTLLQLKGLEDSYEGRLTFPTGRFTIKPLGFLLLQISGDLEDLEPALNKT----------cSALIKLLPGGHDLLVAHNTWNSYQNMLRIIKKYRLQFREGPQEEYPLVAGNNLVFSSYPGTIFSGDDFYILGSGLVTLETTIGNKNPALWKYVQPQGCVLEWIRNVVANRLALDGATWADVFKRFNSGTYNNQWMIVDYKAFLPNGPSPGSRVLTILEQIPGMVVVADKTAELYKTTYWASYNIPYFETVFNASGLQALVAQYGDWFSYTKNPRAKIFQRDQSLVEDMDAMVRLMRYNDFLHDPLSLCEACNPKPNAENAISARSDLNPANGSYPFQALHQRAHGGIDVKVTSFTLAKYMSMLAASGPTWDQCPPFQWSKSPFHSMLHMGQPDLWMFSPIRVP 592
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232     |   -      |252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592
                                                                                                                                                                                                         238        249-OCS
   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 3FBX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3FBX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FBX)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (PLBL2_MOUSE | Q3TCN2)
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:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    GO:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
cellular component
    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: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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  3.1.1.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        PLBL2_MOUSE | Q3TCN2: 3fgr 3fgt 3fgw

(-) Related Entries Specified in the PDB File

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