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(-) Description

Title :  TWO CHAIN FORM OF THE 66.3 KDA PROTEIN AT 1.8 ANGSTROEM
 
Authors :  K. Lakomek, A. Dickmanns, R. Ficner
Date :  08 Dec 08  (Deposition) - 15 Sep 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha Beta, Glycosylated, Disulphide Bonds, N-Terminal Nucleophile Hydrolase Fold, Two Chain Form, Glycoprotein, Hydrolase, Lipid Degradation, Lysosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Lakomek, A. Dickmanns, M. Kettwig, H. Urlaub, R. Ficner, T. Luebke
Initial Insight Into The Function Of The Lysosomal 66. 3 Kda Protein From Mouse By Means Of X-Ray Crystallography
Bmc Struct. Biol. V. 9 56 2009
PubMed-ID: 19706171  |  Reference-DOI: 10.1186/1472-6807-9-56
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE PHOSPHOLIPASE B-LIKE 2 28 KDA FORM
    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
    Fragment: N-TERMINAL DOMAIN, RESIDUES 47-248
    Gene: AAG44101
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: C3H/RV
    Synonym: LAMINA ANCESTOR HOMOLOG 2, LAMA-LIKE PROTEIN 2, 76 KDA PROTEIN, P76, 66.3 KDA PROTEIN
 
Molecule 2 - PUTATIVE PHOSPHOLIPASE B-LIKE 2 40 KDA FORM
    Chains: B
    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
    Fragment: C-TERMINAL DOMAIN, RESIDUES 249-594
    Gene: AAG44101
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: C3H/RV
    Synonym: LAMINA ANCESTOR HOMOLOG 2, LAMA-LIKE PROTEIN 2, 76 KDA PROTEIN, P76, 66.3 KDA PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 23)

Asymmetric/Biological Unit (6, 23)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL11Ligand/IonGLYCEROL
3NA1Ligand/IonSODIUM ION
4NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE
5OCS1Mod. Amino AcidCYSTEINESULFONIC ACID
6XE1Ligand/IonXENON

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWARENAG A:12 , ASN A:115 , SER A:117 , PHE A:207 , THR A:209 , HOH A:258 , HOH A:279 , HOH A:506 , HOH A:716BINDING SITE FOR RESIDUE NAG A 11
02AC2SOFTWARENAG A:11 , GLY A:76 , PHE A:207 , THR A:209 , HOH A:297 , HOH A:381 , HOH A:505BINDING SITE FOR RESIDUE NAG A 12
03AC3SOFTWARELYS A:159 , ASN A:236 , GOL B:11BINDING SITE FOR RESIDUE NAG A 21
04AC4SOFTWAREASN A:93 , THR A:95 , TYR A:105BINDING SITE FOR RESIDUE NAG A 1
05AC5SOFTWAREARG A:188 , THR A:209 , HOH A:290 , HOH A:294 , HOH A:471BINDING SITE FOR RESIDUE GOL A 9
06AC6SOFTWAREASN A:145 , TYR A:146 , CYS A:147 , GLU A:151 , GLU A:153 , LYS A:237BINDING SITE FOR RESIDUE GOL A 10
07AC7SOFTWARETRP A:170 , ARG A:173 , GLU A:174 , HOH B:14 , HOH B:127 , HOH B:185 , PRO B:257 , HOH B:626BINDING SITE FOR RESIDUE ACT A 22
08AC8SOFTWAREHIS A:138 , LEU A:222 , SER A:225 , HOH A:659 , ASN B:270 , ASN B:274 , TYR B:307 , THR B:310BINDING SITE FOR RESIDUE GOL A 3
09AC9SOFTWARENAG B:32 , ASN B:441 , GLN B:446 , HOH B:674 , HOH B:697 , HOH B:789BINDING SITE FOR RESIDUE NAG B 31
10BC1SOFTWARENAG B:31BINDING SITE FOR RESIDUE NAG B 32
11BC2SOFTWAREASN B:520 , HOH B:718BINDING SITE FOR RESIDUE NAG B 41
12BC3SOFTWARENAG A:21 , ALA A:234 , LEU A:235 , TRP B:339 , LYS B:340 , VAL B:342 , GLN B:343 , HOH B:695 , HOH B:734BINDING SITE FOR RESIDUE GOL B 11
13BC4SOFTWARETYR A:183 , HOH B:169 , ASP B:369 , VAL B:370 , ARG B:373 , HOH B:790BINDING SITE FOR RESIDUE GOL B 1
14BC5SOFTWAREGLU A:229 , ASP A:230 , HOH A:277 , HOH A:692 , GLY B:332 , ASN B:333 , LYS B:334 , HOH B:683BINDING SITE FOR RESIDUE GOL B 2
15BC6SOFTWARETYR B:435 , PHE B:436 , GLU B:437 , HOH B:636 , HOH B:849BINDING SITE FOR RESIDUE GOL B 4
16BC7SOFTWAREARG B:373 , ASP B:470 , LEU B:473 , ALA B:479 , ARG B:482 , LEU B:483 , HOH B:741 , HOH B:822BINDING SITE FOR RESIDUE GOL B 5
17BC8SOFTWAREGLN A:193 , HOH A:383 , TYR B:282 , LEU B:284 , ILE B:311 , VAL B:355 , ARG B:359 , HOH B:616BINDING SITE FOR RESIDUE GOL B 6
18BC9SOFTWARETRP B:269 , ILE B:433 , TRP B:455 , ASN B:461 , PRO B:462 , ARG B:463 , GLU B:507 , ASN B:508 , HOH B:743BINDING SITE FOR RESIDUE GOL B 7
19CC1SOFTWAREGLU B:293 , TYR B:294 , PRO B:493 , HOH B:690 , HOH B:815 , HOH B:835BINDING SITE FOR RESIDUE GOL B 8
20CC2SOFTWAREASP B:488 , HIS B:491 , ASP B:492 , HOH B:765 , HOH B:867BINDING SITE FOR RESIDUE ACT B 21
21CC3SOFTWAREPHE A:163 , ASN A:167 , LEU B:349BINDING SITE FOR RESIDUE XE B 606
22CC4SOFTWARESER A:246 , OCS B:249 , ASP B:315 , GLU B:328 , THR B:330 , TYR B:379BINDING SITE FOR RESIDUE NA B 607

(-) SS Bonds  (2, 2)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asp B:315 -Asp B:316
2Asn B:501 -Pro B:502
3Val B:591 -Pro B:592

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FGR)

(-) 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:180
 aligned with PLBL2_MOUSE | Q3TCN2 from UniProtKB/Swiss-Prot  Length:594

    Alignment length:186
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242      
          PLBL2_MOUSE    63 VSRTRSLLLDAASGQLRLEDGFHPDAVAWANLTNAIRETGWAYLDLSTNGRYNDSLQAYAAGVVEASVSEELIYMHWMNTVVNYCGPFEYEVGYCEKLKNFLEANLEWMQREMELNPDSPYWHQVRLTLLQLKGLEDSYEGRLTFPTGRFTIKPLGFLLLQISGDLEDLEPALNKTNTKPSLGSGS 248
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee....eeeeee.......eeeeeeehhhhhh.eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhh...------.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fgr A  63 VSRTRSLLLDAASGQLRLEDGFHPDAVAWANLTNAIRETGWAYLDLSTNGRYNDSLQAYAAGVVEASVSEELIYMHWMNTVVNYCGPFEYEVGYCEKLKNFLEANLEWMQREMELNPDSPYWHQVRLTLLQLKGLEDSYEGRLTFPTGRFTIKPLGFLLLQISGDLEDLEPALNKT------GSGS 248
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232     |   -  |   
                                                                                                                                                                                                         238    245   


Chain B from PDB  Type:PROTEIN  Length:344
 aligned with PLBL2_MOUSE | Q3TCN2 from UniProtKB/Swiss-Prot  Length:594

    Alignment length:344
                                   258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588    
          PLBL2_MOUSE   249 CSALIKLLPGGHDLLVAHNTWNSYQNMLRIIKKYRLQFREGPQEEYPLVAGNNLVFSSYPGTIFSGDDFYILGSGLVTLETTIGNKNPALWKYVQPQGCVLEWIRNVVANRLALDGATWADVFKRFNSGTYNNQWMIVDYKAFLPNGPSPGSRVLTILEQIPGMVVVADKTAELYKTTYWASYNIPYFETVFNASGLQALVAQYGDWFSYTKNPRAKIFQRDQSLVEDMDAMVRLMRYNDFLHDPLSLCEACNPKPNAENAISARSDLNPANGSYPFQALHQRAHGGIDVKVTSFTLAKYMSMLAASGPTWDQCPPFQWSKSPFHSMLHMGQPDLWMFSPIRVP 592
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .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
                 3fgr B 249 cSALIKLLPGGHDLLVAHNTWNSYQNMLRIIKKYRLQFREGPQEEYPLVAGNNLVFSSYPGTIFSGDDFYILGSGLVTLETTIGNKNPALWKYVQPQGCVLEWIRNVVANRLALDGATWADVFKRFNSGTYNNQWMIVDYKAFLPNGPSPGSRVLTILEQIPGMVVVADKTAELYKTTYWASYNIPYFETVFNASGLQALVAQYGDWFSYTKNPRAKIFQRDQSLVEDMDAMVRLMRYNDFLHDPLSLCEACNPKPNAENAISARSDLNPANGSYPFQALHQRAHGGIDVKVTSFTLAKYMSMLAASGPTWDQCPPFQWSKSPFHSMLHMGQPDLWMFSPIRVP 592
                            |      258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588    
                            |                                                                                                                                                                                                                                                                                                                                                       
                          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 3FGR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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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  3fgr
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

3fbx CRYSTAL STRUCTURE OF THE LYSOSOMAL 66.3 KDA PROTEIN FROM MOUSE SOLVED BY S-SAD
3fgt TWO CHAIN FORM OF THE 66.3 KDA PROTEIN FROM MOUSE LACKING THE LINKER PEPTIDE
3fgw ONE CHAIN FORM OF THE 66.3 KDA PROTEIN