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(-) Description

Title :  TWO CHAIN FORM OF THE 66.3 KDA PROTEIN FROM MOUSE LACKING THE LINKER PEPTIDE
 
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 :  2.40
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  (7, 17)

Asymmetric/Biological Unit (7, 17)
No.NameCountTypeFull Name
17PE1Ligand/Ion2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL
2ACT3Ligand/IonACETATE ION
3GOL5Ligand/IonGLYCEROL
4NA1Ligand/IonSODIUM ION
5NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
6OCS1Mod. Amino AcidCYSTEINESULFONIC ACID
7PG42Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARENAG A:12 , ASN A:115 , SER A:117 , PHE A:207 , THR A:209 , HOH A:272 , HOH A:302BINDING SITE FOR RESIDUE NAG A 11
02AC2SOFTWARENAG A:11 , LEU A:71 , PHE A:207BINDING SITE FOR RESIDUE NAG A 12
03AC3SOFTWARELYS A:159 , ASN A:236BINDING SITE FOR RESIDUE NAG A 21
04AC4SOFTWAREHOH B:641BINDING SITE FOR RESIDUE ACT A 249
05AC5SOFTWAREARG A:99 , GLU A:100 , HOH A:327 , PHE B:586BINDING SITE FOR RESIDUE GOL A 3
06AC6SOFTWAREGLU A:165 , LEU A:168 , GLU A:169 , GLN A:172 , PHE A:212 , THR A:213 , ILE A:214 , LYS A:215 , PRO A:216BINDING SITE FOR RESIDUE PG4 A 23
07AC7SOFTWARETYR A:146 , CYS A:147 , GLU A:151 , LYS A:237 , HOH A:463BINDING SITE FOR RESIDUE ACT A 1
08AC8SOFTWAREHOH B:85 , ASN B:441 , GLN B:446 , HOH B:698BINDING SITE FOR RESIDUE NAG B 31
09AC9SOFTWARETRP A:170 , ARG A:173 , GLU A:174 , LEU A:177 , HOH B:120 , HOH B:138 , PRO B:257 , HOH B:616 , HOH B:640BINDING SITE FOR RESIDUE ACT B 12
10BC1SOFTWAREHOH B:221 , ASN B:432 , GLU B:507 , ARG B:531 , HIS B:533BINDING SITE FOR RESIDUE GOL B 1
11BC2SOFTWAREHOH B:104 , HOH B:220 , ASP B:515 , PHE B:565 , GLN B:566 , LYS B:569 , SER B:570 , PRO B:571BINDING SITE FOR RESIDUE GOL B 2
12BC3SOFTWAREHOH B:189 , GLY B:321 , GLY B:323 , TYR B:388 , LYS B:389 , PHE B:391 , LEU B:392 , PRO B:393 , PHE B:543 , HOH B:627BINDING SITE FOR RESIDUE PG4 B 22
13BC4SOFTWAREARG B:373 , ALA B:479 , ARG B:482 , LEU B:483 , 7PE B:607 , HOH B:631BINDING SITE FOR RESIDUE GOL B 5
14BC5SOFTWAREGLU B:293 , TYR B:294 , PRO B:295 , PRO B:493 , HOH B:687BINDING SITE FOR RESIDUE GOL B 4
15BC6SOFTWAREOCS B:249 , ASP B:315 , GLU B:328 , THR B:330 , TYR B:379BINDING SITE FOR RESIDUE NA B 606
16BC7SOFTWAREGOL B:5 , HOH B:124 , HOH B:146 , GLU B:288 , ASP B:369 , ARG B:469 , ARG B:482 , TYR B:486 , GLN B:561BINDING SITE FOR RESIDUE 7PE B 607

(-) SS Bonds  (2, 2)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser A:75 -Gly A:76
2Thr A:238 -Asn A:239
3Asp B:315 -Asp B:316
4Asn B:501 -Pro B:502
5Val B:591 -Pro B:592

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FGT)

(-) 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:180
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239
          PLBL2_MOUSE    60 DPPVSRTRSLLLDAASGQLRLEDGFHPDAVAWANLTNAIRETGWAYLDLSTNGRYNDSLQAYAAGVVEASVSEELIYMHWMNTVVNYCGPFEYEVGYCEKLKNFLEANLEWMQREMELNPDSPYWHQVRLTLLQLKGLEDSYEGRLTFPTGRFTIKPLGFLLLQISGDLEDLEPALNKTN 239
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeee......eeeee.......eeeeeeehhhhhh.eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fgt A  60 DPPVSRTRSLLLDAASGQLRLEDGFHPDAVAWANLTNAIRETGWAYLDLSTNGRYNDSLQAYAAGVVEASVSEELIYMHWMNTVVNYCGPFEYEVGYCEKLKNFLEANLEWMQREMELNPDSPYWHQVRLTLLQLKGLEDSYEGRLTFPTGRFTIKPLGFLLLQISGDLEDLEPALNKTN 239
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239


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
                 3fgt 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 3FGT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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  3fgt
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

3fbx CRYSTAL STRUCTURE OF THE LYSOSOMAL 66.3 KDA PROTEIN FROM MOUSE SOLVED BY S-SAD
3fgr TWO CHAIN FORM OF THE 66.3 KDA PROTEIN AT 1.8 ANGSTROEM
3fgw ONE CHAIN FORM OF THE 66.3 KDA PROTEIN