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(-) Description

Title :  ONE CHAIN FORM OF THE 66.3 KDA PROTEIN
 
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 :  2.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Alpha Beta, Glycosylated, Disulphide Bonds, N-Terminal Hydrolase Fold, Occupied Pocket, One 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
    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  (5, 17)

Asymmetric Unit (5, 17)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2GOL3Ligand/IonGLYCEROL
3IOD7Ligand/IonIODIDE ION
4NA1Ligand/IonSODIUM ION
5NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (4, 32)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2GOL6Ligand/IonGLYCEROL
3IOD14Ligand/IonIODIDE ION
4NA-1Ligand/IonSODIUM ION
5NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARENAG A:12 , ASN A:115 , SER A:117 , PHE A:207BINDING SITE FOR RESIDUE NAG A 11
02AC2SOFTWARENAG A:11 , BMA A:13 , GLY A:76 , PHE A:207 , THR A:209BINDING SITE FOR RESIDUE NAG A 12
03AC3SOFTWARENAG A:12BINDING SITE FOR RESIDUE BMA A 13
04AC4SOFTWARELYS A:159 , ASN A:236BINDING SITE FOR RESIDUE NAG A 21
05AC5SOFTWAREGLU A:437 , ASN A:441 , GLN A:446 , HOH A:651 , HOH A:670 , HOH A:676BINDING SITE FOR RESIDUE NAG A 31
06AC6SOFTWARESER A:64 , ASN A:93 , THR A:95BINDING SITE FOR RESIDUE NAG A 1
07AC7SOFTWAREPHE A:436 , GLU A:437 , THR A:438BINDING SITE FOR RESIDUE GOL A 4
08AC8SOFTWAREGLU A:293 , TYR A:294 , PRO A:493 , HOH A:643BINDING SITE FOR RESIDUE GOL A 8
09AC9SOFTWAREARG A:469 , HOH A:667 , HOH A:697BINDING SITE FOR RESIDUE GOL A 606
10BC1SOFTWAREHOH A:28 , TRP A:170 , GLU A:174BINDING SITE FOR RESIDUE IOD A 607
11BC2SOFTWARESER A:117BINDING SITE FOR RESIDUE IOD A 15
12BC3SOFTWARELYS A:161 , LYS A:215 , LEU A:217BINDING SITE FOR RESIDUE IOD A 16
13BC4SOFTWAREHIS A:577BINDING SITE FOR RESIDUE IOD A 17
14BC5SOFTWAREARG A:373 , HOH A:630BINDING SITE FOR RESIDUE IOD A 608
15BC6SOFTWARELEU A:78 , PHE A:207BINDING SITE FOR RESIDUE IOD A 609
16BC7SOFTWARESER A:248 , CYS A:249 , GLU A:328 , THR A:330 , TYR A:379 , HOH A:712BINDING SITE FOR RESIDUE NA A 610

(-) SS Bonds  (2, 2)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:501 -Pro A:502
2Val A:591 -Pro A:592

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FGW)

(-) 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:529
 aligned with PLBL2_MOUSE | Q3TCN2 from UniProtKB/Swiss-Prot  Length:594

    Alignment length:534
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590    
          PLBL2_MOUSE    61 PPVSRTRSLLLDAASGQLRLEDGFHPDAVAWANLTNAIRETGWAYLDLSTNGRYNDSLQAYAAGVVEASVSEELIYMHWMNTVVNYCGPFEYEVGYCEKLKNFLEANLEWMQREMELNPDSPYWHQVRLTLLQLKGLEDSYEGRLTFPTGRFTIKPLGFLLLQISGDLEDLEPALNKTNTKPSLGSGSCSALIKLLPGGHDLLVAHNTWNSYQNMLRIIKKYRLQFREGPQEEYPLVAGNNLVFSSYPGTIFSGDDFYILGSGLVTLETTIGNKNPALWKYVQPQGCVLEWIRNVVANRLALDGATWADVFKRFNSGTYNNQWMIVDYKAFLPNGPSPGSRVLTILEQIPGMVVVADKTAELYKTTYWASYNIPYFETVFNASGLQALVAQYGDWFSYTKNPRAKIFQRDQSLVEDMDAMVRLMRYNDFLHDPLSLCEACNPKPNAENAISARSDLNPANGSYPFQALHQRAHGGIDVKVTSFTLAKYMSMLAASGPTWDQCPPFQWSKSPFHSMLHMGQPDLWMFSPIRVPWD 594
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee......eeeee.......eeeeeee.......eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh........................hhhhhhhhh....-----.....eeeeee.hhhh.eeeeee.eee.hhh..eeeeee.................eeeeee..........eeee...eeeeeee....hhhhhhhh......hhhhhhhhhhhhh.hhhhhhhhhhh.......eeeeeee...............eeeeeee..eeeeeehhhhhhhhheeee.....hhhhhhhh.hhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhh......hhhhh................hhhhh.......hhhhh...eee.eeeeehhhhhhh..eeeee.................................eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fgw A  61 PPVSRTRSLLLDAASGQLRLEDGFHPDAVAWANLTNAIRETGWAYLDLSTNGRYNDSLQAYAAGVVEASVSEELIYMHWMNTVVNYCGPFEYEVGYCEKLKNFLEANLEWMQREMELNPDSPYWHQVRLTLLQLKGLEDSYEGRLTFPTGRFTIKPLGFLLLQISGDLEDLEPALNKTN-----GSGSCSALIKLLPGGHDLLVAHNTWNSYQNMLRIIKKYRLQFREGPQEEYPLVAGNNLVFSSYPGTIFSGDDFYILGSGLVTLETTIGNKNPALWKYVQPQGCVLEWIRNVVANRLALDGATWADVFKRFNSGTYNNQWMIVDYKAFLPNGPSPGSRVLTILEQIPGMVVVADKTAELYKTTYWASYNIPYFETVFNASGLQALVAQYGDWFSYTKNPRAKIFQRDQSLVEDMDAMVRLMRYNDFLHDPLSLCEACNPKPNAENAISARSDLNPANGSYPFQALHQRAHGGIDVKVTSFTLAKYMSMLAASGPTWDQCPPFQWSKSPFHSMLHMGQPDLWMFSPIRVPWD 594
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        |-    |  250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590    
                                                                                                                                                                                                            239   245
   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 3FGW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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 Related Entries

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

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

(-) 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
3fgt TWO CHAIN FORM OF THE 66.3 KDA PROTEIN FROM MOUSE LACKING THE LINKER PEPTIDE