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(-) Description

Title :  CRYSTAL STRUCTURE OF SCD-MPR MUTANT E19Q/K137M BOUND TO MAN-6-P
 
Authors :  L. J. Olson, G. Sun, R. N. Bohnsack, F. C. Peterson, N. M. Dahms, J. J. P. Ki
Date :  05 Oct 09  (Deposition) - 24 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transport, Lysosome, Mannose, Receptor, Sugar Binding, Glycoprotein, Membrane, Phosphoprotein, Transmembrane, Protein Transport, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. J. Olson, G. Sun, R. N. Bohnsack, F. C. Peterson, N. M. Dahms, J. J. Kim
Intermonomer Interactions Are Essential For Lysosomal Enzym Binding By The Cation-Dependent Mannose 6-Phosphate Receptor.
Biochemistry V. 49 236 2010
PubMed-ID: 19928875  |  Reference-DOI: 10.1021/BI901725X

(-) Compounds

Molecule 1 - CATION-DEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR
    Chains: A, B
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PGAP
    Expression System Strain: X-33
    Expression System Taxid: 4922
    Fragment: UNP RESIDUES 29-182
    Gene: M6PR
    Mutation: YES
    Organism Common: BOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: CD MAN-6-P RECEPTOR, CD-MPR, 46 KDA MANNOSE 6-PHOSPHATE RECEPTOR, MPR 46

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2M6D2Ligand/Ion6-O-PHOSPHONO-BETA-D-MANNOPYRANOSE
3MAN1Ligand/IonALPHA-D-MANNOSE
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:81 , GLU A:82 , NAG A:1300BINDING SITE FOR RESIDUE NAG A 1299
2AC2SOFTWAREHOH A:188 , NAG A:1299 , BMA A:1301 , MAN A:1302BINDING SITE FOR RESIDUE NAG A 1300
3AC3SOFTWARENAG A:1300 , MAN A:1302BINDING SITE FOR RESIDUE BMA A 1301
4AC4SOFTWARENAG A:1300 , BMA A:1301 , HIS B:58BINDING SITE FOR RESIDUE MAN A 1302
5AC5SOFTWARETYR A:45 , GLN A:66 , TYR A:102 , ASP A:103 , ASN A:104 , HIS A:105 , ARG A:111 , GLU A:133 , ARG A:135 , TYR A:143 , HOH A:166 , HOH A:189 , HOH A:191 , HOH A:206BINDING SITE FOR RESIDUE M6D A 500
6AC6SOFTWAREASN B:81 , GLU B:82 , HOH B:166 , NAG B:2300BINDING SITE FOR RESIDUE NAG B 2299
7AC7SOFTWAREARG B:79 , HOH B:232 , NAG B:2299BINDING SITE FOR RESIDUE NAG B 2300
8AC8SOFTWARELYS B:18 , TYR B:45 , GLN B:66 , TYR B:102 , ASP B:103 , ASN B:104 , HIS B:105 , ARG B:111 , GLU B:133 , ARG B:135 , TYR B:143 , HOH B:191 , HOH B:197 , HOH B:207BINDING SITE FOR RESIDUE M6D B 501

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:6 -A:52
2A:106 -A:141
3A:119 -A:153
4B:6 -B:52
5B:106 -B:141
6B:119 -B:153

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:41 -Pro A:42
2Ser B:41 -Pro B:42

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K41)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K41)

(-) Exons   (4, 8)

Asymmetric/Biological Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSBTAT000000242331ENSBTAE00000295015chr5:108383511-108383668158MPRD_BOVIN1-110--
1.2ENSBTAT000000242332ENSBTAE00000197230chr5:108390145-108390324180MPRD_BOVIN1-61612A:4-33 (gaps)
B:4-33		30
30
1.3ENSBTAT000000242333ENSBTAE00000197232chr5:108391558-108391724167MPRD_BOVIN61-117572A:33-89
B:33-89		57
57
1.4ENSBTAT000000242334ENSBTAE00000295014chr5:108392731-108392840110MPRD_BOVIN117-153372A:89-125
B:89-125		37
37
1.5ENSBTAT000000242335ENSBTAE00000197235chr5:108393267-108393397131MPRD_BOVIN154-197442A:126-154
B:126-154		29
29
1.6ENSBTAT000000242336ENSBTAE00000197236chr5:108393940-108394066127MPRD_BOVIN197-239430--
1.7ENSBTAT000000242337ENSBTAE00000197238chr5:108394495-1083960421548MPRD_BOVIN240-279400--

(-) 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:145
 aligned with MPRD_BOVIN | P11456 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:151
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181 
           MPRD_BOVIN    32 KTCDLVGEKGKESEKELALLKRLTPLFNKSFESTVGQSPDMYSYVFRVCREAGNHSSGAGLVQINKSNGKETVVGRFNETQIFNGSNWIMLIYKGGDEYDNHCGREQRRAVVMISCNRHTLADNFNPVSEERGKVQDCFYLFEMDSSLACS 182
               SCOP domains d3k41a      _ A: Cation-dependent mannose 6-phosphate receptor, extracytoplasmic domain                                                                 SCOP domains
               CATH domains 3k41A0      0 A:4-154 Cation-dependent Mannose-6-phosphate Receptor; Chain A                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......------hhhhhhhhhhhhhhh...eeeee......eeeee............eeeeeee.....eeeeeeeeeeeeee...eeeeeeee......hhhhh...eeeeeee......eeeeeeeee.......eeeeeeeehhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:4-33 (gaps)  -------------------------------------------------------Exon 1.4  PDB: A:89-125              Exon 1.5  PDB: A:126-154      Transcript 1 (1)
           Transcript 1 (2) -----------------------------Exon 1.3  PDB: A:33-89 UniProt: 61-117                   ----------------------------------------------------------------- Transcript 1 (2)
                 3k41 A   4 KTCDLV------SEKQLALLKRLTPLFQKSFESTVGQSPDMYSYVFRVCREAGQHSSGAGLVQIQKSNGKETVVGRFNETQIFQGSNWIMLIYKGGDEYDNHCGREQRRAVVMISCNRHTLADNFNPVSEERGMVQDCFYLFEMDSSLACS 154
                                 |   -  |     23        33        43        53        63        73        83        93       103       113       123       133       143       153 
                                 9     16                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:151
 aligned with MPRD_BOVIN | P11456 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:151
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181 
           MPRD_BOVIN    32 KTCDLVGEKGKESEKELALLKRLTPLFNKSFESTVGQSPDMYSYVFRVCREAGNHSSGAGLVQINKSNGKETVVGRFNETQIFNGSNWIMLIYKGGDEYDNHCGREQRRAVVMISCNRHTLADNFNPVSEERGKVQDCFYLFEMDSSLACS 182
               SCOP domains d3k41b_ B: Cation-dependent mannose 6-phosphate receptor, extracytoplasmic domain                                                                       SCOP domains
               CATH domains 3k41B00 B:4-154 Cation-dependent Mannose-6-phosphate Receptor; Chain A                                                                                  CATH domains
           Pfam domains (1) Man-6-P_recep-3k41B01 B:4-154                                                                                                                           Pfam domains (1)
           Pfam domains (2) Man-6-P_recep-3k41B02 B:4-154                                                                                                                           Pfam domains (2)
         Sec.struct. author .........hhhhhhhhhhhhhhhhhh...eeeee......eeeee............eeeeeee.....eeeeeeeeeeeeee...eeeeeeee......hhhhh...eeeeeee......eeeeeeeee.......eeeeeeeehhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:4-33         -------------------------------------------------------Exon 1.4  PDB: B:89-125              Exon 1.5  PDB: B:126-154      Transcript 1 (1)
           Transcript 1 (2) -----------------------------Exon 1.3  PDB: B:33-89 UniProt: 61-117                   ----------------------------------------------------------------- Transcript 1 (2)
                 3k41 B   4 KTCDLVGEKGKESEKQLALLKRLTPLFQKSFESTVGQSPDMYSYVFRVCREAGQHSSGAGLVQIQKSNGKETVVGRFNETQIFQGSNWIMLIYKGGDEYDNHCGREQRRAVVMISCNRHTLADNFNPVSEERGMVQDCFYLFEMDSSLACS 154
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: M6PR (17)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MPRD_BOVIN | P11456)
molecular function
    GO:0005537    mannose binding    Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans.
    GO:0015578    mannose transmembrane transporter activity    Enables the transfer of mannose from one side of the membrane to the other. Mannose is the aldohexose manno-hexose, the C-2 epimer of glucose. The D-(+)-form is widely distributed in mannans and hemicelluloses and is of major importance in the core oligosaccharide of N-linked oligosaccharides of glycoproteins.
biological process
    GO:0015761    mannose transport    The directed movement of mannose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Mannose is the aldohexose manno-hexose, the C-2 epimer of glucose. The D-(+)-form is widely distributed in mannans and hemicelluloses and is of major importance in the core oligosaccharide of N-linked oligosaccharides of glycoproteins.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    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:0005765    lysosomal membrane    The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
    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.
    GO:0000323    lytic vacuole    A vacuole that is maintained at an acidic pH and which contains degradative enzymes, including a wide variety of acid hydrolases.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MPRD_BOVIN | P11456: 1c39 1keo 1m6p 2rl7 2rl8 2rl9 2rlb 3cy4 3k42 3k43

(-) Related Entries Specified in the PDB File

3k42 3k43