3K42 - JenaLib

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Title :   CRYSTAL STRUCTURE OF SCD-MPR MUTANT E19Q/K137M PH 7.0

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 :   2.30

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A (1x),B (1x)

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

Molecule 1 - CATION-DEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Plasmid	:	PPICZALPHAA
	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

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	1GP	2	Ligand/Ion	SN-GLYCEROL-1-PHOSPHATE
2	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 12)

No.	Name	Count	Type	Full Name
1	1GP	2	Ligand/Ion	SN-GLYCEROL-1-PHOSPHATE
2	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	1GP	1	Ligand/Ion	SN-GLYCEROL-1-PHOSPHATE
2	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:79 , ASN A:81 , GLU A:82 , HOH A:592	BINDING SITE FOR RESIDUE NAG A 3001
02	AC2	SOFTWARE	SER A:33 , PHE A:34 , GLU A:35 , ALA A:125 , ASP A:126 , ASN A:127 , PHE A:128 , HOH A:645 , HOH A:665 , HOH A:690 , HOH A:698 , SO4 A:6002	BINDING SITE FOR RESIDUE 1GP A 7000
03	AC3	SOFTWARE	TYR A:102 , ASP A:103 , ASN A:104 , HIS A:105 , ARG A:111	BINDING SITE FOR RESIDUE SO4 A 6000
04	AC4	SOFTWARE	LYS A:32 , SER A:33 , 1GP A:7000	BINDING SITE FOR RESIDUE SO4 A 6002
05	AC5	SOFTWARE	LYS A:32 , LEU A:124 , HOH A:547 , HOH A:662 , ARG B:25	BINDING SITE FOR RESIDUE SO4 A 6003
06	AC6	SOFTWARE	GLU A:35 , SER A:36 , THR A:37 , HOH A:613 , HOH A:645	BINDING SITE FOR RESIDUE SO4 A 6007
07	AC7	SOFTWARE	ASN B:81 , GLU B:82 , HOH B:609 , HOH B:634	BINDING SITE FOR RESIDUE NAG B 4001
08	AC8	SOFTWARE	PHE B:34 , GLU B:35 , ALA B:125 , ASN B:127 , PHE B:128 , HOH B:648	BINDING SITE FOR RESIDUE 1GP B 7001
09	AC9	SOFTWARE	TYR B:102 , ASP B:103 , ASN B:104 , HIS B:105 , ARG B:111	BINDING SITE FOR RESIDUE SO4 B 6001
10	BC1	SOFTWARE	ARG A:25 , CYS A:153 , SER A:154 , HOH A:653 , LEU B:124	BINDING SITE FOR RESIDUE SO4 B 6004
11	BC2	SOFTWARE	SER B:36 , THR B:37 , HOH B:583 , HOH B:623 , HOH B:654	BINDING SITE FOR RESIDUE SO4 B 6005
12	BC3	SOFTWARE	HOH A:606 , HIS B:58 , SER B:59 , SER B:60 , ARG B:79 , HOH B:628	BINDING SITE FOR RESIDUE SO4 B 6006

Asymmetric Unit

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

Asymmetric Unit

No.	Residues
1	Ser A:41	-	Pro A:42

(no "SAP(SNP)/Variant" information available for 3K42)

(no "PROSITE Motif" information available for 3K42)

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSBTAT00000024233	1	ENSBTAE00000295015	chr5:108383511-108383668	158	MPRD_BOVIN	1-1	1	0	-	-
1.2	ENSBTAT00000024233	2	ENSBTAE00000197230	chr5:108390145-108390324	180	MPRD_BOVIN	1-61	61	2	A:3-33 (gaps) B:5-33 (gaps)	31 29
1.3	ENSBTAT00000024233	3	ENSBTAE00000197232	chr5:108391558-108391724	167	MPRD_BOVIN	61-117	57	2	A:33-89 B:33-89	57 57
1.4	ENSBTAT00000024233	4	ENSBTAE00000295014	chr5:108392731-108392840	110	MPRD_BOVIN	117-153	37	2	A:89-125 B:89-125	37 37
1.5	ENSBTAT00000024233	5	ENSBTAE00000197235	chr5:108393267-108393397	131	MPRD_BOVIN	154-197	44	2	A:126-154 (gaps) B:126-154	29 29
1.6	ENSBTAT00000024233	6	ENSBTAE00000197236	chr5:108393940-108394066	127	MPRD_BOVIN	197-239	43	0	-	-
1.7	ENSBTAT00000024233	7	ENSBTAE00000197238	chr5:108394495-108396042	1548	MPRD_BOVIN	240-279	40	0	-	-

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
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Chain A from PDB  Type:PROTEIN  Length:141
 aligned with MPRD_BOVIN | P11456 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:152
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  
           MPRD_BOVIN    31 EKTCDLVGEKGKESEKELALLKRLTPLFNKSFESTVGQSPDMYSYVFRVCREAGNHSSGAGLVQINKSNGKETVVGRFNETQIFNGSNWIMLIYKGGDEYDNHCGREQRRAVVMISCNRHTLADNFNPVSEERGKVQDCFYLFEMDSSLACS 182
               SCOP domains d3k42a_     A: Cation-dependent mannose 6-phosphate receptor, extracytoplasmic domain                                                                    SCOP domains
               CATH domains 3k42A00     A:3-154 Cation-dependent Mannose-6-phosphate Receptor; Chain A                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........----.hhhhhhhhhhhhhhhh..eeeee......eeeee............eeeeeee.....eeeeeeeeeeeeeee..eeeeeeee......hhhhh...eeeeeee......eeeeeee.-------..eeeeeeehhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:3-33 (gaps)   -------------------------------------------------------Exon 1.4  PDB: A:89-125              Exon 1.5 UniProt: 154-197     Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.3  PDB: A:33-89 UniProt: 61-117                   ----------------------------------------------------------------- Transcript 1 (2)
                 3k42 A   3 EKTCDLVG----ESEKQLALLKRLTPLFQKSFESTVGQSPDMYSYVFRVCREAGQHSSGAGLVQIQKSNGKETVVGRFNETQIFQGSNWIMLIYKGGDEYDNHCGREQRRAVVMISCNRHTLADNFNPVSE-------CFYLFEMDSSLACS 154
                                   | -  |     22        32        42        52        62        72        82        92       102       112       122       132|      142       152  
                                  10   15                                                                                                                   133     141

Chain B from PDB  Type:PROTEIN  Length:146
 aligned with MPRD_BOVIN | P11456 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:150
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182
           MPRD_BOVIN    33 TCDLVGEKGKESEKELALLKRLTPLFNKSFESTVGQSPDMYSYVFRVCREAGNHSSGAGLVQINKSNGKETVVGRFNETQIFNGSNWIMLIYKGGDEYDNHCGREQRRAVVMISCNRHTLADNFNPVSEERGKVQDCFYLFEMDSSLACS 182
               SCOP domains d3k42b    _ B: Cation-dependent mannose 6-phosphate receptor, extracytoplasmic domain                                                                  SCOP domains
               CATH domains 3k42B0    0 B:5-154 Cation-dependent Mannose-6-phosphate Receptor; Chain A                                                                             CATH domains
           Pfam domains (1) Man-6-    P_recep-3k42B01 B:5-154                                                                                                                      Pfam domains (1)
           Pfam domains (2) Man-6-    P_recep-3k42B02 B:5-154                                                                                                                      Pfam domains (2)
         Sec.struct. author ......----.hhhhhhhhhhhhhhh...eeeee......eeeee............eeeeeee.....eeeeeeeeeeeeee...eeeeeeee......hhhhh...eeeeeee......eeeee.....hhhhhh.eeeeeeehhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:5-33 (gaps) -------------------------------------------------------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)
                 3k42 B   5 TCDLVG----ESEKQLALLKRLTPLFQKSFESTVGQSPDMYSYVFRVCREAGQHSSGAGLVQIQKSNGKETVVGRFNETQIFQGSNWIMLIYKGGDEYDNHCGREQRRAVVMISCNRHTLADNFNPVSEERGMVQDCFYLFEMDSSLACS 154
                                 |   -|       24        34        44        54        64        74        84        94       104       114       124       134       144       154
                                10   15

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Distorted Sandwich (506)

Topology: Cation-dependent Mannose-6-phosphate Receptor; Chain A (19)

Homologous Superfamily: Cation-dependent Mannose-6-phosphate Receptor; Chain A (19)

Bovine,cow,domestic cattle,domestic cow (Bos taurus) (3)

1a	3k42A00	A:3-154
1b	3k42B00	B:5-154

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: M6PR (17)

Family: Man-6-P_recep (9)

Bos taurus (Bovine) (9)

1a	Man-6-P_recep-3k42B01	B:5-154
1b	Man-6-P_recep-3k42B02	B:5-154

Asymmetric 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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		Ser A:41 - Pro A:42	[ RasMol ]

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	MPRD_BOVIN \| P11456	:	1c39 1keo 1m6p 2rl7 2rl8 2rl9 2rlb 3cy4 3k41 3k43

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SS Bonds (6, 6)

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