1U7P - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   X-RAY CRYSTAL STRUCTURE OF THE HYPOTHETICAL PHOSPHOTYROSINE PHOSPHATASE MDP-1 OF THE HALOACID DEHALOGENASE SUPERFAMILY

Authors :   E. Peisach, J. D. Selengut, D. Dunaway-Mariano, K. N. Allen

Date :   04 Aug 04 (Deposition) - 19 Oct 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Had Superfamily, Phosphoryl Transfer, Phosphotyrosine Phosphatase, Aspartate Nucleophile, Enzyme Evolution, Structural Enzymology, Class Iii, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Peisach, J. D. Selengut, D. Dunaway-Mariano, K. N. Allen
X-Ray Crystal Structure Of The Hypothetical Phosphotyrosine Phosphatase Mdp-1 Of The Haloacid Dehalogenase Superfamily
Biochemistry V. 43 12770 2004
PubMed-ID: 15461449 | Reference-DOI: 10.1021/BI0490688
(for further references see the PDB file header)

Molecule 1 - MAGNESIUM-DEPENDENT PHOSPHATASE-1
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3A
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AF230273
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	MDP-1

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	MG	4	Ligand/Ion	MAGNESIUM ION
2	WO4	2	Ligand/Ion	TUNGSTATE(VI)ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	WO4	1	Ligand/Ion	TUNGSTATE(VI)ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	WO4	-1	Ligand/Ion	TUNGSTATE(VI)ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	WO4	1	Ligand/Ion	TUNGSTATE(VI)ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	WO4	-1	Ligand/Ion	TUNGSTATE(VI)ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:11 , ASP A:13 , ASP A:123 , WO4 A:505 , HOH A:533 , HOH A:564	BINDING SITE FOR RESIDUE MG A 501
2	AC2	SOFTWARE	ASP B:11 , ASP B:13 , THR B:15 , ASP B:122 , ASP B:123 , HOH B:597	BINDING SITE FOR RESIDUE MG B 502
3	AC3	SOFTWARE	ASP C:11 , ASP C:13 , ASP C:123 , WO4 C:506 , HOH C:550 , HOH C:584	BINDING SITE FOR RESIDUE MG C 503
4	AC4	SOFTWARE	ASP D:11 , ASP D:13 , ASP D:122 , ASP D:123 , HOH D:562	BINDING SITE FOR RESIDUE MG D 504
5	AC5	SOFTWARE	ASP A:11 , LEU A:12 , ASP A:13 , SER A:69 , ARG A:70 , THR A:71 , LYS A:100 , MG A:501 , HOH A:571	BINDING SITE FOR RESIDUE WO4 A 505
6	AC6	SOFTWARE	ASP C:11 , LEU C:12 , ASP C:13 , SER C:69 , ARG C:70 , THR C:71 , LYS C:100 , MG C:503 , HOH C:560	BINDING SITE FOR RESIDUE WO4 C 506

(no "SS Bond" information available for 1U7P)

Asymmetric Unit

No.	Residues
1	Pro A:27	-	Pro A:28
2	Pro B:27	-	Pro B:28
3	Pro C:27	-	Pro C:28
4	Pro D:27	-	Pro D:28

(no "SAP(SNP)/Variant" information available for 1U7P)

(no "PROSITE Motif" information available for 1U7P)

(no "Exon" information available for 1U7P)

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:164
 aligned with MGDP1_MOUSE | Q9D967 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
          MGDP1_MOUSE     1 MTRLPKLAVFDLDYTLWPFWVDTHVDPPFHKSSDGTVRDRRGQNIQLYPEVPEVLGRLQSLGVPVAAASRTSEIQGANQLLELFDLGKYFIQREIYPGSKVTHFERLHHKTGVPFSQMVFFDDENRNIIDVGRLGVTCIHIRDGMSLQTLTQGLETFAKAQAGL 164
               SCOP domains d1u7pa_ A: Magnesium-dependent phosphatase-1, Mdp1                                                                                                                   SCOP domains
               CATH domains 1u7pA00 A:1-164  [code=3.40.50.1000, no name defined]                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee..................eee.....eee....ee....hhhhhhhhhhhh...eeeee...hhhhhhhhhhhh.hhhhh.eeee...hhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u7p A   1 MTRLPKLAVFDLDYTLWPFWVDTHVDPPFHKSSDGTVRDRRGQNIQLYPEVPEVLGRLQSLGVPVAAASRTSEIQGANQLLELFDLGKYFIQREIYPGSKVTHFERLHHKTGVPFSQMVFFDDENRNIIDVGRLGVTCIHIRDGMSLQTLTQGLETFAKAQAGL 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain B from PDB  Type:PROTEIN  Length:162
 aligned with MGDP1_MOUSE | Q9D967 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  
          MGDP1_MOUSE     2 TRLPKLAVFDLDYTLWPFWVDTHVDPPFHKSSDGTVRDRRGQNIQLYPEVPEVLGRLQSLGVPVAAASRTSEIQGANQLLELFDLGKYFIQREIYPGSKVTHFERLHHKTGVPFSQMVFFDDENRNIIDVGRLGVTCIHIRDGMSLQTLTQGLETFAKAQAG 163
               SCOP domains d1u7pb_ B: Magnesium-dependent phosphatase-1, Mdp1                                                                                                                 SCOP domains
               CATH domains 1u7pB00 B:2-163  [code=3.40.50.1000, no name defined]                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee...................ee.....ee.....ee....hhhhhhhhhhhhh..eeeee...hhhhhhhhhhhh.hhhhh.eeee...hhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1u7p B   2 TRLPKLAVFDLDYTLWPFWVDTHVDPPFHKSSDGTVRDRRGQNIQLYPEVPEVLGRLQSLGVPVAAASRTSEIQGANQLLELFDLGKYFIQREIYPGSKVTHFERLHHKTGVPFSQMVFFDDENRNIIDVGRLGVTCIHIRDGMSLQTLTQGLETFAKAQAG 163
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain C from PDB  Type:PROTEIN  Length:163
 aligned with MGDP1_MOUSE | Q9D967 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:163
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161   
          MGDP1_MOUSE     2 TRLPKLAVFDLDYTLWPFWVDTHVDPPFHKSSDGTVRDRRGQNIQLYPEVPEVLGRLQSLGVPVAAASRTSEIQGANQLLELFDLGKYFIQREIYPGSKVTHFERLHHKTGVPFSQMVFFDDENRNIIDVGRLGVTCIHIRDGMSLQTLTQGLETFAKAQAGL 164
               SCOP domains d1u7pc_ C: Magnesium-dependent phosphatase-1, Mdp1                                                                                                                  SCOP domains
               CATH domains 1u7pC00 C:2-164  [code=3.40.50.1000, no name defined]                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee...................ee.....ee.....ee....hhhhhhhhhhhhh..eeeee...hhhhhhhhhhhh.hhh.eeeeee...hhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u7p C   2 TRLPKLAVFDLDYTLWPFWVDTHVDPPFHKSSDGTVRDRRGQNIQLYPEVPEVLGRLQSLGVPVAAASRTSEIQGANQLLELFDLGKYFIQREIYPGSKVTHFERLHHKTGVPFSQMVFFDDENRNIIDVGRLGVTCIHIRDGMSLQTLTQGLETFAKAQAGL 164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain D from PDB  Type:PROTEIN  Length:161
 aligned with MGDP1_MOUSE | Q9D967 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:161
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161 
          MGDP1_MOUSE     2 TRLPKLAVFDLDYTLWPFWVDTHVDPPFHKSSDGTVRDRRGQNIQLYPEVPEVLGRLQSLGVPVAAASRTSEIQGANQLLELFDLGKYFIQREIYPGSKVTHFERLHHKTGVPFSQMVFFDDENRNIIDVGRLGVTCIHIRDGMSLQTLTQGLETFAKAQA 162
               SCOP domains d1u7pd_ D: Magnesium-dependent phosphatase-1, Mdp1                                                                                                                SCOP domains
               CATH domains 1u7pD00 D:2-162  [code=3.40.50.1000, no name defined]                                                                                                             CATH domains
           Pfam domains (1) -Acid_PPase-1u7pD01 D:3-160                                                                                                                                    -- Pfam domains (1)
           Pfam domains (2) -Acid_PPase-1u7pD02 D:3-160                                                                                                                                    -- Pfam domains (2)
           Pfam domains (3) -Acid_PPase-1u7pD03 D:3-160                                                                                                                                    -- Pfam domains (3)
           Pfam domains (4) -Acid_PPase-1u7pD04 D:3-160                                                                                                                                    -- Pfam domains (4)
         Sec.struct. author .....eeee...................ee.....ee.....ee....hhhhhhhhhhhh...eeeee...hhhhhhhhhhhh.hhhhh.eeee...hhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u7p D   2 TRLPKLAVFDLDYTLWPFWVDTHVDPPFHKSSDGTVRDRRGQNIQLYPEVPEVLGRLQSLGVPVAAASRTSEIQGANQLLELFDLGKYFIQREIYPGSKVTHFERLHHKTGVPFSQMVFFDDENRNIIDVGRLGVTCIHIRDGMSLQTLTQGLETFAKAQA 162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: HAD-like (349)

Superfamily: HAD-like (349)

Family: Magnesium-dependent phosphatase-1, Mdp1 (3)

Protein domain: Magnesium-dependent phosphatase-1, Mdp1 (2)

Mouse (Mus musculus) [TaxId: 10090] (2)

1a	d1u7pa_	A:
1b	d1u7pb_	B:
1c	d1u7pc_	C:
1d	d1u7pd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1000, no name defined] (211)

House mouse (Mus musculus) (7)

1a	1u7pD00	D:2-162
1b	1u7pB00	B:2-163
1c	1u7pC00	C:2-164
1d	1u7pA00	A:1-164

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HAD (186)

Family: Acid_PPase (3)

Mus musculus (Mouse) (2)

1a	Acid_PPase-1u7pD01	D:3-160
1b	Acid_PPase-1u7pD02	D:3-160
1c	Acid_PPase-1u7pD03	D:3-160
1d	Acid_PPase-1u7pD04	D:3-160

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (MGDP1_MOUSE | Q9D967)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016791	phosphatase activity	Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
	GO:0004721	phosphoprotein phosphatase activity	Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
	GO:0004725	protein tyrosine phosphatase activity	Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0030389	fructosamine metabolic process	The chemical reactions and pathways involving fructosamine, a fructose molecule containing an amino group in place of a hydroxyl group.
	GO:0035335	peptidyl-tyrosine dephosphorylation	The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
	GO:0006470	protein dephosphorylation	The process of removing one or more phosphoric residues from a protein.
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.

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		Pro C:27 - Pro C:28	[ RasMol ]
		Pro D:27 - Pro D:28	[ RasMol ]

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	1u7p
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	MGDP1_MOUSE \| Q9D967	:	1u7o

1u7o	STRUCTURE OF MDP-1 WITHOUT MAGNESIUM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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