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(-) Description

Title :  THE 3-DIMENSIONAL STRUCTURE OF MPGP FROM THERMUS THERMOPHILUS HB27, COVALENTLY BOUND TO VANADATE AND IN COMPLEX WITH ALPHA-MANNOSYLGLYCERATE AND MAGNESIUM
 
Authors :  S. Goncalves, A. M. Esteves, H. Santos, N. Borges, P. M. Matias
Date :  07 Aug 11  (Deposition) - 19 Oct 11  (Release) - 09 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Haloalkanoid Acid Dehalogenase-Like Phosphatase, Had-Like Phosphatase, Crystallographic Snapshot (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Goncalves, A. M. Esteves, H. Santos, N. Borges, P. M. Matias
The Three-Dimensional Structure Of Mannosyl-3- Phosphoglycerate Phosphatase From Thermus Thermophilus Hb27: A New Member Of The Haloalkanoic Acid Dehalogenase Superfamily.
Biochemistry V. 50 9551 2011
PubMed-ID: 21961705  |  Reference-DOI: 10.1021/BI201171H
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MANNOSYL-3-PHOSPHOGLYCERATE PHOSPHATASE
    Chains: A, B
    EC Number: 3.1.3.70
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PKK223-3
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 262724
    Strain: HB27
    Synonym: MPGP

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
12M82Ligand/Ion2-O-ALPHA-MANNOSYL-D-GLYCERATE
2MG2Ligand/IonMAGNESIUM ION
3VN42Ligand/IonOXIDO(DIOXO)VANADIUM

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:6 , ASP A:8 , ASP A:202 , VN4 A:261 , HOH A:2005 , HOH A:2006BINDING SITE FOR RESIDUE MG A 260
2AC2SOFTWAREASP A:6 , LEU A:7 , ASP A:8 , THR A:39 , ALA A:40 , LYS A:177 , ASN A:205 , MG A:260 , 2M8 A:262 , HOH A:2005 , HOH A:2006BINDING SITE FOR RESIDUE VN4 A 261
3AC3SOFTWAREASP A:8 , LYS A:41 , GLU A:45 , TYR A:110 , ARG A:135 , THR A:140 , GLY A:165 , GLY A:166 , ARG A:167 , PHE A:168 , HIS A:170 , VN4 A:261 , HOH A:2135 , HOH A:2176BINDING SITE FOR RESIDUE 2M8 A 262
4AC4SOFTWAREASP B:6 , ASP B:8 , ASP B:202 , VN4 B:261 , HOH B:2006 , HOH B:2010BINDING SITE FOR RESIDUE MG B 260
5AC5SOFTWAREASP B:6 , LEU B:7 , ASP B:8 , THR B:39 , ALA B:40 , LYS B:177 , ASN B:205 , MG B:260 , 2M8 B:262 , HOH B:2006 , HOH B:2010BINDING SITE FOR RESIDUE VN4 B 261
6AC6SOFTWAREASP B:8 , ALA B:40 , LYS B:41 , GLU B:45 , TYR B:110 , ARG B:135 , THR B:140 , GLY B:165 , GLY B:166 , ARG B:167 , PHE B:168 , HIS B:170 , VN4 B:261 , HOH B:2011 , HOH B:2168BINDING SITE FOR RESIDUE 2M8 B 262

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:144 -B:144

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:53 -Pro A:54
2Pro B:53 -Pro B:54

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZX5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZX5)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZX5)

(-) 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:252
 aligned with Q72K29_THET2 | Q72K29 from UniProtKB/TrEMBL  Length:259

    Alignment length:252
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250  
         Q72K29_THET2     1 MIVFTDLDGTLLDERGELGPAREALERLRALGVPVVPVTAKTRKEVEALGLEPPFIVENGGGLYLPRDWPVRAGRPKGGYRVVSLAWPYRKVRARLREAEALAGRPILGYGDLTAEAVARLTGLSREAARRAKAREYDETLVLCPEEVEAVLEALEAVGLEWTHGGRFYHAAKGADKGRAVARLRALWPDPEEARFAVGLGDSLNDLPLFRAVDLAVYVGRGDPPEGVLATPAPGPEGFRYAVERYLLPRLS 252
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..............hhhhhhhhhhhh...eee....hhhhhhhh.....eeehhh.eeeee........eee..eeeee...hhhhhhhhhhhhhhhhh...ee....hhhhhhhhhh.hhhhhhhhhh....eeee.hhhhhhhhhhhhhhh..eeee....eeee...hhhhhhhhhhhh.........eeeee.hhhhhhhhhh..eeee..........ee...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3zx5 A   1 MIVFTDLDGTLLDERGELGPAREALERLRALGVPVVPVTAKTRKEVEALGLEPPFIVENGGGLYLPRDWPVRAGRPKGGYRVVSLAWPYRKVRARLREAEALAGRPILGYGDLTAEAVARLTGLSREAARRAKAREYDETLVLCPEEVEAVLEALEAVGLEWTHGGRFYHAAKGADKGRAVARLRALWPDPEEARFAVGLGDSLNDLPLFRAVDLAVYVGRGDPPEGVLATPAPGPEGFRYAVERYLLPRLS 252
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250  


Chain B from PDB  Type:PROTEIN  Length:252
 aligned with Q72K29_THET2 | Q72K29 from UniProtKB/TrEMBL  Length:259

    Alignment length:252
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250  
         Q72K29_THET2     1 MIVFTDLDGTLLDERGELGPAREALERLRALGVPVVPVTAKTRKEVEALGLEPPFIVENGGGLYLPRDWPVRAGRPKGGYRVVSLAWPYRKVRARLREAEALAGRPILGYGDLTAEAVARLTGLSREAARRAKAREYDETLVLCPEEVEAVLEALEAVGLEWTHGGRFYHAAKGADKGRAVARLRALWPDPEEARFAVGLGDSLNDLPLFRAVDLAVYVGRGDPPEGVLATPAPGPEGFRYAVERYLLPRLS 252
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee.hhhhhh.....hhhhhhhhhhhhhh...eee....hhhhhhhh.....eeehhh.eeeee........eee..eeeee...hhhhhhhhhhhhhhhhh...ee....hhhhhhhhhh.hhhhhhhhh.....eeee.hhhhhhhhhhhhhhh..eeee....eeee...hhhhhhhhhhhh..hhhhhh.eeeee.hhhhhhhhhh..eeee...............hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3zx5 B   1 MIVFTDLDGTLLDERGELGPAREALERLRALGVPVVPVTAKTRKEVEALGLEPPFIVENGGGLYLPRDWPVRAGRPKGGYRVVSLAWPYRKVRARLREAEALAGRPILGYGDLTAEAVARLTGLSREAARRAKAREYDETLVLCPEEVEAVLEALEAVGLEWTHGGRFYHAAKGADKGRAVARLRALWPDPEEARFAVGLGDSLNDLPLFRAVDLAVYVGRGDPPEGVLATPAPGPEGFRYAVERYLLPRLS 252
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3ZX5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZX5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZX5)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q72K29_THET2 | Q72K29)
molecular function
    GO:0050531    mannosyl-3-phosphoglycerate phosphatase activity    Catalysis of the reaction: 2-(alpha-D-mannosyl)-3-phosphoglycerate + H(2)O = 2-(alpha-D-mannosyl)-D-glycerate + phosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0051479    mannosylglycerate biosynthetic process    The chemical reactions and pathways resulting in the formation of mannosylglycerate, a very common compatible solute in thermophilic and hyperthermophilic organisms.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/TrEMBL
        Q72K29_THET2 | Q72K29: 3ztw 3zty 3zu6 3zup 3zw7 3zwd 3zwk 3zx4

(-) Related Entries Specified in the PDB File

3ztw THE 3-DIMENSIONAL STRUCTURE OF APO-MPGP, THE MANNOSYL -3-PHOSPHOGLYCERATE PHOSPHATASE FROM THERMUS THERMOPHILUS HB27 IN ITS APO-FORM
3zty THE 3-DIMENSIONAL STRUCTURE OF THE GADOLINIUM DERIVATIVE OF MPGP, THE MANNOSYL-3-PHOSPHOGLYCERATE PHOSPHATASE FROM THERMUS THERMOPHILUS HB27
3zu6 THE 3-DIMENSIONAL STRUCTURE OF MPGP FROM THERMUS THERMOPHILUS HB27, IN COMPLEX WITH THE ALPHA- MANNOSYLGLYCERATE AND ORTHOPHOSPHATE REACTION PRODUCTS.
3zup THE 3-DIMENSIONAL STRUCTURE OF MPGP FROM THERMUS THERMOPHILUS HB27, IN COMPLEX WITH THE ALPHA- MANNOSYLGLYCERATE AND ORTHOPHOSPHATE REACTION PRODUCTS.
3zw7 THE 3-DIMENSIONAL STRUCTURE OF MPGP FROM THERMUS THERMOPHILUS HB27, IN COMPLEX WITH THE ALPHA- MANNOSYLGLYCERATE AND METAPHOSPHATE.
3zwd THE 3-DIMENSIONAL STRUCTURE OF MPGP FROM THERMUS THERMOPHILUS HB27, IN COMPLEX WITH THE ALPHA- MANNOSYLGLYCERATE.
3zwk THE 3-DIMENSIONAL STRUCTURE OF MPGP FROM THERMUS THERMOPHILUS HB27, IN COMPLEX WITH THE METAVANADATE
3zx4 THE 3-DIMENSIONAL STRUCTURE OF MPGP FROM THERMUS THERMOPHILUS HB27, IN COMPLEX WITH THE ALPHA- MANNOSYLGLYCERATE,ORTHOPHOSPHATE AND MAGNESIUM