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(-) Description

Title :  H309A MUTANT OF MANNOSYL-3-PHOSPHOGLYCERATE SYNTHASE FROM THERMUS THERMOPHILUS HB27 IN COMPLEX WITH GDP-ALPHA-D-MANNOSE AND MG(II)
 
Authors :  S. Goncalves, N. Borges, A. M. Esteves, B. Victor, C. M. Soares, H. Santo P. M. Matias
Date :  19 Oct 09  (Deposition) - 31 Mar 10  (Release) - 19 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.98
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Keywords :  Gt-A Fold, Transferase, Glycosyltransferase, Retaining Mechanism, Glucosyl Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Goncalves, N. Borges, A. M. Esteves, B. Victor, C. M. Soares, H. Santos, P. M. Matias
Structural Analysis Of Thermus Thermophilus Hb27 Mannosyl-3-Phosphoglycerate Synthase Provides Evidence For A Second Catalytic Metal Ion And New Insight Into The Retaining Mechanism Of Glycosyltransferases.
J. Biol. Chem. V. 285 17857 2010
PubMed-ID: 20356840  |  Reference-DOI: 10.1074/JBC.M109.095976
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MANNOSYL-3-PHOSPHOGLYCERATE SYNTHASE
    Chains: A, B
    EC Number: 2.4.1.217
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: ROSETTA
    Mutation: YES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 262724
    Strain: HB27

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1GDD2Ligand/IonGUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
2MG2Ligand/IonMAGNESIUM ION
3ZN3Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GDD2Ligand/IonGUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:60 , THR A:61 , ARG A:62 , GLU A:64 , ALA A:85 , ASN A:87 , GLN A:116 , GLY A:143 , LYS A:144 , ASP A:167 , ALA A:168 , ASP A:169 , ASN A:248 , GLY A:250 , TYR A:268 , GLU A:271 , MG A:401BINDING SITE FOR RESIDUE GDD A 400
2AC2SOFTWAREASP A:169 , GDD A:400BINDING SITE FOR RESIDUE MG A 401
3AC3SOFTWAREPRO B:60 , THR B:61 , ARG B:62 , GLU B:64 , ALA B:85 , ASN B:87 , GLN B:116 , GLY B:143 , LYS B:144 , ASP B:167 , ALA B:168 , ASP B:169 , GLY B:250 , TYR B:268 , GLU B:271 , MG B:401BINDING SITE FOR RESIDUE GDD B 400
4AC4SOFTWAREASP B:169 , GDD B:400BINDING SITE FOR RESIDUE MG B 401
5AC5SOFTWAREHIS A:8 , GLU A:19 , HOH A:2007 , HIS B:105BINDING SITE FOR RESIDUE ZN A1392
6AC6SOFTWAREHIS B:8 , GLU B:19 , ASP B:242 , HOH B:2008BINDING SITE FOR RESIDUE ZN B1392
7AC7SOFTWAREGLU A:292 , HIS A:296 , GLU B:292 , HIS B:296BINDING SITE FOR RESIDUE ZN B1393

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WVM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WVM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WVM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WVM)

(-) Exons   (0, 0)

(no "Exon" information available for 2WVM)

(-) 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:375
 aligned with Q72K30_THET2 | Q72K30 from UniProtKB/TrEMBL  Length:391

    Alignment length:391
                                    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       260       270       280       290       300       310       320       330       340       350       360       370       380       390 
         Q72K30_THET2     1 MRLEIPNHTERFGVVRLHEVQRILELDSGRVRDESPAVGLRRLDDADLRDVLEQTAIVVPTRNERLKLLEGVLSGIPHEALILVASNSSPDRFQMERDLLEEFAHLTERPALIFHQKDPALAEALRAGGYPHPIGEDGLVRSGKAEGMILALVFAALSGRRYVGFIDADNYFPGAVWEYVRAYAAGFLMAKTPFAMVRILWRYKPKLTEDEGVVFRRYGRVSERNNRALNQLIGGVSGFETDVVKTANAGEHAMSLGLALRLPLASGYAVEPQELVSLLELYGGVFPLEDEEVLQHGVEIFQIETRNPHLHENKGDEHIRDMLLACLATVYHSKLATEEVRQSVLEELQAAGALAPGEEPPPPVLYPPLSSLDLQAVRKALRGHFSRFRVP 391
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eeee..eeee..eeeee..............eee.hhhhhhhhhh...........hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhh..............hhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh............----------.hhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhh........hhhhhhhhhhhhhhh......hhhhhhhheeeeeee............hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.------..........hhhhhhhhhhhhhh..hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wvm A   1 MRLEIPNHTERFGVVRLHEVQRILELDSGRVRDESPAVGLRRLDDADLRDVLEQTAIVVPTRNERLKLLEGVLSGIPHEALILVASNSSPDRFQMERDLLEEFAHLTERPALIFHQKDPALAEALRAGGYPHPIGEDGLVRSGKAEGMILALVFAALSGRRYVGFIDADNYFPGAVWEYVRAYAAGFLMAKTPFAMVRILWR----------VVFRRYGRVSERNNRALNQLIGGVSGFETDVVKTANAGEHAMSLGLALRLPLASGYAVEPQELVSLLELYGGVFPLEDEEVLQHGVEIFQIETRNPALHENKGDEHIRDMLLACLATVYHSKLATEEVRQSVLEELQAA------EEPPPPVLYPPLSSLDLQAVRKALRGHFSRFRVP 391
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 |       -  |    220       230       240       250       260       270       280       290       300       310       320       330       340       350|      360       370       380       390 
                                                                                                                                                                                                                                   202        213                                                                                                                                       351    358                                 


Chain B from PDB  Type:PROTEIN  Length:372
 aligned with Q72K30_THET2 | Q72K30 from UniProtKB/TrEMBL  Length:391

    Alignment length:391
                                    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       260       270       280       290       300       310       320       330       340       350       360       370       380       390 
         Q72K30_THET2     1 MRLEIPNHTERFGVVRLHEVQRILELDSGRVRDESPAVGLRRLDDADLRDVLEQTAIVVPTRNERLKLLEGVLSGIPHEALILVASNSSPDRFQMERDLLEEFAHLTERPALIFHQKDPALAEALRAGGYPHPIGEDGLVRSGKAEGMILALVFAALSGRRYVGFIDADNYFPGAVWEYVRAYAAGFLMAKTPFAMVRILWRYKPKLTEDEGVVFRRYGRVSERNNRALNQLIGGVSGFETDVVKTANAGEHAMSLGLALRLPLASGYAVEPQELVSLLELYGGVFPLEDEEVLQHGVEIFQIETRNPHLHENKGDEHIRDMLLACLATVYHSKLATEEVRQSVLEELQAAGALAPGEEPPPPVLYPPLSSLDLQAVRKALRGHFSRFRVP 391
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Osmo_MPGsynth-2wvmB01 B:3-382                                                                                                                                                                                                                                                                                                                                                               --------- Pfam domains (1)
           Pfam domains (2) --Osmo_MPGsynth-2wvmB02 B:3-382                                                                                                                                                                                                                                                                                                                                                               --------- Pfam domains (2)
         Sec.struct. author .eee....eeee..eeee..eeeee..............eee.hhhhhhhhhhh..........hhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhh..............hhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh............-------------hhhhhhhhhhhhhhhhhhhhhhh.................hhhhh...ee...hhhhhhhhhhhhhhh......hhhhhhhheeeeeee.............hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.------.......ee.hhhhhhhhhhhhhh..hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wvm B   1 MRLEIPNHTERFGVVRLHEVQRILELDSGRVRDESPAVGLRRLDDADLRDVLEQTAIVVPTRNERLKLLEGVLSGIPHEALILVASNSSPDRFQMERDLLEEFAHLTERPALIFHQKDPALAEALRAGGYPHPIGEDGLVRSGKAEGMILALVFAALSGRRYVGFIDADNYFPGAVWEYVRAYAAGFLMAKTPFAMVRILWR-------------RRYGRVSERNNRALNQLIGGVSGFETDVVKTANAGEHAMSLGLALRLPLASGYAVEPQELVSLLELYGGVFPLEDEEVLQHGVEIFQIETRNPALHENKGDEHIRDMLLACLATVYHSKLATEEVRQSVLEELQAA------EEPPPPVLYPPLSSLDLQAVRKALRGHFSRFRVP 391
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 |       -     | 220       230       240       250       260       270       280       290       300       310       320       330       340       350|      360       370       380       390 
                                                                                                                                                                                                                                   202           216                                                                                                                                    351    358
   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 2WVM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WVM)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Osmo_MPGsynth] (5)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q72K30_THET2 | Q72K30)
molecular function
    GO:0050504    mannosyl-3-phosphoglycerate synthase activity    Catalysis of the reaction: 3-phospho-D-glycerate + GDP-alpha-D-mannose = 2-(alpha-D-mannosyl)-3-phosphoglycerate + GDP + H(+).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    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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  2.4.1.217
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 Related Entries

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

UniProtKB/TrEMBL
        Q72K30_THET2 | Q72K30: 2wvk 2wvl

(-) Related Entries Specified in the PDB File

2wvk MANNOSYL-3-PHOSPHOGLYCERATE SYNTHASE FROM THERMUS THERMOPHILUS HB27 APOPROTEIN
2wvl MANNOSYL-3-PHOSPHOGLYCERATE SYNTHASE FROM THERMUS THERMOPHILUS HB27 IN COMPLEX WITH GDP-ALPHA-D-MANNOSE AND MG(II)