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(-) Description

Title :  CRYSTAL STRUCTURE OF T. MARITIMA GDP-MANNOSE PYROPHOSPHORYLASE IN COMPLEX WITH MANNOSE-1-PHOSPHATE.
 
Authors :  M. C. Pelissier, S. Lesley, P. Kuhn, Y. Bourne
Date :  15 Feb 10  (Deposition) - 23 Jun 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Nucleotidyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Pelissier, S. Lesley, P. Kuhn, Y. Bourne
Structural Insights Into The Catalytic Mechanism Of Bacterial Guanosine-Diphospho-D-Mannose Pyrophosphorylase And Its Regulation By Divalent Ions.
J. Biol. Chem. V. 285 27468 2010
PubMed-ID: 20573954  |  Reference-DOI: 10.1074/JBC.M109.095182

(-) Compounds

Molecule 1 - MANNOSE-1-PHOSPHATE GUANYLYLTRANSFERASE
    Atcc: 43589
    Chains: A, B
    EC Number: 2.7.7.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMH1
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: ORIGAMI(DE30 PLYSS)
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Other Details: DSM 3109
    Strain: MSB8
    Synonym: GDP-MANNOSE PYROPHOSPHORYLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
1M1P2Ligand/IonALPHA-D-MANNOSE 1-PHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4MRD2Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
5PO41Ligand/IonPHOSPHATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:110 , TYR A:149 , GLY A:150 , GLU A:170 , LYS A:171 , ASN A:189 , SER A:190 , GLY A:191 , ASP A:239 , ASP A:260 , MG A:601 , HOH A:2041 , HOH A:2061 , HOH A:2062 , HOH A:2063 , HOH A:2064 , HOH A:2065BINDING SITE FOR RESIDUE M1P A 600
02AC2SOFTWAREM1P A:600 , HOH A:2023 , HOH A:2061 , HOH A:2062 , HOH A:2063 , HOH A:2064BINDING SITE FOR RESIDUE MG A 601
03AC3SOFTWAREHIS B:110 , TYR B:149 , GLY B:150 , GLU B:170 , LYS B:171 , ASN B:189 , SER B:190 , GLY B:191 , ASP B:239 , TRP B:258 , ASP B:260 , MG B:601 , HOH B:2087 , HOH B:2088 , HOH B:2089BINDING SITE FOR RESIDUE M1P B 600
04AC4SOFTWAREM1P B:600 , HOH B:2031 , HOH B:2087 , HOH B:2088 , HOH B:2089BINDING SITE FOR RESIDUE MG B 601
05AC5SOFTWARESER B:11 , GLY B:12 , GLU B:13 , ARG B:14 , ARG B:326 , HOH B:2090 , HOH B:2091BINDING SITE FOR RESIDUE PO4 B 602
06AC6SOFTWAREPHE A:31 , ARG A:111 , HOH A:2066 , HOH A:2067 , THR B:115BINDING SITE FOR RESIDUE MRD A1335
07AC7SOFTWARETHR A:115 , HOH A:2068 , PHE B:31 , ARG B:111BINDING SITE FOR RESIDUE MRD A1336
08AC8SOFTWARETHR A:274 , GLU A:275 , HOH A:2051 , HOH A:2069 , ASP B:127 , HOH B:2038BINDING SITE FOR RESIDUE MPD A1337
09AC9SOFTWARELYS A:66 , PRO A:70 , ASP A:74BINDING SITE FOR RESIDUE MPD A1338
10BC1SOFTWARELYS A:123 , LYS A:124 , ASP A:127 , HOH A:2070 , HOH A:2071BINDING SITE FOR RESIDUE MPD A1339

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X65)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:16 -Pro A:17
2Trp B:16 -Pro B:17

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2X65)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2X65)

(-) Exons   (0, 0)

(no "Exon" information available for 2X65)

(-) 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:334
 aligned with Q9X0C3_THEMA | Q9X0C3 from UniProtKB/TrEMBL  Length:336

    Alignment length:334
                                    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    
         Q9X0C3_THEMA     1 MMKALILAGGSGERFWPLSTPETPKQFLKLFGNKSLMRWTFERVLEEMDPKDVIVVTHKDYVERTKKELPELPDENIIAEPMKKNTAPACFIGTKLADDDEPVLVLPADHRIPDTKKFWKTVKKALDALEKYDGLFTFGIVPTRPETGYGYIEIGEELEEGVHKVAQFREKPDLETAKKFVESGRFLWNSGMFLWKAREFIEEVKVCEPSIYENLKDVDPRNFEELKKAYEKVPSISVDYAVMEKSKKVRVVKADFEWSDVGNWSSVREIEGYTEESDEVILVDSDRVFVKTHNKPIAVVGLSDVIVIDTPNGILICKEEYAQKVREVVKKLFR 334
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhh........hhhh......hhhhhhhhhhhh..hhh.........hhhhhhhhh...hhh.........hhhhhhhhhhh......eeeeee......hhhhhhhhhhhhhhhhhhhh.eeeeee.........eeeeeeeeee..eeeeeeeee..hhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhh......eeeee.........hhhhhhhhhh.......eeee....eeee.....eeee....eeeeee..eeeeee.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x65 A   1 VMKALILAGGSGERFWPLSTPETPKQFLKLFGNKSLMRWTFERVLEEMDPKDVIVVTHKDYVERTKKELPELPDENIIAEPMKKNTAPACFIGTKLADDDEPVLVLPADHRIPDTKKFWKTVKKALDALEKYDGLFTFGIVPTRPETGYGYIEIGEELEEGVHKVAQFREKPDLETAKKFVESGRFLWNSGMFLWKAREFIEEVKVCEPSIYENLKDVDPRNFEELKKAYEKVPSISVDYAVMEKSKKVRVVKADFEWSDLGNWSSVREIEGYTEESDEVILVDSDRVFVKTHNKPIAVVGLSDVIVIDTPNGILICKEEYAQKVREVVKKLFR 334
                                    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    


Chain B from PDB  Type:PROTEIN  Length:334
 aligned with Q9X0C3_THEMA | Q9X0C3 from UniProtKB/TrEMBL  Length:336

    Alignment length:334
                                    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    
         Q9X0C3_THEMA     1 MMKALILAGGSGERFWPLSTPETPKQFLKLFGNKSLMRWTFERVLEEMDPKDVIVVTHKDYVERTKKELPELPDENIIAEPMKKNTAPACFIGTKLADDDEPVLVLPADHRIPDTKKFWKTVKKALDALEKYDGLFTFGIVPTRPETGYGYIEIGEELEEGVHKVAQFREKPDLETAKKFVESGRFLWNSGMFLWKAREFIEEVKVCEPSIYENLKDVDPRNFEELKKAYEKVPSISVDYAVMEKSKKVRVVKADFEWSDVGNWSSVREIEGYTEESDEVILVDSDRVFVKTHNKPIAVVGLSDVIVIDTPNGILICKEEYAQKVREVVKKLFR 334
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --NTP_transferase-2x65B01 B:3-277                                                                                                                                                                                                                                                    --------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --NTP_transferase-2x65B02 B:3-277                                                                                                                                                                                                                                                    --------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..eeeeee...hhhhh.......hhhhh......hhhhhhhhhhh...hhh.........hhhhhhhhh...hhh.........hhhhhhhhhhh......eeeeee......hhhhhhhhhhhhhhhhhhhh.eeeeee.........eeeeeeeeee..eeeeeeeee..hhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh....hhhhhh......eeeee.........hhhhhhhhhh.......eeee....eeee.....eeee....eeeeee..eeeeee.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x65 B   1 VMKALILAGGSGERFWPLSTPETPKQFLKLFGNKSLMRWTFERVLEEMDPKDVIVVTHKDYVERTKKELPELPDENIIAEPMKKNTAPACFIGTKLADDDEPVLVLPADHRIPDTKKFWKTVKKALDALEKYDGLFTFGIVPTRPETGYGYIEIGEELEEGVHKVAQFREKPDLETAKKFVESGRFLWNSGMFLWKAREFIEEVKVCEPSIYENLKDVDPRNFEELKKAYEKVPSISVDYAVMEKSKKVRVVKADFEWSDLGNWSSVREIEGYTEESDEVILVDSDRVFVKTHNKPIAVVGLSDVIVIDTPNGILICKEEYAQKVREVVKKLFR 334
                                    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
   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 2X65)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2X65)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: GT-A (172)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9X0C3_THEMA | Q9X0C3)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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.
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.

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  2.7.7.13
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 Related Entries

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

UniProtKB/TrEMBL
        Q9X0C3_THEMA | Q9X0C3: 2x5s 2x5z 2x60

(-) Related Entries Specified in the PDB File

2x5s CRYSTAL STRUCTURE OF T. MARITIMA GDP-MANNOSE PYROPHOSPHORYLASE IN APO STATE.
2x5z CRYSTAL STRUCTURE OF T. MARITIMA GDP-MANNOSE PYROPHOSPHORYLASE IN COMPLEX WITH GDP- MANNOSE.
2x60 CRYSTAL STRUCTURE OF T. MARITIMA GDP-MANNOSE PYROPHOSPHORYLASE IN COMPLEX WITH GTP.