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(-) Description

Title :  CRYSTAL STRUCTURE OF T. MARITIMA GDP-MANNOSE PYROPHOSPHORYLASE IN COMPLEX WITH GDP-MANNOSE.
 
Authors :  M. C. Pelissier, S. Lesley, P. Kuhn, Y. Bourne
Date :  12 Feb 10  (Deposition) - 23 Jun 10  (Release) - 01 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Nucleotidyl Transferase (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 (DE3) 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  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1GDD2Ligand/IonGUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:7 , GLY A:9 , GLY A:10 , VAL A:56 , GLU A:80 , LYS A:83 , LYS A:84 , ASN A:85 , THR A:86 , PRO A:107 , ALA A:108 , ASP A:109 , HIS 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 , TRP A:258 , ASP A:260 , MG A:602 , HOH A:2022 , HOH A:2023BINDING SITE FOR RESIDUE GDD A 601
2AC2SOFTWAREASP A:109 , ASP A:260 , GDD A:601 , HOH A:2016 , HOH A:2023BINDING SITE FOR RESIDUE MG A 602
3AC3SOFTWARELEU B:7 , ALA B:8 , GLY B:9 , GLY B:10 , VAL B:56 , GLU B:80 , LYS B:83 , LYS B:84 , ASN B:85 , THR B:86 , PRO B:107 , ALA B:108 , ASP B:109 , HIS 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:239BINDING SITE FOR RESIDUE GDD B 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X5Z)

(-) 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 2X5Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2X5Z)

(-) Exons   (0, 0)

(no "Exon" information available for 2X5Z)

(-) 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:333
 aligned with Q9X0C3_THEMA | Q9X0C3 from UniProtKB/TrEMBL  Length:336

    Alignment length:333
                                    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 MMKALILAGGSGERFWPLSTPETPKQFLKLFGNKSLMRWTFERVLEEMDPKDVIVVTHKDYVERTKKELPELPDENIIAEPMKKNTAPACFIGTKLADDDEPVLVLPADHRIPDTKKFWKTVKKALDALEKYDGLFTFGIVPTRPETGYGYIEIGEELEEGVHKVAQFREKPDLETAKKFVESGRFLWNSGMFLWKAREFIEEVKVCEPSIYENLKDVDPRNFEELKKAYEKVPSISVDYAVMEKSKKVRVVKADFEWSDVGNWSSVREIEGYTEESDEVILVDSDRVFVKTHNKPIAVVGLSDVIVIDTPNGILICKEEYAQKVREVVKKLF 333
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhh.......hhhhh......hhhhhhhhhhhh..hhh.........hhhhhhhhh...hhh.........hhhhhhhhhhhh.....eeeeee..ee..hhhhhhhhhhhhhhhhhhhh.eeeeee.........eeeeeeeeee..eeeeeeeee..hhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhh......eeeee.....ee..hhhhhhhhhh.......eeee....eeee.....eeee....eeeeee..eeeeee.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x5z A   1 VMKALILAGGSGERFWPLSTPETPKQFLKLFGNKSLMRWTFERVLEEMDPKDVIVVTHKDYVERTKKELPELPDENIIAEPMKKNTAPACFIGTKLADDDEPVLVLPADHRIPDTKKFWKTVKKALDALEKYDGLFTFGIVPTRPETGYGYIEIGEELEEGVHKVAQFREKPDLETAKKFVESGRFLWNSGMFLWKAREFIEEVKVCEPSIYENLKDVDPRNFEELKKAYEKVPSISVDYAVMEKSKKVRVVKADFEWSDLGNWSSVREIEGYTEESDEVILVDSDRVFVKTHNKPIAVVGLSDVIVIDTPNGILICKEEYAQKVREVVKKLF 333
                                    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:333
 aligned with Q9X0C3_THEMA | Q9X0C3 from UniProtKB/TrEMBL  Length:336

    Alignment length:333
                                    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 MMKALILAGGSGERFWPLSTPETPKQFLKLFGNKSLMRWTFERVLEEMDPKDVIVVTHKDYVERTKKELPELPDENIIAEPMKKNTAPACFIGTKLADDDEPVLVLPADHRIPDTKKFWKTVKKALDALEKYDGLFTFGIVPTRPETGYGYIEIGEELEEGVHKVAQFREKPDLETAKKFVESGRFLWNSGMFLWKAREFIEEVKVCEPSIYENLKDVDPRNFEELKKAYEKVPSISVDYAVMEKSKKVRVVKADFEWSDVGNWSSVREIEGYTEESDEVILVDSDRVFVKTHNKPIAVVGLSDVIVIDTPNGILICKEEYAQKVREVVKKLF 333
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --NTP_transferase-2x5zB01 B:3-277                                                                                                                                                                                                                                                    -------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --NTP_transferase-2x5zB02 B:3-277                                                                                                                                                                                                                                                    -------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..eeeeee..hhhhhh.......hhhhh......hhhhhhhhhhh...hhh.........hhhhhhhhh...hhh.........hhhhhhhhhhh......eeeeee..ee..hhhhhhhhhhhhhhhhhhhh.eeeeee.........eeeeeeeeee..eeeeeeeee..hhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh....hhhhhh......eeeee.....ee..hhhhhhhhhh.......eeee....eeee.....eeee....eeeee....eeeee.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x5z B   1 VMKALILAGGSGERFWPLSTPETPKQFLKLFGNKSLMRWTFERVLEEMDPKDVIVVTHKDYVERTKKELPELPDENIIAEPMKKNTAPACFIGTKLADDDEPVLVLPADHRIPDTKKFWKTVKKALDALEKYDGLFTFGIVPTRPETGYGYIEIGEELEEGVHKVAQFREKPDLETAKKFVESGRFLWNSGMFLWKAREFIEEVKVCEPSIYENLKDVDPRNFEELKKAYEKVPSISVDYAVMEKSKKVRVVKADFEWSDLGNWSSVREIEGYTEESDEVILVDSDRVFVKTHNKPIAVVGLSDVIVIDTPNGILICKEEYAQKVREVVKKLF 333
                                    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 2X5Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2X5Z)

(-) 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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 Related Entries

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UniProtKB/TrEMBL
        Q9X0C3_THEMA | Q9X0C3: 2x5s 2x60 2x65

(-) Related Entries Specified in the PDB File

2x5s CRYSTAL STRUCTURE OF T. MARITIMA GDP-MANNOSE PYROPHOSPHORYLASE IN APO STATE.
2x60 CRYSTAL STRUCTURE OF T. MARITIMA GDP-MANNOSE PYROPHOSPHORYLASE IN COMPLEX WITH GTP.
2x65 CRYSTAL STRUCTURE OF T. MARITIMA GDP-MANNOSE PYROPHOSPHORYLASE IN COMPLEX WITH MANNOSE-1 -PHOSPHATE.