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(-) Description

Title :  CRYSTAL STRUCTURE OF UDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYLTRANSFERASE FROM AQUIFEX AEOLICUS VF5
 
Authors :  Y. Kitamuta, S. Yokoyama, S. Kuramitsu, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  16 Apr 07  (Deposition) - 16 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym./Biol. Unit :  A
Keywords :  Peptidoglycan, Transferase, Udp-N-Acetylglucosamine, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kitamura, S. Yokoyama, S. Kuramitsu
Crystal Structure Of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Aquifex Aeolicus Vf5
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYLTRANSFERASE
    Chains: A
    EC Number: 2.5.1.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 224324
    Strain: VF5
    Synonym: ENOYLPYRUVATE TRANSFERASE, UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE, EPT

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1EPU1Ligand/IonURIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRICACID
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:98 , MET A:99 , ARG A:100 , ARG A:403 , HOH A:649 , HOH A:705BINDING SITE FOR RESIDUE PO4 A 511
2AC2SOFTWARELYS A:31 , ASN A:32 , ALA A:101 , ARG A:129 , PRO A:130 , ILE A:131 , ASP A:132 , GLN A:133 , LEU A:168 , VAL A:169 , THR A:170 , VAL A:171 , THR A:172 , ASP A:311 , ILE A:333 , PHE A:334 , VAL A:353 , LEU A:376 , HOH A:605 , HOH A:610 , HOH A:616 , HOH A:625 , HOH A:629 , HOH A:634 , HOH A:636 , HOH A:639 , HOH A:641 , HOH A:642 , HOH A:649 , HOH A:806 , HOH A:807 , HOH A:809BINDING SITE FOR RESIDUE EPU A 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:305 -Pro A:306

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YVW)

(-) 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:416
 aligned with MURA_AQUAE | O67315 from UniProtKB/Swiss-Prot  Length:425

    Alignment length:416
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418      
           MURA_AQUAE     9 YRDYFVIRGGKPLTGKVKISGAKNAALPIMFATILTEEPCTITNVPDLLDVRNTLLLLRELGAELEFLNNTVFINPSINSFITNQEIIRRMRASVLSLGPLLGRFGRAVVGLPGGCSIGARPIDQHLKFFKEAGADVEVREGYVYVNLKEKRRVHFKFDLVTVTGTENALLYLASVPEESILENIALEPEVMDLIEVLKKMGAHVKVEGRSAYVKGSENLKGFTHSVIPDRIEAGTFMVGAVLTDGEILLENARINHLRAVVEKLKLIGGEVVEENGNLRVFRKESLRACDIETQVYPGFPTDMQAQFMALLSVAKGKSRIKENIFEHRFHHAQELNRLGANITVRGNTAYVEGVERLYGSEVYSTDLRASASLVLAGLVAQGETVVRDVYHLDRGYEKLEEKLKKLGADIERVSE 424
               SCOP domains d2yvwa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2yvwA01            --2yvwA02 A:30-235  [code=3.65.10.10, no name defined]                                                                                                                                                          -2yvwA01 A:9-27,A:237-424  [code=3.65.10.10, no name defined]                                                                                                                                 CATH domains
               Pfam domains ------EPSP_synthase-2yvwA01 A:15-412                                                                                                                                                                                                                                                                                                                                                                                ------------ Pfam domains
         Sec.struct. author ...eeeee.....eeeee...hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh..eeeee..eeeee......eehhhhhhhhhhhhhhhhhhhhhhheeeee...........hhhhhhhhhhh..eeeee..eeeee.......eee....hhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhh..eeeee..eeeee........eee...hhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhheeeeee..eeeeee........ee.......hhhhhhhhhhhhh....eeeee.......hhhhhhhhh....eeee..eeeee........eee......hhhhhhhhhhh..eeeee.hhhhhhhh.hhhhhhhhh...eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yvw A   9 YRDYFVIRGGKPLTGKVKISGAKNAALPIMFATILTEEPCTITNVPDLLDVRNTLLLLRELGAELEFLNNTVFINPSINSFITNQEIIRRMRASVLSLGPLLGRFGRAVVGLPGGCSIGARPIDQHLKFFKEAGADVEVREGYVYVNLKEKRRVHFKFDLVTVTGTENALLYLASVPEESILENIALEPEVMDLIEVLKKMGAHVKVEGRSAYVKGSENLKGFTHSVIPDRIEAGTFMVGAVLTDGEILLENARINHLRAVVEKLKLIGGEVVEENGNLRVFRKESLRACDIETQVYPGFPTDMQAQFMALLSVAKGKSRIKENIFEHRFHHAQELNRLGANITVRGNTAYVEGVERLYGSEVYSTDLRASASLVLAGLVAQGETVVRDVYHLDRGYEKLEEKLKKLGADIERVSE 424
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: EPT_RTPC (43)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MURA_AQUAE | O67315)
molecular function
    GO:0008760    UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity    Catalysis of the reaction: phosphoenolpyruvate + UDP-N-acetyl-alpha-D-glucosamine = phosphate + UDP-N-acetyl-3-O-(1-carboxyvinyl)-D-glucosamine.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0016765    transferase activity, transferring alkyl or aryl (other than methyl) groups    Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
biological process
    GO:0019277    UDP-N-acetylgalactosamine biosynthetic process    The chemical reactions and pathways resulting in the formation of UDP-N-acetylgalactosamine, a substance composed of N-acetylgalactosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
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 Specified in the PDB File

1uae RELATED ID: AAE001001281.1 RELATED DB: TARGETDB