Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  AQUIFEX AEOLICUS MURA IN COMPLEX WITH UDP-N-ACETYLMURAMIC ACID AND COVALENT ADDUCT OF PEP WITH CYS124
 
Authors :  J. -Y. Zhu, E. Schonbrunn
Date :  13 Jul 11  (Deposition) - 14 Mar 12  (Release) - 02 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym./Biol. Unit :  A
Keywords :  Mura, Close Enzyme State, Cell Wall, Biogenesis/Degradation, Peptidoglycan Synthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Y. Zhu, Y. Yang, H. Han, S. Betzi, S. H. Olesen, F. Marsilio, E. Schonbrunn
Functional Consequence Of Covalent Reaction Of Phosphoenolpyruvate With Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase (Mura).
J. Biol. Chem. V. 287 12657 2012
PubMed-ID: 22378791  |  Reference-DOI: 10.1074/JBC.M112.342725

(-) 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
    Gene: MURA, AQ_1281
    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  (6, 19)

Asymmetric/Biological Unit (6, 19)
No.NameCountTypeFull Name
1EDO11Ligand/Ion1,2-ETHANEDIOL
2EPZ1Ligand/Ion(2R)-2-{[(2R,3R,4R,5S,6R)-3-(ACETYLAMINO)-2-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-5-HYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-4-YL]OXY}PROPANOICACID
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
4PG43Ligand/IonTETRAETHYLENE GLYCOL
5PGE1Ligand/IonTRIETHYLENE GLYCOL
6QPA1Mod. Amino AcidS-[(1S)-1-CARBOXY-1-(PHOSPHONOOXY)ETHYL]-L-CYSTEINE

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:132 , LYS A:139 , VAL A:145 , ASN A:350 , HOH A:898 , HOH A:928BINDING SITE FOR RESIDUE PG4 A 501
02AC2SOFTWARELYS A:326 , THR A:352 , TYR A:359 , GLU A:361BINDING SITE FOR RESIDUE PG4 A 502
03AC3SOFTWAREGLU A:255 , LEU A:257 , ARG A:267 , ARG A:288 , HOH A:703 , HOH A:935BINDING SITE FOR RESIDUE PG4 A 503
04AC4SOFTWARELYS A:165 , PHE A:166 , ASP A:167 , ASN A:192BINDING SITE FOR RESIDUE PGE A 504
05AC5SOFTWAREPRO A:47 , THR A:49 , PHE A:231 , THR A:232 , HOH A:901BINDING SITE FOR RESIDUE PEG A 505
06AC6SOFTWAREALA A:323 , LYS A:324 , VAL A:363 , GLU A:364 , HOH A:845BINDING SITE FOR RESIDUE PEG A 506
07AC7SOFTWAREILE A:90 , TYR A:151 , TYR A:153BINDING SITE FOR RESIDUE EDO A 507
08AC8SOFTWAREASN A:83BINDING SITE FOR RESIDUE EDO A 508
09AC9SOFTWAREARG A:112 , GLY A:114BINDING SITE FOR RESIDUE EDO A 509
10BC1SOFTWAREGLU A:146 , ARG A:148 , TYR A:153BINDING SITE FOR RESIDUE EDO A 510
11BC2SOFTWAREARG A:60 , ARG A:67BINDING SITE FOR RESIDUE EDO A 511
12BC3SOFTWAREPHE A:290BINDING SITE FOR RESIDUE EDO A 512
13BC4SOFTWAREASN A:284 , GLY A:285 , ASN A:286BINDING SITE FOR RESIDUE EDO A 513
14BC5SOFTWARELYS A:214 , TYR A:221 , ARG A:365BINDING SITE FOR RESIDUE EDO A 514
15BC6SOFTWAREHIS A:163 , GLU A:191BINDING SITE FOR RESIDUE EDO A 515
16BC7SOFTWAREGLU A:187 , LYS A:223 , GLN A:390BINDING SITE FOR RESIDUE EDO A 516
17BC8SOFTWARELEU A:43 , GLU A:45 , GLU A:226 , HOH A:701 , HOH A:863BINDING SITE FOR RESIDUE EDO A 517
18BC9SOFTWARELYS 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 , THR A:170 , VAL A:171 , THR A:172 , THR A:310 , ASP A:311 , ILE A:333 , PHE A:334 , VAL A:353 , LEU A:376 , HOH A:604 , HOH A:609 , HOH A:615 , HOH A:624 , HOH A:628 , HOH A:633 , HOH A:635 , HOH A:638 , HOH A:640 , HOH A:641 , HOH A:648 , HOH A:804 , HOH A:805 , HOH A:807BINDING SITE FOR RESIDUE EPZ A 518

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SWG)

(-) 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 3SWG)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3SWG)

(-) 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:417
 aligned with MURA_AQUAE | O67315 from UniProtKB/Swiss-Prot  Length:425

    Alignment length:417
                                    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 YRDYFVIRGGKPLTGKVKISGAKNAALPIMFATILTEEPCTITNVPDLLDVRNTLLLLRELGAELEFLNNTVFINPSINSFITNQEIIRRMRASVLSLGPLLGRFGRAVVGLPGGCSIGARPIDQHLKFFKEAGADVEVREGYVYVNLKEKRRVHFKFDLVTVTGTENALLYLASVPEESILENIALEPEVMDLIEVLKKMGAHVKVEGRSAYVKGSENLKGFTHSVIPDRIEAGTFMVGAVLTDGEILLENARINHLRAVVEKLKLIGGEVVEENGNLRVFRKESLRACDIETQVYPGFPTDMQAQFMALLSVAKGKSRIKENIFEHRFHHAQELNRLGANITVRGNTAYVEGVERLYGSEVYSTDLRASASLVLAGLVAQGETVVRDVYHLDRGYEKLEEKLKKLGADIERVSEL 425
               SCOP domains d3swga_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 3swg A   9 YRDYFVIRGGKPLTGKVKISGAKNAALPIMFATILTEEPCTITNVPDLLDVRNTLLLLRELGAELEFLNNTVFINPSINSFITNQEIIRRMRASVLSLGPLLGRFGRAVVGLPGGcSIGARPIDQHLKFFKEAGADVEVREGYVYVNLKEKRRVHFKFDLVTVTGTENALLYLASVPEESILENIALEPEVMDLIEVLKKMGAHVKVEGRSAYVKGSENLKGFTHSVIPDRIEAGTFMVGAVLTDGEILLENARINHLRAVVEKLKLIGGEVVEENGNLRVFRKESLRACDIETQVYPGFPTDMQAQFMALLSVAKGKSRIKENIFEHRFHHAQELNRLGANITVRGNTAYVEGVERLYGSEVYSTDLRASASLVLAGLVAQGETVVRDVYHLDRGYEKLEEKLKKLGADIERVSEL 425
                                    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       
                                                                                                                                             124-QPA
   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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EPZ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PGE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    QPA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Tyr A:305 - Pro A:306   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3swg
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MURA_AQUAE | O67315
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.5.1.7
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  MURA_AQUAE | O67315
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MURA_AQUAE | O67315: 2yvw

(-) Related Entries Specified in the PDB File

2yvw THIS ENTRY 3SWD REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA R2YVWSF