Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS MEMBRANE-BOUND TRANSGLYCOSYLASE: APOENZYME
 
Authors :  C. Y. Huang, H. W. Shih, L. Y. Lin, Y. W. Tien, T. J. R. Cheng, W. C. Cheng, C. C. Ma
Date :  15 Dec 11  (Deposition) - 18 Apr 12  (Release) - 17 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.52
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transmembrane, Glycosyltransferase, Bacterial Cell Wall Synthesis, Membrane, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Y. Huang, H. W. Shih, L. Y. Lin, Y. W. Tien, T. J. R. Cheng, W. C. Cheng, C. H. Wong, C. Ma
Crystal Structure Of Staphylococcus Aureus Transglycosylase In Complex With A Lipid Ii Analog And Elucidation Of Peptidoglycan Synthesis Mechanism
Proc. Natl. Acad. Sci. Usa V. 109 6496 2012
PubMed-ID: 22493270  |  Reference-DOI: 10.1073/PNAS.1203900109

(-) Compounds

Molecule 1 - MONOFUNCTIONAL GLYCOSYLTRANSFERASE
    Chains: A, B
    EC Number: 2.4.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 28-269
    Gene: MGT
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 158878
    Strain: MU50
    Synonym: MGT, PEPTIDOGLYCAN TGASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:111 , THR A:115 , GLY A:131 , GLN A:136BINDING SITE FOR RESIDUE MG A 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Thr A:66 -Arg A:67
2Arg A:67 -Asp A:68
3Gly A:130 -Gly A:131
4Thr B:66 -Arg B:67
5Arg B:67 -Asp B:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VMQ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3VMQ)

(-) 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:223
 aligned with MGT_STAAM | Q99T05 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:229
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260         
            MGT_STAAM    41 RILLKILLTILIIIALFIGIMYFLSTRDNVDELRKIENKSSFVSADNMPEYVKGAFISMEDERFYNHHGFDLKGTTRALFSTISDRDVQGGSTITQQVVKNYFYDNDRSFTRKVKELFVAHRVEKQYNKNEILSFYLNNIYFGDNQYTLEGAANHYFGTTVNKNSTTMSHITVLQSAILASKVNAPSVYNINNMSENFTQRVSTNLEKMKQQNYINETQYQQAMSQLNR 269
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.........hhhhhhhh....------....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh.............hhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vmq A  41 RILLKILLTILIIIALFIGIMYFLSTRDNVDELRKIENKSSFVSADNMPEYVKGAFISMEDERFYNHHGFDLKGTTRALFST------QGGSTITQQVVKNYFYDNDRSFTRKVKELFVAHRVEKQYNKNEILSFYLNNIYFGDNQYTLEGAANHYFGTTVNKNSTTMSHITVLQSAILASKVNAPSVYNINNMSENFTQRVSTNLEKMKQQNYINETQYQQAMSQLNR 269
                                    50        60        70        80        90       100       110       120 |     130       140       150       160       170       180       190       200       210       220       230       240       250       260         
                                                                                                           122    129                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:217
 aligned with MGT_STAAM | Q99T05 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:229
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260         
            MGT_STAAM    41 RILLKILLTILIIIALFIGIMYFLSTRDNVDELRKIENKSSFVSADNMPEYVKGAFISMEDERFYNHHGFDLKGTTRALFSTISDRDVQGGSTITQQVVKNYFYDNDRSFTRKVKELFVAHRVEKQYNKNEILSFYLNNIYFGDNQYTLEGAANHYFGTTVNKNSTTMSHITVLQSAILASKVNAPSVYNINNMSENFTQRVSTNLEKMKQQNYINETQYQQAMSQLNR 269
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh....hhhhhhhhhhhhhhhhhh.........hhhhhhhh.------------.hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh.ee........ee.hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vmq B  41 RILLKILLTILIIIALFIGIMYFLSTRDNVDELRKIENKSSFVSADNMPEYVKGAFISMEDERFYNHHGFDLKGTTRAL------------STITQQVVKNYFYDNDRSFTRKVKELFVAHRVEKQYNKNEILSFYLNNIYFGDNQYTLEGAANHYFGTTVNKNSTTMSHITVLQSAILASKVNAPSVYNINNMSENFTQRVSTNLEKMKQQNYINETQYQQAMSQLNR 269
                                    50        60        70        80        90       100       110        |-         - |     140       150       160       170       180       190       200       210       220       230       240       250       260         
                                                                                                        119          132
   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 3VMQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MGT_STAAM | Q99T05)
molecular function
    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: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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

 Visualization

(-) Interactive Views

Asymmetric 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
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:67 - Asp A:68   [ RasMol ]  
    Arg B:67 - Asp B:68   [ RasMol ]  
    Gly A:130 - Gly A:131   [ RasMol ]  
    Thr A:66 - Arg A:67   [ RasMol ]  
    Thr B:66 - Arg B:67   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  3vmq
    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
  MGT_STAAM | Q99T05
    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)
  2.4.-.-
    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
  MGT_STAAM | Q99T05
    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
        MGT_STAAM | Q99T05: 3vmr 3vms 3vmt

(-) Related Entries Specified in the PDB File

3vmr 3vms 3vmt