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(-) Description

Title :  GLUTAMATE RACEMASE (MURI) FROM E. FAECALIS IN COMPLEX WITH A 9-BENZYL PURINE INHIBITOR
 
Authors :  B. Geng, G. Breault, J. Comita-Prevoir, R. Petrichko, C. Eyermann, T. Lundqvist, P. Doig, E. Gorseth, B. Noonan
Date :  11 Jun 08  (Deposition) - 24 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Isomerase, Glutamate Racemase, Peptidoglycan Synthesis, Cell Wall Biogenesis/Degradation, Cell Shape, Benzyl Purine, Muri Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Geng, G. Breault, J. Comita-Prevoir, R. Petrichko, C. Eyermann, T. Lundqvist, P. Doig, E. Gorseth, B. Noonan
Exploring 9-Benzyl Purines As Inhibitors Of Glutamate Racemase (Muri) In Gram-Positive Bacteria.
Bioorg. Med. Chem. Lett. V. 18 4368 2008
PubMed-ID: 18614367  |  Reference-DOI: 10.1016/J.BMCL.2008.06.068

(-) Compounds

Molecule 1 - GLUTAMATE RACEMASE
    ChainsA, B
    EC Number5.1.1.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRESIDUES 1-270
    Organism ScientificENTEROCOCCUS FAECALIS
    Organism Taxid1351

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1DGL2Ligand/IonD-GLUTAMIC ACID
2I242Ligand/Ion2-BUTOXY-9-(2,6-DIFLUOROBENZYL)-N-(2-MORPHOLIN-4-YLETHYL)-9H-PURIN-6-AMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:14 , VAL A:152 , GLU A:153 , ASN A:155 , HIS A:187 , LEU A:190 , MET A:246 , ILE A:250 , HOH A:2194 , HOH A:2313 , HOH A:2314BINDING SITE FOR RESIDUE I24 A1269
2AC2SOFTWAREASN A:197 , GLY A:200 , SER A:201 , HIS A:202 , HOH A:2235 , VAL B:152 , GLU B:153 , ASN B:155 , GLU B:249 , ILE B:250 , HOH B:2355 , HOH B:2386BINDING SITE FOR RESIDUE I24 B1269
3AC3SOFTWAREASP A:11 , SER A:12 , PRO A:42 , TYR A:43 , GLY A:44 , CYS A:74 , ASN A:75 , THR A:76 , THR A:118 , CYS A:185 , THR A:186 , HOH A:2021 , HOH A:2230 , HOH A:2315BINDING SITE FOR RESIDUE DGL A1270
4AC4SOFTWAREASP B:11 , SER B:12 , PRO B:42 , TYR B:43 , GLY B:44 , CYS B:74 , ASN B:75 , THR B:76 , THR B:118 , CYS B:185 , THR B:186 , HIS B:187 , HOH B:2282 , HOH B:2388BINDING SITE FOR RESIDUE DGL B1270

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Cys A:41 -Pro A:42
2Cys B:41 -Pro B:42

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ASP_GLU_RACEMASE_1PS00923 Aspartate and glutamate racemases signature 1.MURI_ENTFA71-79
 
  2A:71-79
B:71-79
2ASP_GLU_RACEMASE_2PS00924 Aspartate and glutamate racemases signature 2.MURI_ENTFA181-191
 
  2A:181-191
B:181-191

(-) Exons   (0, 0)

(no "Exon" information available for 2VVT)

(-) 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:270
 aligned with MURI_ENTFA | Q836J0 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:275
                                  1                                                                                                                                                                                                                                                                            
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264     
           MURI_ENTFA     - ------MSNQEAIGLIDSGVGGLTVLKEALKQLPNERLIYLGDTARCPYGPRPAEQVVQFTWEMADFLLKKRIKMLVIACNTATAVALEEIKAALPIPVVGVILPGARAAVKVTKNNKIGVIGTLGTIKSASYEIAIKSKAPTIEVTSLDCPKFVPIVESNQYRSSVAKKIVAETLQALQLKGLDTLILGCTHYPLLRPVIQNVMGSHVTLIDSGAETVGEVSMLLDYFDIAHTPEAPTQPHEFYTTGSAKMFEEIASSWLGIENLKAQQIHLGG 269
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh.eeeee....hhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhh....hhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhh......-----..eeee..hhhhhhhhhhhhhh.....eee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------ASP_GLU_R-----------------------------------------------------------------------------------------------------ASP_GLU_RAC------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vvt A  -5 VPRGSHMSNQEAIGLIDSGVGGLTVLKEALKQLPNERLIYLGDTARCPYGPRPAEQVVQFTWEMADFLLKKRIKMLVIACNTATAVALEEIKAALPIPVVGVILPGARAAVKVTKNNKIGVIGTLGTIKSASYEIAIKSKAPAIEVTSLACPKFVPIVESNQYRSSVAKKIVAETLQALQLKGLDTLILGCTHYPLLRPVIQNVMGSHVTLIDSGAETVGEVSMLLDYFDIAHTP-----PHEFYTTGSAKMFEEIASSWLGIENLKAQQIHLGG 269
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224    |    -|      244       254       264     
                                                                                                                                                                                                                                                                    229   235                                  

Chain B from PDB  Type:PROTEIN  Length:266
 aligned with MURI_ENTFA | Q836J0 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:266
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262      
           MURI_ENTFA     3 NQEAIGLIDSGVGGLTVLKEALKQLPNERLIYLGDTARCPYGPRPAEQVVQFTWEMADFLLKKRIKMLVIACNTATAVALEEIKAALPIPVVGVILPGARAAVKVTKNNKIGVIGTLGTIKSASYEIAIKSKAPTIEVTSLDCPKFVPIVESNQYRSSVAKKIVAETLQALQLKGLDTLILGCTHYPLLRPVIQNVMGSHVTLIDSGAETVGEVSMLLDYFDIAHTPEAPTQPHEFYTTGSAKMFEEIASSWLGIENLKAQQIHLG 268
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----Asp_Glu_race-2vvtB01 B:7-217                                                                                                                                                                                       --------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----Asp_Glu_race-2vvtB02 B:7-217                                                                                                                                                                                       --------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....eeeee....hhhhhhhhhhhh....eeeee.hhhh.....hhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhh....hhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhh.............eeee..hhhhhhhhhhhhhh......ee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------ASP_GLU_R-----------------------------------------------------------------------------------------------------ASP_GLU_RAC----------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vvt B   3 NQEAIGLIDSGVGGLTVLKEALKQLPNERLIYLGDTARCPYGPRPAEQVVQFTWEMADFLLKKRIKMLVIACNTATAVALEEIKAALPIPVVGVILPGARAAVKVTKNNKIGVIGTLGTIKSASYEIAIKSKAPAIEVTSLACPKFVPIVESNQYRSSVAKKIVAETLQALQLKGLDTLILGCTHYPLLRPVIQNVMGSHVTLIDSGAETVGEVSMLLDYFDIAHTPEAPTQPHEFYTTGSAKMFEEIASSWLGIENLKAQQIHLG 268
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262      

   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 2VVT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MURI_ENTFA | Q836J0)
molecular function
    GO:0008881    glutamate racemase activity    Catalysis of the reaction: L-glutamate = D-glutamate.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0036361    racemase activity, acting on amino acids and derivatives    Catalysis of the interconversion of the two enantiomers of a chiral amino acid or amino acid derivative.
    GO:0016855    racemase and epimerase activity, acting on amino acids and derivatives    Catalysis of a reaction that alters the configuration of one or more chiral centers in an amino acid.
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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0006807    nitrogen compound metabolic process    The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MURI_ENTFA | Q836J02jfo 2jfp

(-) Related Entries Specified in the PDB File

2jfo CRYSTAL STRUCTURE OF ENTEROCOCCUS FAECALIS GLUTAMATE RACEMASE IN COMPLEX WITH D- AND L-GLUTAMATE
2jfp CRYSTAL STRUCTURE OF ENTEROCOCCUS FAECALIS GLUTAMATE RACEMASE IN COMPLEX WITH D- GLUTAMATE