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(-) Description

Title :  CRYSTAL STRUCTURE OF ESCHERICHIA COLI GLUTAMATE RACEMASE IN COMPLEX WITH L-GLUTAMATE AND ACTIVATOR UDP-MURNAC-ALA
 
Authors :  T. Lundqvist
Date :  03 Feb 07  (Deposition) - 03 Jul 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Cell Wall, Isomerase, Cell Shape, Udp- Murnac-Ala, Peptidoglycan Biosynthesis, Glutamate Racemase, Peptidoglycan Synthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Lundqvist, S. L. Fisher, G. Kern, R. H. A. Folmer, Y. Xue, D. T. Newton, T. A. Keating, R. A. Alm, B. L. M. De Jonge
Exploitation Of Structural And Regulatory Diversity In Glutamate Racemases
Nature V. 447 817 2007
PubMed-ID: 17568739  |  Reference-DOI: 10.1038/NATURE05689

(-) Compounds

Molecule 1 - GLUTAMATE RACEMASE
    Chains: A
    EC Number: 5.1.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 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
1GLU1Mod. Amino AcidGLUTAMIC ACID
2UMA1Ligand/IonURIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:28 , SER A:29 , PHE A:58 , PRO A:59 , TYR A:60 , GLY A:61 , CYS A:92 , ASN A:93 , THR A:94 , CYS A:204 , THR A:205 , HIS A:206 , HOH A:2089BINDING SITE FOR RESIDUE GLU A1287
2AC2SOFTWARELEU A:100 , ARG A:104 , VAL A:112 , GLY A:113 , VAL A:114 , VAL A:115 , PRO A:116 , ALA A:117 , LYS A:119 , PRO A:120 , SER A:227 , ALA A:230 , ILE A:231 , ARG A:233 , ARG A:234 , HOH A:2084 , HOH A:2166 , HOH A:2213 , HOH A:2214 , HOH A:2215 , HOH A:2217 , HOH A:2218 , HOH A:2220 , HOH A:2221BINDING SITE FOR RESIDUE UMA A1286

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:58 -Pro A:59

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ASP_GLU_RACEMASE_1PS00923 Aspartate and glutamate racemases signature 1.MURI_ECOLI89-97  1A:89-97
2ASP_GLU_RACEMASE_2PS00924 Aspartate and glutamate racemases signature 2.MURI_ECOLI200-210  1A:200-210

(-) Exons   (0, 0)

(no "Exon" information available for 2JFN)

(-) 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:267
 aligned with MURI_ECOLI | P22634 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:267
                                                                                                                                                                                                                                                                                                   285 
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279     | 
          MURI_ECOLI     20 PRPTVLVFDSGVGGLSVYDEIRHLLPDLHYIYAFDNVAFPYGEKSEAFIVERVVAIVTAVQERYPLALAVVACNTASTVSLPALREKFDFPVVGVVPAIKPAARLTANGIVGLLATRGTVKRSYTHELIARFANECQIEMLGSAEMVELAEAKLHGEDVSLDALKRILRPWLRMKEPPDTVVLGCTHFPLLQEELLQVLPEGTRLVDSGAAIARRTAWLLEHEAPDAKSADANIAFCMAMTPGAEQLLPVLQRYGFETLEKLAVLG-    -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----Asp_Glu_race-2jfnA01 A:24-236                                                                                                                                                                                        -------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...hhhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhh...ee....hhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhh....hhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhh....ee....eeee...hhhhhhhhhhhhhh...eeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------ASP_GLU_R------------------------------------------------------------------------------------------------------ASP_GLU_RAC---------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2jfn A   20 PRPTVLVFDSGVGGLSVYDEIRHLLPDLHYIYAFDNVAFPYGEKSEAFIVERVVAIVTAVQERYPLALAVVACNTASTVSLPALREKFDFPVVGVVPAIKPAARLTANGIVGLLATRGTVKRSYTHELIARFANECQIEMLGSAEMVELAEAKLHGEDVSLDALKRILRPWLRMKEPPDTVVLGCTHFPLLQEELLQVLPEGTRLVDSGAAIARRTAWLLEHEAPDAKSADANIAFCMAMTPGAEQLLPVLQRYGFETLEKLAVLGE 1287
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279     ||
                                                                                                                                                                                                                                                                                                   285|
                                                                                                                                                                                                                                                                                                   1287
   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 2JFN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Asp-glut_race (23)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MURI_ECOLI | P22634)
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

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(-) Related Entries Specified in the PDB File

2jfo CRYSTAL STRUCTURE OF E. FAECALIS GLUTAMATE RACEMASE IN COMPLEX WITH D- AND L- GLUTAMATE
2jfp CRYSTAL STRUCTURE OF E. FAECALIS GLUTAMATE RACEMASE IN COMPLEX WITH D-GLUTAMATE
2jfq CRYSTAL STRUCTURE OF S. AUREUS GLUTAMATE RACEMASE IN COMPLEX WITH D-GLUTAMATE
2jfu CRYSTAL STRUCTURE OF E. FAECIUM GLUTAMATE RACEMASE IN COMPLEX WITH PHOSPHATE