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(-) Description

Title :  CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS GLUTAMATE RACEMASE IN COMPLEX WITH D-GLUTAMATE
 
Authors :  T. Lundqvist
Date :  04 Feb 07  (Deposition) - 03 Jul 07  (Release) - 06 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cell Wall, Isomerase, Cell Shape, Glutamate Racemase, Peptidoglycan Synthesis, Peptidoglycan Biosynthesis (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, B
    EC Number: 5.1.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1DGL2Ligand/IonD-GLUTAMIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:9 , SER A:10 , PRO A:40 , TYR A:41 , GLY A:42 , CYS A:72 , ASN A:73 , THR A:74 , THR A:116 , CYS A:184 , THR A:185 , HIS A:186 , HOH A:2002 , HOH A:2039BINDING SITE FOR RESIDUE DGL A1267
2AC2SOFTWAREASP B:9 , SER B:10 , PRO B:40 , TYR B:41 , GLY B:42 , CYS B:72 , ASN B:73 , THR B:74 , THR B:116 , CYS B:184 , THR B:185 , HIS B:186 , HOH B:2003 , HOH B:2061BINDING SITE FOR RESIDUE DGL B1267

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Cys A:39 -Pro A:40
2Cys B:39 -Pro B:40

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ASP_GLU_RACEMASE_1PS00923 Aspartate and glutamate racemases signature 1.MURI_STAAR69-77
 		  2A:69-77
B:69-77
2ASP_GLU_RACEMASE_2PS00924 Aspartate and glutamate racemases signature 2.MURI_STAAR180-190
 		  2A:180-190
B:180-190

(-) Exons   (0, 0)

(no "Exon" information available for 2JFQ)

(-) 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:266
 aligned with MURI_STAAR | Q6GHT5 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:266
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      
           MURI_STAAR     1 MNKPIGVIDSGVGGLTVAKEIMRQLPNETIYYLGDIGRCPYGPRPGEQVKQYTVEIARKLMEFDIKMLVIACNTATAVALEYLQKTLSIPVIGVIEPGARTAIMTTRNQNVLVLGTEGTIKSEAYRTHIKRINPHVEVHGVACPGFVPLVEQMRYSDPTITSIVIHQTLKRWRNSESDTVILGCTHYPLLYKPIYDYFGGKKTVISSGLETAREVSALLTFSNEHASYTEHPDHRFFATGDTTHITNIIKEWLNLSVNVERISVND 266
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2jfqA01 A:1-93,A:208-266  [code=3.40.50.1860, no name defined]                               2jfqA02 A:94-207  [code=3.40.50.1860, no name defined]                                                            2jfqA01 A:1-93,A:208-266                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....hhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhh....hhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhh............eeee...hhhhhhhhhhhhh.....ee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------ASP_GLU_R------------------------------------------------------------------------------------------------------ASP_GLU_RAC---------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jfq A   1 MNKPIGVIDSGVGGLTVAKEIMRQLPNETIYYLGDIGRCPYGPRPGEQVKQYTVEIARKLMEFDIKMLVIACNTATAVALEYLQKTLSISVIGVIEPGARTAIMTTRNQNVLVLGTEGTIKSEAYRTHIKRINPHVEVHGVACPGFVPLVEQMRYSDPTITSIVIHQTLKRWRNSESDTVILGCTHYPLLYKPIYDYFGGKKTVISSGLETAREVSALLTFSNEHASYTEHPDHRFFATGDTTHITNIIKEWLNLSVNVERISVND 266
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      


Chain B from PDB  Type:PROTEIN  Length:266
 aligned with MURI_STAAR | Q6GHT5 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:266
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      
           MURI_STAAR     1 MNKPIGVIDSGVGGLTVAKEIMRQLPNETIYYLGDIGRCPYGPRPGEQVKQYTVEIARKLMEFDIKMLVIACNTATAVALEYLQKTLSIPVIGVIEPGARTAIMTTRNQNVLVLGTEGTIKSEAYRTHIKRINPHVEVHGVACPGFVPLVEQMRYSDPTITSIVIHQTLKRWRNSESDTVILGCTHYPLLYKPIYDYFGGKKTVISSGLETAREVSALLTFSNEHASYTEHPDHRFFATGDTTHITNIIKEWLNLSVNVERISVND 266
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2jfqB01 B:1-93,B:208-266  [code=3.40.50.1860, no name defined]                               2jfqB02 B:94-207  [code=3.40.50.1860, no name defined]                                                            2jfqB01 B:1-93,B:208-266                                    CATH domains
           Pfam domains (1) ----Asp_Glu_race-2jfqB01 B:5-216                                                                                                                                                                                        -------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----Asp_Glu_race-2jfqB02 B:5-216                                                                                                                                                                                        -------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....eeeee....hhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhh...hhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhh............eeee...hhhhhhhhhhhhh.....ee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------ASP_GLU_R------------------------------------------------------------------------------------------------------ASP_GLU_RAC---------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jfq B   1 MNKPIGVIDSGVGGLTVAKEIMRQLPNETIYYLGDIGRCPYGPRPGEQVKQYTVEIARKLMEFDIKMLVIACNTATAVALEYLQKTLSISVIGVIEPGARTAIMTTRNQNVLVLGTEGTIKSEAYRTHIKRINPHVEVHGVACPGFVPLVEQMRYSDPTITSIVIHQTLKRWRNSESDTVILGCTHYPLLYKPIYDYFGGKKTVISSGLETAREVSALLTFSNEHASYTEHPDHRFFATGDTTHITNIIKEWLNLSVNVERISVND 266
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260
   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 2JFQ)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MURI_STAAR | Q6GHT5)
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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