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(-) Description

Title :  CRYSTAL STRUCTURE OF GLUTAMATE RACEMASE FROM FRANCISELLA TULARENSIS SUBSP. TULARENSIS SCHU S4 IN COMPLEX WITH D-GLUTAMATE.
 
Authors :  E. V. Filippova, Z. Wawrzak, O. Onopriyenko, M. Kudriska, A. Edwards, A. Savchenko, F. W. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
Date :  15 Sep 10  (Deposition) - 29 Sep 10  (Release) - 29 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Biol. Unit 2:  A,C  (1x)
Biol. Unit 3:  B  (2x)
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Glutamate Racemase, Muri, Cell Envelope, Francisella Tularensis Subsp. Tularensis Schu S4, Center For Structural Genomics Of Infectious Diseases (Csgid), Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. V. Filippova, Z. Wawrzak, O. Onopriyenko, M. Kudriska, A. Edwards, A. Savchenko, F. W. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of Glutamate Racemase From Francisella Tularensis Subsp. Tularensis Schu S4 In Complex With D-Glutamate.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLUTAMATE RACEMASE
    Chains: A, B, C
    EC Number: 5.1.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21-CODONPLUS(DE3)-RIPL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FTT_1197C, MURI
    Organism Scientific: FRANCISELLA TULARENSIS SUBSP. TULARENSIS
    Organism Taxid: 119856

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC
Biological Unit 2 (1x): A C
Biological Unit 3 (2x):  B 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric Unit (2, 18)
No.NameCountTypeFull Name
1DGL3Ligand/IonD-GLUTAMIC ACID
2MSE15Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 36)
No.NameCountTypeFull Name
1DGL6Ligand/IonD-GLUTAMIC ACID
2MSE30Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 12)
No.NameCountTypeFull Name
1DGL2Ligand/IonD-GLUTAMIC ACID
2MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 12)
No.NameCountTypeFull Name
1DGL2Ligand/IonD-GLUTAMIC ACID
2MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:12 , GLY A:13 , PRO A:42 , TYR A:43 , GLY A:44 , ASN A:75 , THR A:76 , CYS A:183 , THR A:184 , HOH A:271 , HOH A:274 , HOH A:285 , HOH A:297BINDING SITE FOR RESIDUE DGL A 266
2AC2SOFTWARESER B:12 , GLY B:13 , PRO B:42 , TYR B:43 , GLY B:44 , CYS B:74 , ASN B:75 , THR B:76 , CYS B:183 , THR B:184 , HOH B:267 , HOH B:279 , HOH B:282 , HOH B:285BINDING SITE FOR RESIDUE DGL B 266
3AC3SOFTWARESER C:12 , GLY C:13 , PRO C:42 , TYR C:43 , GLY C:44 , CYS C:74 , ASN C:75 , THR C:76 , THR C:116 , CYS C:183 , THR C:184 , HOH C:269 , HOH C:280 , HOH C:283 , HOH C:299BINDING SITE FOR RESIDUE DGL C 266

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ile A:41 -Pro A:42
2Ile B:41 -Pro B:42
3Ile C:41 -Pro C:42

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OUT)

(-) 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:263
 aligned with Q5NFN6_FRATT | Q5NFN6 from UniProtKB/TrEMBL  Length:265

    Alignment length:264
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261    
         Q5NFN6_FRATT     2 LDNRPIGVFDSGIGGLTIVKNLMSILPNEDIIYFGDIARIPYGTKSRATIQKFAAQTAKFLIDQEVKAIIIACNTISAIAKDIVQEIAKAIPVIDVITAGVSLVDNLNTVGVIATPATINSNAYALQIHKKNPNIEVYSNPCGLFVSMIEEGFVSGHIVELVAKEYLSYFHDKNIQALILGCTHYPIIKESIAKILDVKLIDPSLQASKMLYSLLFENKLLNTTKSNPEYRFYVTDIPLKFRSVGEMFLQTEMQHLEIVSLDSY 265
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee....hhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh...eeehhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhh....hhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhh.......-...eeeee.....hhhhhhhhhhh....eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3out A   2 LDNRPIGVFDSGIGGLTIVKNLmSILPNEDIIYFGDIARIPYGTKSRATIQKFAAQTAKFLIDQEVKAIIIACNTISAIAKDIVQEIAKAIPVIDVITAGVSLVDNLNTVGVIATPATINSNAYALQIHKKNPNIEVYSNPCGLFVSmIEEGFVSGHIVELVAKEYLSYFHDKNIQALILGCTHYPIIKESIAKILDVKLIDPSLQASKmLYSLLFENKLLNTTK-NPEYRFYVTDIPLKFRSVGEmFLQTEmQHLEIVSLDSY 265
                                    11        21  |     31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221    | |231       241      |251  |    261    
                                                 24-MSE                                                                                                                      149-MSE                                                       211-MSE        226 |                 248-MSE |           
                                                                                                                                                                                                                                                            228                       254-MSE       


Chain B from PDB  Type:PROTEIN  Length:264
 aligned with Q5NFN6_FRATT | Q5NFN6 from UniProtKB/TrEMBL  Length:265

    Alignment length:264
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261    
         Q5NFN6_FRATT     2 LDNRPIGVFDSGIGGLTIVKNLMSILPNEDIIYFGDIARIPYGTKSRATIQKFAAQTAKFLIDQEVKAIIIACNTISAIAKDIVQEIAKAIPVIDVITAGVSLVDNLNTVGVIATPATINSNAYALQIHKKNPNIEVYSNPCGLFVSMIEEGFVSGHIVELVAKEYLSYFHDKNIQALILGCTHYPIIKESIAKILDVKLIDPSLQASKMLYSLLFENKLLNTTKSNPEYRFYVTDIPLKFRSVGEMFLQTEMQHLEIVSLDSY 265
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee....hhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh...eeehhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhh....hhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhh...........eeeee.....hhhhhhhhhhh....eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3out B   2 LDNRPIGVFDSGIGGLTIVKNLmSILPNEDIIYFGDIARIPYGTKSRATIQKFAAQTAKFLIDQEVKAIIIACNTISAIAKDIVQEIAKAIPVIDVITAGVSLVDNLNTVGVIATPATINSNAYALQIHKKNPNIEVYSNPCGLFVSmIEEGFVSGHIVELVAKEYLSYFHDKNIQALILGCTHYPIIKESIAKILDVKLIDPSLQASKmLYSLLFENKLLNTTKSNPEYRFYVTDIPLKFRSVGEmFLQTEmQHLEIVSLDSY 265
                                    11        21  |     31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241      |251  |    261    
                                                 24-MSE                                                                                                                      149-MSE                                                       211-MSE                              248-MSE |           
                                                                                                                                                                                                                                                                                      254-MSE       


Chain C from PDB  Type:PROTEIN  Length:264
 aligned with Q5NFN6_FRATT | Q5NFN6 from UniProtKB/TrEMBL  Length:265

    Alignment length:264
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261    
         Q5NFN6_FRATT     2 LDNRPIGVFDSGIGGLTIVKNLMSILPNEDIIYFGDIARIPYGTKSRATIQKFAAQTAKFLIDQEVKAIIIACNTISAIAKDIVQEIAKAIPVIDVITAGVSLVDNLNTVGVIATPATINSNAYALQIHKKNPNIEVYSNPCGLFVSMIEEGFVSGHIVELVAKEYLSYFHDKNIQALILGCTHYPIIKESIAKILDVKLIDPSLQASKMLYSLLFENKLLNTTKSNPEYRFYVTDIPLKFRSVGEMFLQTEMQHLEIVSLDSY 265
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----Asp_Glu_race-3outC01 C:7-213                                                                                                                                                                                   ---------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----Asp_Glu_race-3outC02 C:7-213                                                                                                                                                                                   ---------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -----Asp_Glu_race-3outC03 C:7-213                                                                                                                                                                                   ---------------------------------------------------- Pfam domains (3)
         Sec.struct. author .....eeeee....hhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhh....eeehhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhh....hhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhh..eeehhhhhhhhhhhhhhhhh...........eeeee.....hhhhhhhhhhh.....eee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3out C   2 LDNRPIGVFDSGIGGLTIVKNLmSILPNEDIIYFGDIARIPYGTKSRATIQKFAAQTAKFLIDQEVKAIIIACNTISAIAKDIVQEIAKAIPVIDVITAGVSLVDNLNTVGVIATPATINSNAYALQIHKKNPNIEVYSNPCGLFVSmIEEGFVSGHIVELVAKEYLSYFHDKNIQALILGCTHYPIIKESIAKILDVKLIDPSLQASKmLYSLLFENKLLNTTKSNPEYRFYVTDIPLKFRSVGEmFLQTEmQHLEIVSLDSY 265
                                    11        21  |     31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241      |251  |    261    
                                                 24-MSE                                                                                                                      149-MSE                                                       211-MSE                              248-MSE |           
                                                                                                                                                                                                                                                                                      254-MSE
   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 3OUT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 3)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q5NFN6_FRATT | Q5NFN6)
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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