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(-) Description

Title :  CRYSTAL STRUCTURE OF GLUTAMATE RACEMASE FROM LISTERIA MONOCYTOGENES
 
Authors :  K. A. Majorek, M. Chruszcz, M. D. Zimmerman, M. M. Klimecka, M. Cymborow T. Skarina, O. Onopriyenko, J. Stam, Z. Otwinowski, W. F. Anderson, A. Savchenko, W. Minor, Center For Structural Genomics Of Infec Diseases (Csgid)
Date :  12 May 09  (Deposition) - 09 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glutamate Racemase, Structural Genomics, Sad, Cell Shape, Cell Wall Biogenesis/Degradation, Isomerase, Peptidoglycan Synthesis, Center For Structural Genomics Of Infectious Diseases, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. A. Majorek, M. Chruszcz, M. D. Zimmerman, M. M. Klimecka, M. Cymborowski, T. Skarina, O. Onopriyenko, J. Stam, Z. Otwinowski, W. F. Anderson, A. Savchenko, W. Minor, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of Glutamate Racemase From Listeria Monocytogenes
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLUTAMATE RACEMASE
    Chains: A, B
    EC Number: 5.1.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19C
    Expression System Strain: BL21 DE3 STAR MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LMO1237, MURI, RACE
    Organism Scientific: LISTERIA MONOCYTOGENES
    Organism Taxid: 1639
    Strain: LISTERIA MONOCYTOGENES EGD-E

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 20)

Asymmetric/Biological Unit (3, 20)
No.NameCountTypeFull Name
16JZ3Ligand/Ion3,6,9,12,15-PENTAOXAHEPTADECANE
2CL3Ligand/IonCHLORIDE ION
3MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:74 , THR A:116 , THR A:119 , HOH A:272BINDING SITE FOR RESIDUE CL A 267
2AC2SOFTWARETHR A:116 , LEU A:117BINDING SITE FOR RESIDUE CL A 268
3AC3SOFTWARETYR A:81 , ASN B:222BINDING SITE FOR RESIDUE 6JZ A 269
4AC4SOFTWARELYS A:156 , ASP A:246BINDING SITE FOR RESIDUE 6JZ A 270
5AC5SOFTWAREASN B:73 , CYS B:183 , THR B:184 , HOH B:333BINDING SITE FOR RESIDUE CL B 267
6AC6SOFTWARETYR A:220 , HIS A:221 , ASP B:88 , TYR B:220 , HIS B:221BINDING SITE FOR RESIDUE 6JZ B 268

(-) SS Bonds  (0, 0)

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

(-) 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 3HFR)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ASP_GLU_RACEMASE_1PS00923 Aspartate and glutamate racemases signature 1.MURI_LISMO69-77
 		  2A:69-77
B:69-77
2ASP_GLU_RACEMASE_2PS00924 Aspartate and glutamate racemases signature 2.MURI_LISMO179-189
 		  2A:179-189
B:179-189

(-) Exons   (0, 0)

(no "Exon" information available for 3HFR)

(-) 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_LISMO | Q8Y7N7 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:266
                             1                                                                                                                                                                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259      
           MURI_LISMO     - -MKQAIGFIDSGVGGLTVVREVLKQLPHEQVYYLGDTARCPYGPRDKEEVAKFTWEMTNFLVDRGIKMLVIACNTATAAALYDIREKLDIPVIGVIQPGSRAALKATRNNKIGVLGTLGTVESMAYPTALKGLNRRVEVDSLACPKFVSVVESGEYKSAIAKKVVAESLLPLKSTKIDTVILGCTHYPLLKPIIENFMGDGVAVINSGEETASEVSALLDYHNLLDATDEEIEHRFFTTGSTQIFKDIAKDWLNMPDMTVEHIKLG 265
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3hfrA01 A:0-93,A:207-265  [code=3.40.50.1860, no name defined]                                3hfrA02 A:94-206  [code=3.40.50.1860, no name defined]                                                           3hfrA01 A:0-93,A:207-265                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....hhhhhhhhhhhh....eeeee.hhhh.....hhhhhhhhhhhhhhhhhhhheeeeee.hhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhh....hhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhh............eeee..hhhhhhhhhhhhh......eee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------ASP_GLU_R-----------------------------------------------------------------------------------------------------ASP_GLU_RAC---------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hfr A   0 AmKQAIGFIDSGVGGLTVVREVLKQLPHEQVYYLGDTARCPYGPRDKEEVAKFTWEmTNFLVDRGIKmLVIACNTATAAALYDIREKLDIPVIGVIQPGSRAALKATRNNKIGVLGTLGTVESmAYPTALKGLNRRVEVDSLACPKFVSVVESGEYKSAIAKKVVAESLLPLKSTKIDTVILGCTHYPLLKPIIENFmGDGVAVINSGEETASEVSALLDYHNLLDATDEEIEHRFFTTGSTQIFKDIAKDWLNmPDmTVEHIKLG 265
                             |       9        19        29        39        49      | 59       |69        79        89        99       109       119   |   129       139       149       159       169       179       189       199       209       219       229       239       249    |  259      
                             |                                                     56-MSE     67-MSE                                                 123-MSE                                                                   197-MSE                                                  254-MSE       
                             1-MSE                                                                                                                                                                                                                                                         257-MSE    


Chain B from PDB  Type:PROTEIN  Length:266
 aligned with MURI_LISMO | Q8Y7N7 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_LISMO     1 MKQAIGFIDSGVGGLTVVREVLKQLPHEQVYYLGDTARCPYGPRDKEEVAKFTWEMTNFLVDRGIKMLVIACNTATAAALYDIREKLDIPVIGVIQPGSRAALKATRNNKIGVLGTLGTVESMAYPTALKGLNRRVEVDSLACPKFVSVVESGEYKSAIAKKVVAESLLPLKSTKIDTVILGCTHYPLLKPIIENFMGDGVAVINSGEETASEVSALLDYHNLLDATDEEIEHRFFTTGSTQIFKDIAKDWLNMPDMTVEHIKLGK 266
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -3hfrB01 B:2-93,B:207-266  [code=3.40.50.1860, no name defined]                              3hfrB02 B:94-206  [code=3.40.50.1860, no name defined]                                                           3hfrB01 B:2-93,B:207-266                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....hhhhhhhhhhhh....eeeee.hhhh.....hhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhh............eeee..hhhhhhhhhhhhh......eee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------ASP_GLU_R-----------------------------------------------------------------------------------------------------ASP_GLU_RAC----------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hfr B   1 mKQAIGFIDSGVGGLTVVREVLKQLPHEQVYYLGDTARCPYGPRDKEEVAKFTWEmTNFLVDRGIKmLVIACNTATAAALYDIREKLDIPVIGVIQPGSRAALKATRNNKIGVLGTLGTVESmAYPTALKGLNRRVEVDSLACPKFVSVVESGEYKSAIAKKVVAESLLPLKSTKIDTVILGCTHYPLLKPIIENFmGDGVAVINSGEETASEVSALLDYHNLLDATDEEIEHRFFTTGSTQIFKDIAKDWLNmPDmTVEHIKLGK 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      
                            1-MSE                                                 56-MSE     67-MSE                                                 123-MSE                                                                   197-MSE                                                  254-MSE        
                                                                                                                                                                                                                                                                                          257-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 3HFR)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MURI_LISMO | Q8Y7N7)
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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        MURI_LISMO | Q8Y7N7: 3ist 3isv

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