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(-) Description

Title :  CRYSTAL STRUCTURE OF B.SUBTILIS GLUTAMATE RACEMASE (RACE) WITH D-GLU
 
Authors :  S. N. Ruzheinikov, M. A. Taal, S. E. Sedelnikova, P. J. Baker, D. W. Rice
Date :  01 Jun 05  (Deposition) - 06 Dec 05  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B  (2x)
Keywords :  Glutamate Racemase; (R)-Glutamate; Peptidoglycan Biosynthesis, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. N. Ruzheinikov, M. A. Taal, S. E. Sedelnikova, P. J. Baker, D. W. Rice
Substrate-Induced Conformational Changes In Bacillus Subtilis Glutamate Racemase And Their Implications For Drug Discovery
Structure V. 13 1707 2005
PubMed-ID: 16271894  |  Reference-DOI: 10.1016/J.STR.2005.07.024
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUTAMATE RACEMASE 1
    ChainsA, B, C
    EC Number5.1.1.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneRACE
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1DGL3Ligand/IonD-GLUTAMIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1DGL2Ligand/IonD-GLUTAMIC ACID
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1DGL2Ligand/IonD-GLUTAMIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:10 , SER A:11 , PRO A:41 , TYR A:42 , GLY A:43 , CYS A:74 , ASN A:75 , THR A:76 , THR A:118 , CYS A:185 , THR A:186 , HIS A:187 , HOH A:1318 , HOH A:1326BINDING SITE FOR RESIDUE DGL A 1301
2AC2SOFTWAREASP B:10 , SER B:11 , PRO B:41 , TYR B:42 , GLY B:43 , CYS B:74 , ASN B:75 , THR B:76 , CYS B:185 , THR B:186 , HIS B:187 , HOH B:2318 , HOH B:2341BINDING SITE FOR RESIDUE DGL B 2301
3AC3SOFTWAREASP C:10 , SER C:11 , PRO C:41 , TYR C:42 , GLY C:43 , CYS C:74 , ASN C:75 , THR C:76 , THR C:118 , CYS C:185 , THR C:186 , HIS C:187 , HOH C:3302 , HOH C:3304BINDING SITE FOR RESIDUE DGL C 3301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZUW)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Cys A:40 -Pro A:41
2Cys B:40 -Pro B:41
3Cys C:40 -Pro C:41

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZUW)

(-) PROSITE Motifs  (2, 6)

Asymmetric Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ASP_GLU_RACEMASE_1PS00923 Aspartate and glutamate racemases signature 1.MURI1_BACSU71-79
 
 
  3A:71-79
B:71-79
C:71-79
2ASP_GLU_RACEMASE_2PS00924 Aspartate and glutamate racemases signature 2.MURI1_BACSU181-191
 
 
  3A:181-191
B:181-191
C:181-191
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ASP_GLU_RACEMASE_1PS00923 Aspartate and glutamate racemases signature 1.MURI1_BACSU71-79
 
 
  2A:71-79
-
C:71-79
2ASP_GLU_RACEMASE_2PS00924 Aspartate and glutamate racemases signature 2.MURI1_BACSU181-191
 
 
  2A:181-191
-
C:181-191
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ASP_GLU_RACEMASE_1PS00923 Aspartate and glutamate racemases signature 1.MURI1_BACSU71-79
 
 
  2-
B:71-79
-
2ASP_GLU_RACEMASE_2PS00924 Aspartate and glutamate racemases signature 2.MURI1_BACSU181-191
 
 
  2-
B:181-191
-

(-) Exons   (0, 0)

(no "Exon" information available for 1ZUW)

(-) 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:261
 aligned with MURI1_BACSU | P94556 from UniProtKB/Swiss-Prot  Length:272

    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      
          MURI1_BACSU     1 MLEQPIGVIDSGVGGLTVAKEIMRQLPKENIIYVGDTKRCPYGPRPEEEVLQYTWELTNYLLENHHIKMLVIACNTATAIALDDIQRSVGIPVVGVIQPGARAAIKVTDNQHIGVIGTENTIKSNAYEEALLALNPDLKVENLACPLLVPFVESGKFLDKTADEIVKTSLYPLKDTSIDSLILGCTHYPILKEAIQRYMGEHVNIISSGDETAREVSTILSYKGLLNQSPIAPDHQFLTTGARDQFAKIADDWFGHEVGHVECISL 266
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1zuwA01 A:1-95,A:209-266  [code=3.40.50.1860, no name defined]                                 1zuwA02 A:96-208  [code=3.40.50.1860, no name defined]                                                           1zuwA01 A:1-95,A:209-266                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....hhhhhhhhhhhh....eeeee.hhhh.....hhhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhh....hhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhh..........eeeee..hhhhhhhhhhhhh-----.eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------ASP_GLU_R-----------------------------------------------------------------------------------------------------ASP_GLU_RAC--------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zuw A   1 MLEQPIGVIDSGVGGLTVAKEIMRQLPKENIIYVGDTKRCPYGPRPEEEVLQYTWELTNYLLENHHIKMLVIACNTATAIALDDIQRSVGIPVVGVIQPGARAAIKVTDNQHIGVIGTENTIKSNAYEEALLALNPDLKVENLACPLLVPFVESGKFLDQTADEIVKTSLYPLKDTSIDSLILGCTHYPILKEAIQRYMGEHVNIISSGDETAREVSTILSYKGLLNQSPIAPDHQFLTTGARDQFAKIADDWF-----HVECISL 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      
                                                                                                                                                                                                                                                                                       254   260      

Chain B from PDB  Type:PROTEIN  Length:256
 aligned with MURI1_BACSU | P94556 from UniProtKB/Swiss-Prot  Length:272

    Alignment length: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     
          MURI1_BACSU     2 LEQPIGVIDSGVGGLTVAKEIMRQLPKENIIYVGDTKRCPYGPRPEEEVLQYTWELTNYLLENHHIKMLVIACNTATAIALDDIQRSVGIPVVGVIQPGARAAIKVTDNQHIGVIGTENTIKSNAYEEALLALNPDLKVENLACPLLVPFVESGKFLDKTADEIVKTSLYPLKDTSIDSLILGCTHYPILKEAIQRYMGEHVNIISSGDETAREVSTILSYKGLLNQSPIAPDHQFLTTGARDQFAKIADDWFGHEVGHVECISL 266
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1zuwB01 B:2-95,B:209-266  [code=3.40.50.1860, no name defined]                                1zuwB02 B:96-208  [code=3.40.50.1860, no name defined]                                                           1zuwB01 B:2-95,B:209-266                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....hhhhhhhhhhhh....eeeee.hhhh.....hhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhh....hhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhh...........eeeee....--..-hhhhhh------.ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------ASP_GLU_R-----------------------------------------------------------------------------------------------------ASP_GLU_RAC--------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zuw B   2 LEQPIGVIDSGVGGLTVAKEIMRQLPKENIIYVGDTKRCPYGPRPEEEVLQYTWELTNYLLENHHIKMLVIACNTATAIALDDIQRSVGIPVVGVIQPGARAAIKVTDNQHIGVIGTENTIKSNAYEEALLALNPDLKVENLACPLLVPFVESGKFLDQTADEIVKTSLYPLKDTSIDSLILGCTHYPILKEAIQRYMGEHVNIISSGDETAREVSTILSYKGLLNQSPIAPDHQFLTTGAR--FA-IADDWF------VECISL 266
                                    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     
                                                                                                                                                                                                                                                                           243  || |  254    261     
                                                                                                                                                                                                                                                                              246| |                 
                                                                                                                                                                                                                                                                               247 |                 
                                                                                                                                                                                                                                                                                 249                 

Chain C from PDB  Type:PROTEIN  Length:262
 aligned with MURI1_BACSU | P94556 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:267
                                    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       
          MURI1_BACSU     2 LEQPIGVIDSGVGGLTVAKEIMRQLPKENIIYVGDTKRCPYGPRPEEEVLQYTWELTNYLLENHHIKMLVIACNTATAIALDDIQRSVGIPVVGVIQPGARAAIKVTDNQHIGVIGTENTIKSNAYEEALLALNPDLKVENLACPLLVPFVESGKFLDKTADEIVKTSLYPLKDTSIDSLILGCTHYPILKEAIQRYMGEHVNIISSGDETAREVSTILSYKGLLNQSPIAPDHQFLTTGARDQFAKIADDWFGHEVGHVECISLQE 268
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1zuwC01 C:2-95,C:209-268  [code=3.40.50.1860, no name defined]                                1zuwC02 C:96-208  [code=3.40.50.1860, no name defined]                                                           1zuwC01 C:2-95,C:209-268                                     CATH domains
           Pfam domains (1) ----Asp_Glu_race-1zuwC01 C:6-217                                                                                                                                                                                        --------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----Asp_Glu_race-1zuwC02 C:6-217                                                                                                                                                                                        --------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ----Asp_Glu_race-1zuwC03 C:6-217                                                                                                                                                                                        --------------------------------------------------- Pfam domains (3)
         Sec.struct. author ....eeeee....hhhhhhhhhhhh....eeeee.hhhh.....hhhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhh..hhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhh...........eeeee..hhhhhhhhhhhhh-----.eee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------ASP_GLU_R-----------------------------------------------------------------------------------------------------ASP_GLU_RAC----------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zuw C   2 LEQPIGVIDSGVGGLTVAKEIMRQLPKENIIYVGDTKRCPYGPRPEEEVLQYTWELTNYLLENHHIKMLVIACNTATAIALDDIQRSVGIPVVGVIQPGARAAIKVTDNQHIGVIGTENTIKSNAYEEALLALNPDLKVENLACPLLVPFVESGKFLDQTADEIVKTSLYPLKDTSIDSLILGCTHYPILKEAIQRYMGEHVNIISSGDETAREVSTILSYKGLLNQSPIAPDHQFLTTGARDQFAKIADDWF-----HVECISLQE 268
                                    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       
                                                                                                                                                                                                                                                                                      254   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 1ZUW)

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (MURI1_BACSU | P94556)
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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