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(-) Description

Title :  CRYSTAL STRUCTURE OF ENOLASE SUPERFAMILY MEMBER FROM BORDETELLA BRONCHISEPTICA COMPLEXED WITH MG AND M-XYLARATE
 
Authors :  A. A. Fedorov, E. V. Fedorov, D. Wichelecki, J. A. Gerlt, S. C. Almo
Date :  27 Sep 10  (Deposition) - 28 Sep 11  (Release) - 28 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Alpha Barrel, Enolase Superfamily Member, M-Xylarate, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Fedorov, E. V. Fedorov, D. Wichelecki, J. A. Gerlt, S. C. Almo
Crystal Structure Of Enolase Superfamily Member From Bordetella Bronchiseptica Complexed With Mg And M-Xylarate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE MANDELATE RACEMASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BB4687
    Organism Common: ALCALIGENES BRONCHISEPTICUS
    Organism Scientific: BORDETELLA BRONCHISEPTICA
    Organism Taxid: 518

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric/Biological Unit (4, 15)
No.NameCountTypeFull Name
1ACY6Ligand/IonACETIC ACID
2DXL1Ligand/IonD-XYLARIC ACID
3GOL4Ligand/IonGLYCEROL
4MG4Ligand/IonMAGNESIUM ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:201 , GLU A:227 , GLU A:254 , HOH A:972 , HOH A:1031 , HOH A:1032BINDING SITE FOR RESIDUE MG A 390
02AC2SOFTWAREASP B:201 , GLU B:227 , GLU B:254 , DXL B:392 , HOH B:971BINDING SITE FOR RESIDUE MG B 390
03AC3SOFTWAREHIS A:86 , HIS A:90 , HOH A:1024 , HOH B:978BINDING SITE FOR RESIDUE MG A 391
04AC4SOFTWAREHOH A:976 , HIS B:86 , HIS B:90 , HOH B:734BINDING SITE FOR RESIDUE MG B 391
05AC5SOFTWARESER B:25 , LYS B:30 , TYR B:147 , LYS B:171 , LYS B:173 , ASP B:201 , ASN B:203 , GLU B:227 , GLU B:254 , HIS B:304 , PHE B:306 , GLU B:329 , MG B:390 , HOH B:531 , HOH B:971BINDING SITE FOR RESIDUE DXL B 392
06AC6SOFTWAREHIS A:99 , ARG A:100 , ASP A:264 , HOH A:405 , ARG B:100 , LEU B:256 , ALA B:261 , ASP B:264 , HOH B:498 , HOH B:588BINDING SITE FOR RESIDUE GOL B 393
07AC7SOFTWAREARG A:63 , GLU A:92 , ASP B:57 , GLU B:378 , PRO B:379 , HOH B:521 , HOH B:525 , HOH B:615 , HOH B:623 , HOH B:763BINDING SITE FOR RESIDUE GOL B 394
08AC8SOFTWAREASP A:57 , GLU A:378 , HOH A:508 , HOH A:525 , HOH A:559 , HOH A:605 , ARG B:63 , ASP B:67 , GLU B:92 , HOH B:508BINDING SITE FOR RESIDUE GOL A 392
09AC9SOFTWAREGLU A:197 , GLY A:222 , CYS A:223 , PRO A:247 , ARG A:249 , HOH A:484 , HOH A:611 , HOH A:675BINDING SITE FOR RESIDUE GOL A 393
10BC1SOFTWAREHOH A:741 , ARG B:22 , HOH B:571 , HOH B:820 , HOH B:868BINDING SITE FOR RESIDUE ACY B 395
11BC2SOFTWAREGLY B:207 , ARG B:208 , HIS B:298 , HOH B:483 , HOH B:487 , HOH B:540 , HOH B:850BINDING SITE FOR RESIDUE ACY B 396
12BC3SOFTWAREASP B:149 , ARG B:176 , ASP B:181 , HOH B:538 , HOH B:634BINDING SITE FOR RESIDUE ACY B 397
13BC4SOFTWAREGLY A:207 , ARG A:208 , HIS A:298 , HOH A:496 , HOH A:500 , HOH A:542 , HOH A:807 , HOH A:996BINDING SITE FOR RESIDUE ACY A 394
14BC5SOFTWAREASP A:149 , ARG A:176 , ASP A:181 , HOH A:447 , HOH A:581BINDING SITE FOR RESIDUE ACY A 395
15BC6SOFTWARESER A:25 , ALA A:27 , LYS A:30 , TYR A:147 , LYS A:173 , ASN A:203 , HOH A:1035BINDING SITE FOR RESIDUE ACY A 396

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:54 -Pro A:55
2Ser A:144 -Ser A:145
3Gly B:54 -Pro B:55
4Ser B:144 -Ser B:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OZY)

(-) 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:386
 aligned with A0A0H3LT39_B | A0A0H3LT39 from UniProtKB/TrEMBL  Length:387

    Alignment length:386
                             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       269       279       289       299       309       319       329       339       349       359       369       379      
         A0A0H3LT39_B     - -MKITEVKAHALSTPIPERMRVESGAGLKLNRQMILVEVRTDEGVTGVGSPSGPYDLAVLKRAIEDVIGPQLIGEDPANINYLWHKVFHGEVSRNLGHRSVGIAAMSGVDIALWDLKGRAMNQPIYQLLGGKFHTRGVRAYASSIYWDLTPDQAADELAGWVEQGFTAAKLKVGRAPRKDAANLRAMRQRVGADVEILVDANQSLGRHDALAMLRILDEAGCYWFEEPLSIDDIEGHRILRAQGTPVRIATGENLYTRNAFNDYIRNDAIDVLQADASRAGGITEALAISASAASAHLAWNPHTFNDIITVAANLHLVAASPHPAMFEWDITHNDLMTRLASYDLKLENGLVQPPQGPGLGFEIDWDFVAAHAWKGEPAIGAGHGM 385
               SCOP domains d3ozya1 A:2-132 automated matches                                                                                                  d3ozya2 A:133-387 automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeee.hhhhh.ee..ee..eeeeeeeeeee.....eee......hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh........eeeeeeee....hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh...eee......hhhhhhhhhh.....eeee....hhhhhhhhhhhh....ee........hhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhh.....eeee...hhhhh............ee............hhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ozy A   2 SLKITEVKAHALSTPIPERMRVESGAGLKLNRQMILVEVRTDEGVTGVGSPSGPYDLAVLKRAIEDVIGPQLIGEDPANINYLWHKVFHGEVSRNLGHRSVGIAAMSGVDIALWDLKGRAMNQPIYQLLGGKFHTRGVRAYASSIYWDLTPDQAADELAGWVEQGFTAAKLKVGRAPRKDAANLRAMRQRVGADVEILVDANQSLGRHDALAMLRILDEAGCYWFEEPLSIDDIEGHRILRAQGTPVRIATGENLYTRNAFNDYIRNDAIDVLQADASRAGGITEALAISASAASAHLAWNPHTFNDIITVAANLHLVAASPHPAMFEWDITHNDLMTRLASYDLKLENGLVQPPQGPGLGFEIDWDFVAAHAWKGEPAIGAGHGM 387
                                    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       271       281       291       301       311       321       331       341       351       361       371       381      


Chain B from PDB  Type:PROTEIN  Length:386
 aligned with A0A0H3LT39_B | A0A0H3LT39 from UniProtKB/TrEMBL  Length:387

    Alignment length:386
                             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       269       279       289       299       309       319       329       339       349       359       369       379      
         A0A0H3LT39_B     - -MKITEVKAHALSTPIPERMRVESGAGLKLNRQMILVEVRTDEGVTGVGSPSGPYDLAVLKRAIEDVIGPQLIGEDPANINYLWHKVFHGEVSRNLGHRSVGIAAMSGVDIALWDLKGRAMNQPIYQLLGGKFHTRGVRAYASSIYWDLTPDQAADELAGWVEQGFTAAKLKVGRAPRKDAANLRAMRQRVGADVEILVDANQSLGRHDALAMLRILDEAGCYWFEEPLSIDDIEGHRILRAQGTPVRIATGENLYTRNAFNDYIRNDAIDVLQADASRAGGITEALAISASAASAHLAWNPHTFNDIITVAANLHLVAASPHPAMFEWDITHNDLMTRLASYDLKLENGLVQPPQGPGLGFEIDWDFVAAHAWKGEPAIGAGHGM 385
               SCOP domains d3ozyb1 B:2-132 automated matches                                                                                                  d3ozyb2 B:133-387 automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeee.hhhhh.ee..ee..eeeeeeeeeee.....eee......hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh........eeeeeeee....hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh...eee......hhhhhhhhhh.....eeee....hhhhhhhhhhhh....ee........hhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhh.....eeee...hhhhhh...........ee............hhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ozy B   2 SLKITEVKAHALSTPIPERMRVESGAGLKLNRQMILVEVRTDEGVTGVGSPSGPYDLAVLKRAIEDVIGPQLIGEDPANINYLWHKVFHGEVSRNLGHRSVGIAAMSGVDIALWDLKGRAMNQPIYQLLGGKFHTRGVRAYASSIYWDLTPDQAADELAGWVEQGFTAAKLKVGRAPRKDAANLRAMRQRVGADVEILVDANQSLGRHDALAMLRILDEAGCYWFEEPLSIDDIEGHRILRAQGTPVRIATGENLYTRNAFNDYIRNDAIDVLQADASRAGGITEALAISASAASAHLAWNPHTFNDIITVAANLHLVAASPHPAMFEWDITHNDLMTRLASYDLKLENGLVQPPQGPGLGFEIDWDFVAAHAWKGEPAIGAGHGM 387
                                    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       271       281       291       301       311       321       331       341       351       361       371       381
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3OZY)

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  3ozy
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 Related Entries

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UniProtKB/TrEMBL
        A0A0H3LT39_B | A0A0H3LT39: 3h12 3op2 3ozm

(-) Related Entries Specified in the PDB File

3ozm THE SAME PROTEIN COMPLEXED WITH DIFFERENT LIGANDS AND CRYSTALLIZED IN DIFFERENT SPACE GROUP