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(-) Description

Title :  CRYSTAL STRUCTURE OF A MANDELATE RACEMASE/MUCONATE LACTONIZING ENZYME-LIKE PROTEIN FROM RUBROBACTER XYLANOPHILUS
 
Authors :  J. B. Bonanno, J. Freeman, K. T. Bain, F. Zhang, J. Bravo, D. Smith, S. Was J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center Structural Genomics (Nysgxrc)
Date :  25 Apr 08  (Deposition) - 06 May 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Structural Genomics, Isomerase, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Bonanno, J. Freeman, K. T. Bain, F. Zhang, J. Bravo, D. Smith, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of A Mandelate Racemase/Muconate Lactonizing Enzyme-Like Protein From Rubrobacter Xylanophilus.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MANDELATE RACEMASE/MUCONATE LACTONIZING ENZYME-LIKE PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: MODIFIED PET26
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Gene: RXYL_2719
    Organism Scientific: RUBROBACTER XYLANOPHILUS DSM 9941
    Organism Taxid: 266117
    Strain: DSM 9941 / NBRC 16129

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NA2Ligand/IonSODIUM ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2NA-1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:192 , ASN A:194 , GLU A:219 , GLU A:220 , GLU A:247BINDING SITE FOR RESIDUE NA A 371
2AC2SOFTWAREASP C:192 , ASN C:194 , GLU C:219 , GLU C:220 , GLU C:247BINDING SITE FOR RESIDUE NA C 371
3AC3SOFTWAREASP A:24 , TRP A:29 , LYS A:164 , HIS A:295 , PHE A:317 , ARG B:88 , ASN B:89BINDING SITE FOR RESIDUE GOL A 372
4AC4SOFTWAREASP C:24 , TRP C:29 , LYS C:164 , ASN C:194 , HIS C:295 , ARG D:88 , ASN D:89BINDING SITE FOR RESIDUE GOL C 372

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CYJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CYJ)

(-) 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:359
 aligned with Q1ASJ4_RUBXD | Q1ASJ4 from UniProtKB/TrEMBL  Length:362

    Alignment length:359
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353         
         Q1ASJ4_RUBXD     4 PRVERLEVSAYTVPTDYPESDGTLQWDSTTMILVEAHGGGRKGLGYTYGDVSVGRFVESKLAGVAEGSDALSPPAVWARMQAAIRNAGRPGVGAMAVSAVDIALWDLKARLLGLPLADALPRFHAEVPVYGSGGFTSYPLRRLQEQLGGWAAAGIPRVKMKVGREPEKDPERVRAAREAIGESVELMVDANGAYTRKQALYWAGAFAREAGISYLEEPVSSEDREGLRLLRDRGPGGVAIAAGEYEWTLPQLHDLAGCVDILQADVTRCGGITGLLRVDGICRGHQIPFSAHCAPAVSAHACCAVESLLHLEYFHDHARVERLLFDGTLDPEGGSLRPDPDRPGLGLELKRSEAGKYAA 362
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cyjA01 A:4-116,A:354-362 Enolase-like, N-terminal domain                                                        3cyjA02 A:117-353 Enolase superfamily                                                                                                                                                                                                        3cyjA01   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..hhhhhh......eeeeee......hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhh....eeee.....hhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhh..eee..hhhhhhhhhhhh..eeeeeeehhhhhhhhhhee....hhh.ee...........eehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cyj A   4 PRVERLEVSAYTVPTDYPESDGTLQWDSTTMILVEAHGGGRKGLGYTYGDVSVGRFVESKLAGVAEGSDALSPPAVWARMQAAIRNAGRPGVGAMAVSAVDIALWDLKARLLGLPLADALPRFHAEVPVYGSGGFTSYPLRRLQEQLGGWAAAGIPRVKMKVGREPEKDPERVRAAREAIGESVELMVDANGAYTRKQALYWAGAFAREAGISYLEEPVSSEDREGLRLLRDRGPGGVAIAAGEYEWTLPQLHDLAGCVDILQADVTRCGGITGLLRVDGICRGHQIPFSAHCAPAVSAHACCAVESLLHLEYFHDHARVERLLFDGTLDPEGGSLRPDPDRPGLGLELKRSEAGKYAA 362
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353         


Chain B from PDB  Type:PROTEIN  Length:359
 aligned with Q1ASJ4_RUBXD | Q1ASJ4 from UniProtKB/TrEMBL  Length:362

    Alignment length:359
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353         
         Q1ASJ4_RUBXD     4 PRVERLEVSAYTVPTDYPESDGTLQWDSTTMILVEAHGGGRKGLGYTYGDVSVGRFVESKLAGVAEGSDALSPPAVWARMQAAIRNAGRPGVGAMAVSAVDIALWDLKARLLGLPLADALPRFHAEVPVYGSGGFTSYPLRRLQEQLGGWAAAGIPRVKMKVGREPEKDPERVRAAREAIGESVELMVDANGAYTRKQALYWAGAFAREAGISYLEEPVSSEDREGLRLLRDRGPGGVAIAAGEYEWTLPQLHDLAGCVDILQADVTRCGGITGLLRVDGICRGHQIPFSAHCAPAVSAHACCAVESLLHLEYFHDHARVERLLFDGTLDPEGGSLRPDPDRPGLGLELKRSEAGKYAA 362
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cyjB01 B:4-116,B:354-362 Enolase-like, N-terminal domain                                                        3cyjB02 B:117-353 Enolase superfamily                                                                                                                                                                                                        3cyjB01   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeeeeee....eeeeeeeeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eeeeee......hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhh....eeee.....hhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhh..eee..hhhhhhhhhhhh..eeeeeeehhhhhhhhhhee........ee...........eehhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cyj B   4 PRVERLEVSAYTVPTDYPESDGTLQWDSTTMILVEAHGGGRKGLGYTYGDVSVGRFVESKLAGVAEGSDALSPPAVWARMQAAIRNAGRPGVGAMAVSAVDIALWDLKARLLGLPLADALPRFHAEVPVYGSGGFTSYPLRRLQEQLGGWAAAGIPRVKMKVGREPEKDPERVRAAREAIGESVELMVDANGAYTRKQALYWAGAFAREAGISYLEEPVSSEDREGLRLLRDRGPGGVAIAAGEYEWTLPQLHDLAGCVDILQADVTRCGGITGLLRVDGICRGHQIPFSAHCAPAVSAHACCAVESLLHLEYFHDHARVERLLFDGTLDPEGGSLRPDPDRPGLGLELKRSEAGKYAA 362
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353         


Chain C from PDB  Type:PROTEIN  Length:359
 aligned with Q1ASJ4_RUBXD | Q1ASJ4 from UniProtKB/TrEMBL  Length:362

    Alignment length:359
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353         
         Q1ASJ4_RUBXD     4 PRVERLEVSAYTVPTDYPESDGTLQWDSTTMILVEAHGGGRKGLGYTYGDVSVGRFVESKLAGVAEGSDALSPPAVWARMQAAIRNAGRPGVGAMAVSAVDIALWDLKARLLGLPLADALPRFHAEVPVYGSGGFTSYPLRRLQEQLGGWAAAGIPRVKMKVGREPEKDPERVRAAREAIGESVELMVDANGAYTRKQALYWAGAFAREAGISYLEEPVSSEDREGLRLLRDRGPGGVAIAAGEYEWTLPQLHDLAGCVDILQADVTRCGGITGLLRVDGICRGHQIPFSAHCAPAVSAHACCAVESLLHLEYFHDHARVERLLFDGTLDPEGGSLRPDPDRPGLGLELKRSEAGKYAA 362
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cyjC01 C:4-116,C:354-362 Enolase-like, N-terminal domain                                                        3cyjC02 C:117-353 Enolase superfamily                                                                                                                                                                                                        3cyjC01   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeeeeeeee..eeeeeeeeeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..hhhhhh......eeeeee......hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhh....eeee.....hhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhh...eee..hhhhhhhhhhhh..eeeeeeehhhhhhhhhhee........ee...........eehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cyj C   4 PRVERLEVSAYTVPTDYPESDGTLQWDSTTMILVEAHGGGRKGLGYTYGDVSVGRFVESKLAGVAEGSDALSPPAVWARMQAAIRNAGRPGVGAMAVSAVDIALWDLKARLLGLPLADALPRFHAEVPVYGSGGFTSYPLRRLQEQLGGWAAAGIPRVKMKVGREPEKDPERVRAAREAIGESVELMVDANGAYTRKQALYWAGAFAREAGISYLEEPVSSEDREGLRLLRDRGPGGVAIAAGEYEWTLPQLHDLAGCVDILQADVTRCGGITGLLRVDGICRGHQIPFSAHCAPAVSAHACCAVESLLHLEYFHDHARVERLLFDGTLDPEGGSLRPDPDRPGLGLELKRSEAGKYAA 362
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353         


Chain D from PDB  Type:PROTEIN  Length:359
 aligned with Q1ASJ4_RUBXD | Q1ASJ4 from UniProtKB/TrEMBL  Length:362

    Alignment length:359
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353         
         Q1ASJ4_RUBXD     4 PRVERLEVSAYTVPTDYPESDGTLQWDSTTMILVEAHGGGRKGLGYTYGDVSVGRFVESKLAGVAEGSDALSPPAVWARMQAAIRNAGRPGVGAMAVSAVDIALWDLKARLLGLPLADALPRFHAEVPVYGSGGFTSYPLRRLQEQLGGWAAAGIPRVKMKVGREPEKDPERVRAAREAIGESVELMVDANGAYTRKQALYWAGAFAREAGISYLEEPVSSEDREGLRLLRDRGPGGVAIAAGEYEWTLPQLHDLAGCVDILQADVTRCGGITGLLRVDGICRGHQIPFSAHCAPAVSAHACCAVESLLHLEYFHDHARVERLLFDGTLDPEGGSLRPDPDRPGLGLELKRSEAGKYAA 362
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cyjD01 D:4-116,D:354-362 Enolase-like, N-terminal domain                                                        3cyjD02 D:117-353 Enolase superfamily                                                                                                                                                                                                        3cyjD01   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eeeeee......hhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhh....eeee.....hhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhh...eee..hhhhhhhhhhhh..eeeeeeehhhhhhhhhhee........ee...........eehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cyj D   4 PRVERLEVSAYTVPTDYPESDGTLQWDSTTMILVEAHGGGRKGLGYTYGDVSVGRFVESKLAGVAEGSDALSPPAVWARMQAAIRNAGRPGVGAMAVSAVDIALWDLKARLLGLPLADALPRFHAEVPVYGSGGFTSYPLRRLQEQLGGWAAAGIPRVKMKVGREPEKDPERVRAAREAIGESVELMVDANGAYTRKQALYWAGAFAREAGISYLEEPVSSEDREGLRLLRDRGPGGVAIAAGEYEWTLPQLHDLAGCVDILQADVTRCGGITGLLRVDGICRGHQIPFSAHCAPAVSAHACCAVESLLHLEYFHDHARVERLLFDGTLDPEGGSLRPDPDRPGLGLELKRSEAGKYAA 362
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353
   Legend:   → Mismatch (orange background)
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  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 3CYJ)

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q1ASJ4_RUBXD | Q1ASJ4)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    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.

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