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(-) Description

Title :  CRYSTAL STRUCTURE OF 5-CARBOXYVANILLATE DECARBOXYLASE LIGW2 (TARGET EFI-505250) FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 COMPLEXED WITH MANGANESE
 
Authors :  Y. Patskovsky, A. Vladimirova, R. Toro, R. Bhosle, J. A. Gerlt, F. M. Rau S. C. Almo
Date :  07 Jul 14  (Deposition) - 20 Aug 14  (Release) - 20 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.47
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Amidohydrolase, Metal Binding Site, Decarboxylase, Ligw2, Manganese, Enzyme Function Initiative, Efi, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, A. Vladimirova, R. Toro, R. Bhosle, F. M. Raushel, S. C. Almo
Crystal Structure Of 5-Carboxyvanillate Decarboxylase Ligw2 From Novosphingobium Aromaticivorans
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 5-CARBOXYVANILLATE DECARBOXYLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SARO_0799
    Organism Scientific: NOVOSPHINGOBIUM AROMATICIVORANS
    Organism Taxid: 279238
    Strain: DSM 12444 / F199

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MN2Ligand/IonMANGANESE (II) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:19 , HIS A:188 , ASP A:314 , HOH A:662 , HOH A:688 , HOH A:875BINDING SITE FOR RESIDUE MN A 401
2AC2SOFTWARETYR A:255 , GLN A:258 , ALA A:259 , ARG A:262 , HOH A:579 , HOH A:871 , HOH A:873 , ASP B:331BINDING SITE FOR RESIDUE GOL A 402
3AC3SOFTWAREASP A:41 , GLN A:162 , PRO A:193 , ASP A:194 , HOH A:744BINDING SITE FOR RESIDUE GOL A 403
4AC4SOFTWAREGLU B:19 , HIS B:188 , ASP B:314 , HOH B:610 , HOH B:685 , HOH B:788BINDING SITE FOR RESIDUE MN B 401
5AC5SOFTWAREASP B:41 , GLN B:162 , PRO B:193 , ASP B:194 , HOH B:686 , HOH B:748BINDING SITE FOR RESIDUE GOL B 402
6AC6SOFTWAREASP B:307 , LYS B:339 , THR B:343 , ASN B:344 , LYS B:347 , HOH B:554BINDING SITE FOR RESIDUE GOL B 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QTG)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser A:91 -Pro A:92
2Tyr A:315 -Pro A:316
3Ser B:91 -Pro B:92
4Tyr B:315 -Pro B:316

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QTG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QTG)

(-) Exons   (0, 0)

(no "Exon" information available for 4QTG)

(-) 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:348
                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............eeeeeee.hhhhhhhhhhhhhh...hhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhh.....eee..........hhhhhhhhhhhhhhh..eee.........hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhh...hhhhhhhhhhhhhhh...........hhhhhhhhheeee.....hhhhhhhhhhhhh...ee.........hhhhhhhhhh...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4qtg A   4 DLKTGGEQGYLRIATEEAFATREIIDVYLRMIRDGTADKGMVSLWGFYAQSPSERATQILERLLDLGERRIADMDATGIDKAILALTSPGVQPLHDLDEARTLATRANDTLADACQKYPDRFIGMGTVAPQDPEWSAREIHRGARELGFKGIQINSHTQGRYLDEEFFDPIFRALVEVDQPLYIHPATSPDSMIDPMLEAGLDGAIFGFGVETGMHLLRLITIGIFDKYPSLQIMVGHMGEALPYWLYRLDYMHQAGVRSQRYERMKPLKKTIEGYLKSNVLVTNSGVAWEPAIKFCQQVMGEDRVMYAMDYPYQYVADEVRAMDAMDMSAQTKKKFFQTNAEKWFKL 351
                                    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        


Chain B from PDB  Type:PROTEIN  Length:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeee.hhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhh.....eee..........hhhhhhhhhhhhhhh..eee.........hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh....eeehhhhh....hhhhhhhhhhhhhhh...........hhhhhhhhheeee.....hhhhhhhhhhhhh...ee.........hhhhhhhhhh...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qtg B   3 QDLKTGGEQGYLRIATEEAFATREIIDVYLRMIRDGTADKGMVSLWGFYAQSPSERATQILERLLDLGERRIADMDATGIDKAILALTSPGVQPLHDLDEARTLATRANDTLADACQKYPDRFIGMGTVAPQDPEWSAREIHRGARELGFKGIQINSHTQGRYLDEEFFDPIFRALVEVDQPLYIHPATSPDSMIDPMLEAGLDGAIFGFGVETGMHLLRLITIGIFDKYPSLQIMVGHMGEALPYWLYRLDYMHQAGVRSQRYERMKPLKKTIEGYLKSNVLVTNSGVAWEPAIKFCQQVMGEDRVMYAMDYPYQYVADEVRAMDAMDMSAQTKKKFFQTNAEKWFKL 351
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342
   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 4QTG)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QTG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QTG)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q2GA79_NOVAD | Q2GA79: 4inf 4qrn 4qs5 4qs6

(-) Related Entries Specified in the PDB File

4qrn COMPLEX WITH MANGANESE AND 4-HYDROXY-3-METHOXY-5- NITROBENZOIC ACID
4qs5 D314N MUTANT, COMPLEX WITH MANGANESE AND 4-HYDROXY-3- METHOXY-5-NITROBENZOIC ACID
4qs6 D314N MUTANT, COMPLEX WITH 4-HYDROXY-3-METHOXY-5- NITROBENZOIC ACID RELATED ID: EFI-505250 RELATED DB: TARGETTRACK