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(-) Description

Title :  CRYSTAL STRUCTURE OF 5-CARBOXYVANILLATE DECARBOXYLASE LIGW2 FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 (TARGET EFI-505250) WITH BOUND 4-HYDROXY-3-METHOXY-5-NITROBENZOIC ACID, NO METAL, THE D314N MUTANT
 
Authors :  Y. Patskovsky, A. Vladimirova, R. Toro, R. Bhosle, J. A. Gerlt, F. M. Rau S. C. Almo
Date :  03 Jul 14  (Deposition) - 06 Aug 14  (Release) - 06 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Amidohydrolase, Metal Binding Site, Decarboxylase (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 Ligw2 Decarboxylase From Novosphingobium Aromaticivorans
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LIGW2 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  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
11DF2Ligand/Ion4-HYDROXY-3-METHOXY-5-NITROBENZOIC ACID
2CL2Ligand/IonCHLORIDE ION
3GOL3Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:255 , GLN A:258 , ALA A:259 , ARG A:262 , HOH A:577 , HOH A:677 , HOH A:751 , ARG B:58 , ASP B:331BINDING SITE FOR RESIDUE GOL A 401
2AC2SOFTWAREARG A:262 , SER B:333 , ALA B:334BINDING SITE FOR RESIDUE CL A 402
3AC3SOFTWAREASP A:41 , PRO A:193 , ASP A:194BINDING SITE FOR RESIDUE CL A 403
4AC4SOFTWAREGLU A:19 , TYR A:51 , ARG A:58 , THR A:90 , SER A:91 , HIS A:188 , PHE A:212 , HIS A:241 , ASN A:314 , TYR A:317 , HOH A:502 , HOH A:509 , HOH A:657 , HOH A:876 , ARG B:252 , MET B:256BINDING SITE FOR RESIDUE 1DF A 404
5AC5SOFTWAREASP B:41 , GLN B:162 , PRO B:193 , ASP B:194 , HOH B:757BINDING SITE FOR RESIDUE GOL B 401
6AC6SOFTWAREASP B:307 , LYS B:339 , THR B:343 , ASN B:344 , LYS B:347 , HOH B:643BINDING SITE FOR RESIDUE GOL B 402
7AC7SOFTWAREARG A:252 , MET A:256 , GLU B:19 , TYR B:51 , THR B:90 , SER B:91 , HIS B:188 , HIS B:241 , ASN B:314 , TYR B:317 , HOH B:501 , HOH B:502 , HOH B:608 , HOH B:617 , HOH B:671 , HOH B:861BINDING SITE FOR RESIDUE 1DF B 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QS6)

(-) 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 4QS6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QS6)

(-) Exons   (0, 0)

(no "Exon" information available for 4QS6)

(-) 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:349
                                                                                                                                                                                                                                                                                                                                                                                             
               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.........hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhheeee.....hhhhhhhhhhhhh...ee.........hhhhhhhhhh...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qs6 A   3 QDLKTGGEQGYLRIATEEAFATREIIDVYLRMIRDGTADKGMVSLWGFYAQSPSERATQILERLLDLGERRIADMDATGIDKAILALTSPGVQPLHDLDEARTLATRANDTLADACQKYPDRFIGMGTVAPQDPEWSAREIHRGARELGFKGIQINSHTQGRYLDEEFFDPIFRALVEVDQPLYIHPATSPDSMIDPMLEAGLDGAIFGFGVETGMHLLRLITIGIFDKYPSLQIMVGHMGEALPYWLYRLDYMHQAGVRSQRYERMKPLKKTIEGYLKSNVLVTNSGVAWEPAIKFCQQVMGEDRVMYAMNYPYQYVADEVRAMDAMDMSAQTKKKFFQTNAEKWFKL 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         


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...hhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhh.....eee..........hhhhhhhhhhhhhhh..eee.....hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhh...hhhhhhhhhhhhhhh...........hhhhhhhhheeee.....hhhhhhhhhhhhh...ee.........hhhhhhhhhh...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qs6 B   3 QDLKTGGEQGYLRIATEEAFATREIIDVYLRMIRDGTADKGMVSLWGFYAQSPSERATQILERLLDLGERRIADMDATGIDKAILALTSPGVQPLHDLDEARTLATRANDTLADACQKYPDRFIGMGTVAPQDPEWSAREIHRGARELGFKGIQINSHTQGRYLDEEFFDPIFRALVEVDQPLYIHPATSPDSMIDPMLEAGLDGAIFGFGVETGMHLLRLITIGIFDKYPSLQIMVGHMGEALPYWLYRLDYMHQAGVRSQRYERMKPLKKTIEGYLKSNVLVTNSGVAWEPAIKFCQQVMGEDRVMYAMNYPYQYVADEVRAMDAMDMSAQTKKKFFQTNAEKWFKL 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)
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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 4QS6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QS6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QS6)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

(-) Related Entries Specified in the PDB File

4qrn 4qs5