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(-) Description

Title :  HIGH-RESOLUTION CRYSTAL STRUCTURE OF 5-CARBOXYVANILLATE DECARBOXYLASE (TARGET EFI-505250) FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 COMPLEXED WITH MANGANESE AND 4-HYDROXY-3-METHOXY-5-NITROBENZOIC ACID
 
Authors :  Y. Patskovsky, A. Vladimirova, R. Toro, R. Bhosle, J. A. Gerlt, F. M. Rau S. C. Almo
Date :  01 Jul 14  (Deposition) - 06 Aug 14  (Release) - 06 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.07
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Hydrolase, Decarboxylase, Enzyme Function Initiative, Efi, Hydrolase- Hydrolase Inhibitor Complex (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 From Novosphingobium Aromaticivorans
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 5-CARBOXYVANILLATE DECARBOXYLASE
    Chains: A, B, C, D
    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

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 23)

Asymmetric Unit (5, 23)
No.NameCountTypeFull Name
11DF4Ligand/Ion4-HYDROXY-3-METHOXY-5-NITROBENZOIC ACID
2ACT1Ligand/IonACETATE ION
3CL8Ligand/IonCHLORIDE ION
4GOL6Ligand/IonGLYCEROL
5MN4Ligand/IonMANGANESE (II) ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
11DF2Ligand/Ion4-HYDROXY-3-METHOXY-5-NITROBENZOIC ACID
2ACT1Ligand/IonACETATE ION
3CL-1Ligand/IonCHLORIDE ION
4GOL3Ligand/IonGLYCEROL
5MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
11DF2Ligand/Ion4-HYDROXY-3-METHOXY-5-NITROBENZOIC ACID
2ACT-1Ligand/IonACETATE ION
3CL-1Ligand/IonCHLORIDE ION
4GOL3Ligand/IonGLYCEROL
5MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:19 , HIS A:188 , ASP A:314 , 1DF A:402 , HOH A:572BINDING SITE FOR RESIDUE MN A 401
02AC2SOFTWAREGLU A:19 , TYR A:51 , ARG A:58 , THR A:90 , SER A:91 , HIS A:188 , PHE A:212 , HIS A:241 , ASP A:314 , TYR A:317 , MN A:401 , HOH A:512 , HOH A:535 , HOH A:546 , HOH A:610 , ARG B:252 , MET B:256BINDING SITE FOR RESIDUE 1DF A 402
03AC3SOFTWAREASP A:41 , GLN A:162 , PRO A:193 , ASP A:194 , CL A:406 , HOH A:692 , HOH A:850 , HOH A:916BINDING SITE FOR RESIDUE GOL A 403
04AC4SOFTWAREASP A:331 , HOH A:861 , HOH A:887 , HOH A:997BINDING SITE FOR RESIDUE GOL A 404
05AC5SOFTWAREVAL A:179 , TYR A:232 , PRO A:233 , SER A:234 , HOH A:815 , HOH A:961BINDING SITE FOR RESIDUE CL A 405
06AC6SOFTWAREASP A:194 , SER A:195 , GOL A:403 , HOH A:768 , HOH B:707BINDING SITE FOR RESIDUE CL A 406
07AC7SOFTWARETYR A:121 , PRO A:122 , ASP A:123 , HOH A:843BINDING SITE FOR RESIDUE CL A 407
08AC8SOFTWAREGLN A:134 , ARG A:164 , HOH A:680 , HOH A:725 , HOH A:925BINDING SITE FOR RESIDUE ACT A 408
09AC9SOFTWAREGLU B:19 , HIS B:188 , ASP B:314 , 1DF B:402 , HOH B:564BINDING SITE FOR RESIDUE MN B 401
10BC1SOFTWAREARG A:252 , MET A:256 , GLU B:19 , TYR B:51 , ARG B:58 , THR B:90 , SER B:91 , HIS B:188 , PHE B:212 , HIS B:241 , ASP B:314 , TYR B:317 , MN B:401 , HOH B:512 , HOH B:515 , HOH B:540 , HOH B:584BINDING SITE FOR RESIDUE 1DF B 402
11BC2SOFTWAREASP B:41 , GLN B:162 , PRO B:193 , ASP B:194 , HOH B:822 , HOH B:843 , HOH B:966BINDING SITE FOR RESIDUE GOL B 403
12BC3SOFTWARESER A:263 , HOH A:664 , ARG B:58 , HOH B:880BINDING SITE FOR RESIDUE CL B 404
13BC4SOFTWAREGLU C:19 , HIS C:188 , ASP C:314 , 1DF C:402 , HOH C:575BINDING SITE FOR RESIDUE MN C 401
14BC5SOFTWAREGLU C:19 , TYR C:51 , ARG C:58 , THR C:90 , SER C:91 , HIS C:188 , HIS C:241 , ASP C:314 , TYR C:317 , MN C:401 , HOH C:512 , HOH C:536 , HOH C:593 , HOH C:614 , ARG D:252 , MET D:256BINDING SITE FOR RESIDUE 1DF C 402
15BC6SOFTWAREASP C:41 , GLN C:162 , PRO C:193 , ASP C:194 , HOH C:684 , HOH C:755 , HOH C:1006BINDING SITE FOR RESIDUE GOL C 403
16BC7SOFTWARETYR C:255 , GLN C:258 , ALA C:259 , ARG C:262 , HOH C:534 , HOH C:691 , HOH C:819 , HOH C:921BINDING SITE FOR RESIDUE GOL C 404
17BC8SOFTWAREARG C:58 , SER D:263 , HOH D:674BINDING SITE FOR RESIDUE CL C 405
18BC9SOFTWAREGLU C:169 , ARG C:268 , HOH C:753BINDING SITE FOR RESIDUE CL C 406
19CC1SOFTWAREGLU D:19 , HIS D:188 , ASP D:314 , 1DF D:402 , HOH D:542BINDING SITE FOR RESIDUE MN D 401
20CC2SOFTWAREARG C:252 , MET C:256 , GLU D:19 , TYR D:51 , ARG D:58 , THR D:90 , SER D:91 , HIS D:188 , HIS D:241 , ASP D:314 , TYR D:317 , MN D:401 , HOH D:509 , HOH D:545 , HOH D:582 , HOH D:610BINDING SITE FOR RESIDUE 1DF D 402
21CC3SOFTWAREASP D:41 , GLN D:162 , PRO D:193 , ASP D:194 , HOH D:691 , HOH D:800 , HOH D:809 , HOH D:881BINDING SITE FOR RESIDUE GOL D 403
22CC4SOFTWARETYR D:121 , PRO D:122 , ASP D:123BINDING SITE FOR RESIDUE CL D 404
23CC5SOFTWAREVAL D:179 , TYR D:232 , PRO D:233 , SER D:234BINDING SITE FOR RESIDUE CL D 405

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric 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
5Ser C:91 -Pro C:92
6Tyr C:315 -Pro C:316
7Ser D:91 -Pro D:92
8Tyr D:315 -Pro D:316

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QRN)

(-) 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:352
                                                                                                                                                                                                                                                                                                                                                                                                
               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....eeehhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhheeee.....hhhhhhhhhhhhh...ee.........hhhhhhhhhh...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qrn A   0 SMTQDLKTGGEQGYLRIATEEAFATREIIDVYLRMIRDGTADKGMVSLWGFYAQSPSERATQILERLLDLGERRIADMDATGIDKAILALTSPGVQPLHDLDEARTLATRANDTLADACQKYPDRFIGMGTVAPQDPEWSAREIHRGARELGFKGIQINSHTQGRYLDEEFFDPIFRALVEVDQPLYIHPATSPDSMIDPMLEAGLDGAIFGFGVETGMHLLRLITIGIFDKYPSLQIMVGHMGEALPYWLYRLDYMHQAGVRSQRYERMKPLKKTIEGYLKSNVLVTNSGVAWEPAIKFCQQVMGEDRVMYAMDYPYQYVADEVRAMDAMDMSAQTKKKFFQTNAEKWFKL 351
                                     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  


Chain B 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....eeehhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhheeee.....hhhhhhhhhhhhh...ee.........hhhhhhhhhh...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4qrn B   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 C 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....eeehhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhheeee.....hhhhhhhhhhhhh...ee.........hhhhhhhhhh...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4qrn C   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 D from PDB  Type:PROTEIN  Length:350
                                                                                                                                                                                                                                                                                                                                                                                              
               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.........hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhheeee.....hhhhhhhhhhhhh...ee.........hhhhhhhhhh...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qrn D   2 TQDLKTGGEQGYLRIATEEAFATREIIDVYLRMIRDGTADKGMVSLWGFYAQSPSERATQILERLLDLGERRIADMDATGIDKAILALTSPGVQPLHDLDEARTLATRANDTLADACQKYPDRFIGMGTVAPQDPEWSAREIHRGARELGFKGIQINSHTQGRYLDEEFFDPIFRALVEVDQPLYIHPATSPDSMIDPMLEAGLDGAIFGFGVETGMHLLRLITIGIFDKYPSLQIMVGHMGEALPYWLYRLDYMHQAGVRSQRYERMKPLKKTIEGYLKSNVLVTNSGVAWEPAIKFCQQVMGEDRVMYAMDYPYQYVADEVRAMDAMDMSAQTKKKFFQTNAEKWFKL 351
                                    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
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  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 4QRN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

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  4qrn
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  Q2GA79_NOVAD | Q2GA79
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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