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(-) Description

Title :  CRYSTAL STRUCTURE OF PPUT_1285, A PUTATIVE HYDROXYPROLINE EPIMERASE FROM PSEUDOMONAS PUTIDA F1 (TARGET EFI-506500), OPEN FORM, SPACE GROUP P212121, BOUND SULFATE
 
Authors :  M. W. Vetting, R. Toro, R. Bhosle, N. F. Al Obaidi, L. L. Morisco, S. R. Wa S. Sojitra, E. Washington, A. Scott Glenn, S. Chowdhury, B. Evans, J. M. Stead, B. Hillerich, J. Love, R. D. Seidel, H. J. Imker, J. A. Gerlt, S Enzyme Function Initiative (Efi)
Date :  24 Feb 13  (Deposition) - 06 Mar 13  (Release) - 06 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,D
Biol. Unit 1:  A (1x),D (1x)
Keywords :  Putative Hydroxyproline Epimerase, Enzyme Function Initiative, Efi, Structural Genomics, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. W. Vetting, R. Toro, R. Bhosle, N. F. Al Obaidi, L. L. Morisco, S. R. Wasserman, S. Sojitra, E. Washington, A. Scott Glenn, S. Chowdhury, B. Evans, J. Hammonds, M. Stead, B. Hillerich, J. Love, R. D. Seidel, H. J. Imker, J. A. Gerlt, S. C. Almo
Crystal Structure Of Pput_1285, A Putative Hydroxyproline Epimerase From Pseudomonas Putida F1 (Target Efi-506500), Open Form, Space Group P212121, Bound Sulfate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROLINE RACEMASE
    Chains: A, 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: PPUT_1285
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 351746
    Strain: F1 / ATCC 700007

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AD
Biological Unit 1 (1x): A (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 14)

Asymmetric Unit (1, 14)
No.NameCountTypeFull Name
1SO414Ligand/IonSULFATE ION
Biological Unit 1 (1, 7)
No.NameCountTypeFull Name
1SO47Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:41 , HIS A:42 , ARG A:44 , TRP A:45 , HOH A:562 , HOH A:590 , HOH A:790 , HOH A:821BINDING SITE FOR RESIDUE SO4 A 401
02AC2SOFTWAREGLY A:89 , HIS A:90 , GLY A:237 , THR A:238 , HOH A:657 , HOH A:729BINDING SITE FOR RESIDUE SO4 A 402
03AC3SOFTWARELYS A:2 , ARG A:44 , GLN A:141 , HOH A:709BINDING SITE FOR RESIDUE SO4 A 403
04AC4SOFTWAREHIS A:124 , GLU A:125 , HOH A:574 , HOH A:656BINDING SITE FOR RESIDUE SO4 A 404
05AC5SOFTWAREASP A:177 , ARG A:179 , HOH A:730BINDING SITE FOR RESIDUE SO4 A 405
06AC6SOFTWAREARG A:233 , HOH A:514 , HOH A:534 , HOH A:674 , HOH D:631 , HOH D:861BINDING SITE FOR RESIDUE SO4 A 406
07AC7SOFTWARETYR A:-3 , ASN A:146 , PRO A:148 , GLY A:149 , HIS A:150 , GLY A:151 , GLN D:100 , HIS D:101 , HOH D:717BINDING SITE FOR RESIDUE SO4 A 407
08AC8SOFTWAREPRO D:24 , LEU D:41 , HIS D:42 , ARG D:44 , TRP D:45 , HOH D:551 , HOH D:593 , HOH D:766BINDING SITE FOR RESIDUE SO4 D 401
09AC9SOFTWAREGLY D:89 , HIS D:90 , CYS D:236 , GLY D:237 , THR D:238 , HOH D:605 , HOH D:672 , HOH D:727 , HOH D:775BINDING SITE FOR RESIDUE SO4 D 402
10BC1SOFTWARELYS D:2 , ARG D:44 , GLU D:300 , HOH D:740BINDING SITE FOR RESIDUE SO4 D 403
11BC2SOFTWAREARG D:39 , ALA D:82 , GLY D:83 , TYR D:84 , HOH D:791 , HOH D:846BINDING SITE FOR RESIDUE SO4 D 404
12BC3SOFTWAREHIS D:124 , GLU D:125 , HOH D:571 , HOH D:585 , HOH D:894BINDING SITE FOR RESIDUE SO4 D 405
13BC4SOFTWARETHR D:73 , HIS D:110 , HOH D:584 , HOH D:695BINDING SITE FOR RESIDUE SO4 D 406
14BC5SOFTWAREARG D:279 , HOH D:698 , HOH D:742 , HOH D:841BINDING SITE FOR RESIDUE SO4 D 407

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JD7)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:52 -Pro A:53
2Glu D:52 -Pro D:53

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JD7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JD7)

(-) Exons   (0, 0)

(no "Exon" information available for 4JD7)

(-) 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:314
                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4jd7a_ A: automated matches                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeee..eeeeeeee........hhhhhhhhhhhhhhhhhhhhhh........eeeeee........eeeeee........hhhhhhhhhhhhhhh.....eeeeeee..eeeeeee.....eeee....eeeeeeeeeee...eeeeeeeee...eeeeee......hhhhhhhhhhhhhhhhhhhhhh...hhhhh...eeeeeeee..eeeeeeeee...ee....hhhhhhhhhhhhhhh........eeee.....eeeeeeeee..eeeeeeee.eeeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jd7 A  -5 NLYFQSMKQIHVIDSHTGGEPTRLVMKGFPQLHGRSMAEQRDELRELHDRWRRACLLEPRGNDVLVGALYCPPVSADATCGVIFFNNAGYLNMCGHGTIGLVASLQHLGLIAPGVHKIDTPVGQVSATLHEDGAITVANVPSYRYRQHVAVNVPGHGVVHGDIAWGGNWFFLVAEHGQRIELDNREVLTEYTWAMLKALEAQGITGENGAPIDHVELFADDPNADSRNFVMCPGKAYDRSPCGTGTSAKLACLAADGTLAEGQTWVQASITGSQFHGRYERDGERIRPFITGRAHMTADSTLLIDEQDPFAWGI 308
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304    


Chain D from PDB  Type:PROTEIN  Length:312
                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4jd7d_ D: automated matches                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhheeeeeeeeee..eeeeeeee........hhhhhhhhhhhhhhhhhhhhhh........eeeeee......eeeeeeee........hhhhhhhhhhhhhhh.....eeeeeee..eeeeeee.....eeee....eeeeeeeeeee...eeeeeeeee...eeeeee......hhhhhhhhhhhhhhhhhhhhhh...hhhhh...eeeeeeee..eeeeeeeeehhhee....hhhhhhhhhhhhhhh........eeee.....eeeeeeeee..eeeeeeee.eeeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jd7 D  -3 YFQSMKQIHVIDSHTGGEPTRLVMKGFPQLHGRSMAEQRDELRELHDRWRRACLLEPRGNDVLVGALYCPPVSADATCGVIFFNNAGYLNMCGHGTIGLVASLQHLGLIAPGVHKIDTPVGQVSATLHEDGAITVANVPSYRYRQHVAVNVPGHGVVHGDIAWGGNWFFLVAEHGQRIELDNREVLTEYTWAMLKALEAQGITGENGAPIDHVELFADDPNADSRNFVMCPGKAYDRSPCGTGTSAKLACLAADGTLAEGQTWVQASITGSQFHGRYERDGERIRPFITGRAHMTADSTLLIDEQDPFAWGI 308
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JD7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JD7)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

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    Glu A:52 - Pro A:53   [ RasMol ]  
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