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(-) Description

Title :  STRUCTURE OF THE ISOLEUCINE 2-EPIMERASE FROM LACTOBACILLUS BUCHNERI (PLP COMPLEX FORM)
 
Authors :  J. -B. Reiser, R. Awad, P. Gans
Date :  26 Jul 16  (Deposition) - 12 Apr 17  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Racemase, Epimerase, Isoleucine, Plp, Lactobacillus Buchneri, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Awad, P. Gans, J. B. Reiser
Structural Insights Into The Substrate Recognition And Reaction Specificity Of The Plp-Dependent Fold-Type I Isoleucine 2-Epimerase From Lactobacillus Buchneri.
Biochimie V. 137 165 2017
PubMed-ID: 28344038  |  Reference-DOI: 10.1016/J.BIOCHI.2017.03.015

(-) Compounds

Molecule 1 - ISOLEUCINE 2-EPIMERASE
    Chains: A, B, C, D
    EC Number: 5.1.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: LACTOBACILLUS BUCHNERI
    Organism Taxid: 1581
    Synonym: BCAA RACEMASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1PLP4Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:114 , GLY A:115 , SER A:116 , ASN A:119 , TYR A:142 , HIS A:143 , GLU A:217 , ASP A:250 , VAL A:252 , ASN A:253 , LYS A:280 , HOH A:1101 , HOH A:1110 , HOH A:1122 , PHE B:308 , THR B:309binding site for residue PLP A 1000
2AC2SOFTWAREPHE A:308 , THR A:309 , HOH A:1102 , ALA B:54 , ALA B:56 , SER B:114 , GLY B:115 , SER B:116 , ASN B:119 , TYR B:142 , HIS B:143 , GLU B:217 , ASP B:250 , VAL B:252 , ASN B:253 , GLY B:279 , SER B:281 , LEU B:282 , GLY B:285 , HOH B:1101 , HOH B:1104 , HOH B:1116binding site for Di-peptide PLP B 1000 and LYS B 280
3AC3SOFTWAREALA C:54 , ALA C:56 , SER C:114 , GLY C:115 , SER C:116 , TYR C:142 , HIS C:143 , GLU C:217 , ASP C:250 , VAL C:252 , ASN C:253 , GLY C:279 , SER C:281 , LEU C:282 , GLY C:285 , HOH C:1101 , HOH C:1103 , HOH C:1115 , HOH C:1206 , PHE D:308 , THR D:309 , HOH D:1106binding site for Di-peptide PLP C 1000 and LYS C 280
4AC4SOFTWAREPHE C:308 , THR C:309 , ALA D:54 , ALA D:56 , SER D:114 , GLY D:115 , SER D:116 , ASN D:119 , TYR D:142 , HIS D:143 , GLU D:217 , ASP D:250 , VAL D:252 , ASN D:253 , GLY D:279 , SER D:281 , LEU D:282 , GLY D:285 , HOH D:1101 , HOH D:1102 , HOH D:1105 , HOH D:1125binding site for Di-peptide PLP D 1000 and LYS D 280

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LL3)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Gly A:164 -Pro A:165
2Ala A:303 -Pro A:304
3Gly B:164 -Pro B:165
4Ala B:303 -Pro B:304
5Gly C:164 -Pro C:165
6Ala C:303 -Pro C:304
7Gly D:164 -Pro D:165

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LL3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LL3)

(-) Exons   (0, 0)

(no "Exon" information available for 5LL3)

(-) 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:417
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhhhh........eehhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhh..hhhhh.........eeee............hhhhhhhhhhhhhhhhhh...hhh.eeeeee..ee.....ee.hhhhhhhhhhhhhhhh.eeeee............hhhhhh......eeeehhhhhh....eeeeeehhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeee.........hhhhhhhhhhhhhhh.ee.eee...eeee......hhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ll3 A  25 NYYNLVIDHAHGATLVDVDGNKYIDLLASASAINVGHTHEKVVKAIADQAQKLIHYTPAYFHHVPGMELSEKLAKIAPGNSPKMVSFGNSGSDANDAIIKFARAYTGRQYIVSYMGSYHGSTYGSQTLSGSSLNMTRKIGPMLPSVVHVPYPDSYRTYPGETEHDVSLRYFNEFKKPFESFLPADETACVLIEPIQGDGGIIKAPEEYMQLVYKFCHEHGILFAIDEVNQGLGRTGKMWAIQQFKDIEPDLMSVGKSLASGMPLSAVIGKKEVMQSLDAPAHLFTTAGNPVCSAASLATLDVIEYEGLVEKSATDGAYAKQRFLEMQQRHPMIGDVRMWGLNGGIELVKDPKTKEPDSDAATKVIYYAFAHGVVIITLAGNILRFQPPLVIPREQLDQALQVLDDAFTAVENGEVTI 441
                                    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       314       324       334       344       354       364       374       384       394       404       414       424       434       


Chain B from PDB  Type:PROTEIN  Length:417
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhhhh........eehhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhh.hhhhh..........eeee............hhhhhhhhhhhhhhhhhh...hhh.eeeeee..ee.....ee.hhhhhhhhhhhhhhhh.eeeee............hhhhhh......eeeehhhhhh....eeeeeehhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeee.........hhhhhhhhhhhhhhh.ee.eee...eeee......hhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ll3 B  25 NYYNLVIDHAHGATLVDVDGNKYIDLLASASAINVGHTHEKVVKAIADQAQKLIHYTPAYFHHVPGMELSEKLAKIAPGNSPKMVSFGNSGSDANDAIIKFARAYTGRQYIVSYMGSYHGSTYGSQTLSGSSLNMTRKIGPMLPSVVHVPYPDSYRTYPGETEHDVSLRYFNEFKKPFESFLPADETACVLIEPIQGDGGIIKAPEEYMQLVYKFCHEHGILFAIDEVNQGLGRTGKMWAIQQFKDIEPDLMSVGKSLASGMPLSAVIGKKEVMQSLDAPAHLFTTAGNPVCSAASLATLDVIEYEGLVEKSATDGAYAKQRFLEMQQRHPMIGDVRMWGLNGGIELVKDPKTKEPDSDAATKVIYYAFAHGVVIITLAGNILRFQPPLVIPREQLDQALQVLDDAFTAVENGEVTI 441
                                    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       314       324       334       344       354       364       374       384       394       404       414       424       434       


Chain C from PDB  Type:PROTEIN  Length:417
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhhhh........eehhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhh..hhhhh.........eeee............hhhhhhhhhhhhhhhhhh...hhh.eeeeee..ee.....ee.hhhhhhhhhhhhhhhh.eeeee............hhhhhh......eeeehhhhhh....eeeeeehhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeee.........hhhhhhhhhhhhhhh.ee.eee...eeee......hhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ll3 C  25 NYYNLVIDHAHGATLVDVDGNKYIDLLASASAINVGHTHEKVVKAIADQAQKLIHYTPAYFHHVPGMELSEKLAKIAPGNSPKMVSFGNSGSDANDAIIKFARAYTGRQYIVSYMGSYHGSTYGSQTLSGSSLNMTRKIGPMLPSVVHVPYPDSYRTYPGETEHDVSLRYFNEFKKPFESFLPADETACVLIEPIQGDGGIIKAPEEYMQLVYKFCHEHGILFAIDEVNQGLGRTGKMWAIQQFKDIEPDLMSVGKSLASGMPLSAVIGKKEVMQSLDAPAHLFTTAGNPVCSAASLATLDVIEYEGLVEKSATDGAYAKQRFLEMQQRHPMIGDVRMWGLNGGIELVKDPKTKEPDSDAATKVIYYAFAHGVVIITLAGNILRFQPPLVIPREQLDQALQVLDDAFTAVENGEVTI 441
                                    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       314       324       334       344       354       364       374       384       394       404       414       424       434       


Chain D from PDB  Type:PROTEIN  Length:417
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhhhh........eehhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhh.hhhhh..........eeee............hhhhhhhhhhhhhhhhhh...hhh.eeeeee..ee.....ee.hhhhhhhhhhhhhhhh.eeeee............hhhhhh......eeeehhhhhh....eeeeeehhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeee.........hhhhhhhhhhhhhhh.ee.eee...eeee......hhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ll3 D  25 NYYNLVIDHAHGATLVDVDGNKYIDLLASASAINVGHTHEKVVKAIADQAQKLIHYTPAYFHHVPGMELSEKLAKIAPGNSPKMVSFGNSGSDANDAIIKFARAYTGRQYIVSYMGSYHGSTYGSQTLSGSSLNMTRKIGPMLPSVVHVPYPDSYRTYPGETEHDVSLRYFNEFKKPFESFLPADETACVLIEPIQGDGGIIKAPEEYMQLVYKFCHEHGILFAIDEVNQGLGRTGKMWAIQQFKDIEPDLMSVGKSLASGMPLSAVIGKKEVMQSLDAPAHLFTTAGNPVCSAASLATLDVIEYEGLVEKSATDGAYAKQRFLEMQQRHPMIGDVRMWGLNGGIELVKDPKTKEPDSDAATKVIYYAFAHGVVIITLAGNILRFQPPLVIPREQLDQALQVLDDAFTAVENGEVTI 441
                                    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       314       324       334       344       354       364       374       384       394       404       414       424       434
   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 5LL3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LL3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LL3)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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    Gly D:164 - Pro D:165   [ RasMol ]  
 

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UniProtKB/Swiss-Prot
        ILE2E_LACBU | M1GRN3: 4ysn 4ysv 5ll2 5wya 5wyf

(-) Related Entries Specified in the PDB File

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