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(-) Description

Title :  STRUCTURE OF AMINOACID RACEMASE IN COMPLEX WITH PLP
 
Authors :  H. Sakuraba, Y. Mutaguchi, J. Hayashi, T. Ohshima
Date :  17 Mar 15  (Deposition) - 20 Apr 16  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Fold Type I Of Plp-Dependent Enzyme, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Hayashi, Y. Mutaguchi, Y. Minemura, N. Nakagawa, K. Yoneda, T. Ohmori, T. Ohshima, H. Sakuraba
Crystal Structure Of The Novel Amino-Acid Racemase Isoleucine 2-Epimerase From Lactobacillus Buchneri.
Acta Crystallogr D Struct V. 73 428 2017 Biol
PubMed-ID: 28471367  |  Reference-DOI: 10.1107/S2059798317005332

(-) Compounds

Molecule 1 - PUTATIVE 4-AMINOBUTYRATE AMINOTRANSFERASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCOLD PROS2
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: LACTOBACILLUS BUCHNERI
    Organism Taxid: 1581

 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 , TYR A:142 , HIS A:143 , GLU A:217 , ASP A:222 , ASP A:250 , VAL A:252 , ASN A:253 , LYS A:280 , HOH A:1121 , HOH A:1144 , HOH A:1158 , PHE B:308 , THR B:309binding site for Di-peptide PLP A 1001 and LYS A 280
2AC2SOFTWAREPHE A:308 , THR A:309 , ALA B:54 , ALA B:56 , SER B:114 , GLY B:115 , SER B:116 , 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:1122 , HOH B:1150 , HOH B:1158 , HOH B:1179 , HOH B:1281binding site for Di-peptide PLP B 1001 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:222 , ASP C:250 , VAL C:252 , ASN C:253 , GLY C:279 , SER C:281 , LEU C:282 , GLY C:285 , HOH C:1135 , HOH C:1145 , HOH C:1163 , HOH C:1168 , PHE D:308 , THR D:309binding site for Di-peptide PLP C 1001 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 , TYR D:142 , HIS D:143 , GLU D:217 , ASP D:222 , ASP D:250 , VAL D:252 , ASN D:253 , GLY D:279 , SER D:281 , LEU D:282 , GLY D:285 , HOH D:1108 , HOH D:1141 , HOH D:1143 , HOH D:1152 , HOH D:1186binding site for Di-peptide PLP D 1001 and LYS D 280

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

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
8Ala D:303 -Pro D:304

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YSN)

(-) 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:446
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh...hhhhh.......eeeee..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
                 4ysn A  -3 HMELMGKLDKASKLIDEENKYYARSARINYYNLVIDHAHGATLVDVDGNKYIDLLASASAINVGHTHEKVVKAIADQAQKLIHYTPAYFHHVPGMELSEKLAKIAPGNSPKMVSFGNSGSDANDAIIKFARAYTGRQYIVSYMGSYHGSTYGSQTLSGSSLNMTRKIGPMLPSVVHVPYPDSYRTYPGETEHDVSLRYFNEFKKPFESFLPADETACVLIEPIQGDGGIIKAPEEYMQLVYKFCHEHGILFAIDEVNQGLGRTGKMWAIQQFKDIEPDLMSVGKSLASGMPLSAVIGKKEVMQSLDAPAHLFTTAGNPVCSAASLATLDVIEYEGLVEKSATDGAYAKQRFLEMQQRHPMIGDVRMWGLNGGIELVKDPKTKEPDSDAATKVIYYAFAHGVVIITLAGNILRFQPPLVIPREQLDQALQVLDDAFTAVENGEVTIP 442
                                     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       316       326       336       346       356       366       376       386       396       406       416       426       436      


Chain B from PDB  Type:PROTEIN  Length:443
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh......eeeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh.....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
                 4ysn B  -1 ELMGKLDKASKLIDEENKYYARSARINYYNLVIDHAHGATLVDVDGNKYIDLLASASAINVGHTHEKVVKAIADQAQKLIHYTPAYFHHVPGMELSEKLAKIAPGNSPKMVSFGNSGSDANDAIIKFARAYTGRQYIVSYMGSYHGSTYGSQTLSGSSLNMTRKIGPMLPSVVHVPYPDSYRTYPGETEHDVSLRYFNEFKKPFESFLPADETACVLIEPIQGDGGIIKAPEEYMQLVYKFCHEHGILFAIDEVNQGLGRTGKMWAIQQFKDIEPDLMSVGKSLASGMPLSAVIGKKEVMQSLDAPAHLFTTAGNPVCSAASLATLDVIEYEGLVEKSATDGAYAKQRFLEMQQRHPMIGDVRMWGLNGGIELVKDPKTKEPDSDAATKVIYYAFAHGVVIITLAGNILRFQPPLVIPREQLDQALQVLDDAFTAVENGEVTI 441
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438   


Chain C from PDB  Type:PROTEIN  Length:448
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh...hhhhh......eeeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhhhh........eehhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhh..hhhhh.........eeee............hhhhhhhhhhhhhhhhhh...hhh.eeeeee..ee.....ee.hhhhhhhhhhhhhhh..eeeee............hhhhhh......eeeehhhhhh....eeeeeehhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeee.........hhhhhhhhhhhhhhh.ee.eee...eeee......hhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ysn C  -6 EGRHMELMGKLDKASKLIDEENKYYARSARINYYNLVIDHAHGATLVDVDGNKYIDLLASASAINVGHTHEKVVKAIADQAQKLIHYTPAYFHHVPGMELSEKLAKIAPGNSPKMVSFGNSGSDANDAIIKFARAYTGRQYIVSYMGSYHGSTYGSQTLSGSSLNMTRKIGPMLPSVVHVPYPDSYRTYPGETEHDVSLRYFNEFKKPFESFLPADETACVLIEPIQGDGGIIKAPEEYMQLVYKFCHEHGILFAIDEVNQGLGRTGKMWAIQQFKDIEPDLMSVGKSLASGMPLSAVIGKKEVMQSLDAPAHLFTTAGNPVCSAASLATLDVIEYEGLVEKSATDGAYAKQRFLEMQQRHPMIGDVRMWGLNGGIELVKDPKTKEPDSDAATKVIYYAFAHGVVIITLAGNILRFQPPLVIPREQLDQALQVLDDAFTAVENGEVTI 441
                                     3        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       353       363       373       383       393       403       413       423       433        


Chain D from PDB  Type:PROTEIN  Length:442
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh...hhhhh......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
                 4ysn D  -1 ELMGKLDKASKLIDEENKYYARSARINYYNLVIDHAHGATLVDVDGNKYIDLLASASAINVGHTHEKVVKAIADQAQKLIHYTPAYFHHVPGMELSEKLAKIAPGNSPKMVSFGNSGSDANDAIIKFARAYTGRQYIVSYMGSYHGSTYGSQTLSGSSLNMTRKIGPMLPSVVHVPYPDSYRTYPGETEHDVSLRYFNEFKKPFESFLPADETACVLIEPIQGDGGIIKAPEEYMQLVYKFCHEHGILFAIDEVNQGLGRTGKMWAIQQFKDIEPDLMSVGKSLASGMPLSAVIGKKEVMQSLDAPAHLFTTAGNPVCSAASLATLDVIEYEGLVEKSATDGAYAKQRFLEMQQRHPMIGDVRMWGLNGGIELVKDPKTKEPDSDAATKVIYYAFAHGVVIITLAGNILRFQPPLVIPREQLDQALQVLDDAFTAVENGEVT 440
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438
   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 4YSN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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        ILE2E_LACBU | M1GRN3: 4ysv 5ll2 5ll3 5wya 5wyf

(-) Related Entries Specified in the PDB File

4ysv