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(-) Description

Title :  CRYSTAL STRUCTURE OF CYSTATHIONINE GAMMA LYASE (XOMETC) FROM XANTHOMONAS ORYZAE PV. ORYZAE IN COMPLEX WITH E-SITE SERINE, A-SITE EXTERNAL ALDIMINE STRUCTURE WITH SERINE AND A-SITE EXTERNAL ALDIMINE STRUCTURE WITH AMINOACRYLATE INTERMEDIATES
 
Authors :  H. P. T. Ngo, J. K. Kim, L. W. Kang
Date :  28 Jan 13  (Deposition) - 29 Jan 14  (Release) - 26 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Xocgl, Serine External Schiff Base, Aminoacrylate External Schiff Base, Plp Dependent Enzyme, Lyase, Cys-Met Metabolism Plp Dependent Enzyme, Cystathionine Gamma Lyase, Plp Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. P. Ngo, N. M. Cerqueira, J. K. Kim, M. K. Hong, P. A. Fernandes, M. J. Ramos, L. W. Kang
Plp Undergoes Conformational Changes During The Course Of A Enzymatic Reaction.
Acta Crystallogr. , Sect. D V. 70 596 2014
PubMed-ID: 24531493  |  Reference-DOI: 10.1107/S1399004713031283

(-) Compounds

Molecule 1 - CYSTATHIONINE GAMMA-LYASE-LIKE PROTEIN
    Chains: A, B, C, D
    EC Number: 4.4.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: METB, XOCGL, XOO0778
    Organism Scientific: XANTHOMONAS ORYZAE PV. ORYZAE
    Organism Taxid: 291331
    Strain: KACC 10331/KXO85

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 13)

Asymmetric/Biological Unit (6, 13)
No.NameCountTypeFull Name
10JO1Ligand/Ion2-{[(E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE]AMINO}PROP-2-ENOICACID
2GOL2Ligand/IonGLYCEROL
3KOU3Ligand/Ion(E)-N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE)-L-SERINE
4PYR2Ligand/IonPYRUVIC ACID
5SER4Mod. Amino AcidSERINE
6SO41Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:112 , ARG A:117 , GLU A:338 , TYR B:58 , ARG B:60 , THR B:61 , ASN B:240 , HOH B:818BINDING SITE FOR RESIDUE SER A 401
02AC2SOFTWAREASP A:167 , ILE A:168 , ALA A:169 , ARG A:304 , GLN A:305 , ALA C:294 , SER C:295 , HOH C:699BINDING SITE FOR RESIDUE GOL A 402
03AC3SOFTWAREGLU A:280 , THR A:281 , HIS A:282 , ILE A:285 , ARG D:176 , LEU D:197 , SER D:198 , GLY D:200BINDING SITE FOR RESIDUE GOL A 403
04AC4SOFTWAREARG A:117 , ARG A:121 , HOH A:630 , HOH A:704 , HOH A:837 , PHE B:237 , VAL B:300BINDING SITE FOR RESIDUE SO4 A 404
05AC5SOFTWARESER A:87 , GLY A:88 , MET A:89 , TYR A:112 , ASN A:160 , ASP A:185 , SER A:207 , THR A:209 , LYS A:210 , SER A:339 , LEU A:340 , THR A:354 , ARG A:374 , TYR B:58 , ARG B:60BINDING SITE FOR RESIDUE 0JO A 405
06AC6SOFTWAREGLU A:57 , TYR A:58 , ARG A:60 , THR A:61 , ASN A:240 , TYR B:112 , ARG B:117 , GLU B:338 , KOU B:403 , HOH B:777BINDING SITE FOR RESIDUE SER B 401
07AC7SOFTWAREARG A:121 , ARG A:125 , GLN B:234 , PHE B:237 , LYS B:303 , HOH B:698 , HOH B:704BINDING SITE FOR RESIDUE PYR B 402
08AC8SOFTWARETYR A:58 , ARG A:60 , SER B:87 , GLY B:88 , MET B:89 , TYR B:112 , ASN B:160 , ASP B:185 , SER B:207 , THR B:209 , LYS B:210 , GLU B:338 , SER B:339 , LEU B:340 , THR B:354 , ARG B:374 , SER B:401BINDING SITE FOR RESIDUE KOU B 403
09AC9SOFTWARETYR C:112 , ARG C:117 , GLU C:338 , KOU C:402 , HOH C:681 , GLU D:57 , TYR D:58 , ARG D:60 , THR D:61 , ASN D:240BINDING SITE FOR RESIDUE SER C 401
10BC1SOFTWARESER C:87 , GLY C:88 , MET C:89 , TYR C:112 , ASN C:160 , ASP C:185 , SER C:207 , THR C:209 , LYS C:210 , GLU C:338 , SER C:339 , THR C:354 , ARG C:374 , SER C:401 , TYR D:58 , ARG D:60BINDING SITE FOR RESIDUE KOU C 402
11BC2SOFTWAREGLU C:57 , TYR C:58 , ARG C:60 , THR C:61 , ASN C:240 , TYR D:112 , ARG D:117 , GLU D:338 , KOU D:403BINDING SITE FOR RESIDUE SER D 401
12BC3SOFTWAREASN D:271 , ILE D:379 , GLU D:380 , ASP D:381 , LEU D:382 , HOH D:503 , HOH D:565 , HOH D:610 , HOH D:845BINDING SITE FOR RESIDUE PYR D 402
13BC4SOFTWARETYR C:58 , ARG C:60 , SER D:87 , GLY D:88 , MET D:89 , TYR D:112 , ASN D:160 , ASP D:185 , SER D:207 , THR D:209 , LYS D:210 , SER D:339 , THR D:354 , ARG D:374 , SER D:401BINDING SITE FOR RESIDUE KOU D 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IY7)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Thr A:157 -Pro A:158
2Asn A:160 -Pro A:161
3Thr B:157 -Pro B:158
4Asn B:160 -Pro B:161
5Thr C:157 -Pro C:158
6Asn C:160 -Pro C:161
7Thr D:157 -Pro D:158
8Asn D:160 -Pro D:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IY7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IY7)

(-) Exons   (0, 0)

(no "Exon" information available for 4IY7)

(-) 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:382
                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4iy7a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh......................................hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhh...eeeeeee..........hhhhhhhhhhhh..eeeee.........hhhhhh..eeeee.............eeeee..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhh.....eeeeee.hhhhhhhhhhhhh...ee.........eee..........hhhhhhhhh....eeeee....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iy7 A  14 ALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSRTHNPTRFAYERCVAALEGGTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERALVS 401
                                    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||
                                                                                                                                                                                                                                                                                                                                                                                                                      394|
                                                                                                                                                                                                                                                                                                                                                                                                                       401


Chain B from PDB  Type:PROTEIN  Length:382
                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4iy7b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh......................................hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhh...eeeeeee..........hhhhhhhhhhhh..eeeee.........hhhhhh..eeeee.............eeeee..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhh.....eeeeee.hhhhhhhhhhhhh...ee.........eee..........hhhhhhhhh....eeeee....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iy7 B  14 ALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSRTHNPTRFAYERCVAALEGGTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERALVS 401
                                    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||
                                                                                                                                                                                                                                                                                                                                                                                                                      394|
                                                                                                                                                                                                                                                                                                                                                                                                                       401


Chain C from PDB  Type:PROTEIN  Length:382
                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4iy7c_ C: automated matches                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh......................................hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhh...eeeeeee..........hhhhhhhhhhhh..eeeee.........hhhhhh..eeeee.............eeeee..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhh.....eeeeee.hhhhhhhhhhhhh...ee.........eee..........hhhhhhhhh....eeeee....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iy7 C  14 ALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSRTHNPTRFAYERCVAALEGGTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERALVS 401
                                    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||
                                                                                                                                                                                                                                                                                                                                                                                                                      394|
                                                                                                                                                                                                                                                                                                                                                                                                                       401


Chain D from PDB  Type:PROTEIN  Length:384
                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4iy7d_ D: automated matches                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhh......................................hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhh...eeeeeee..........hhhhhhhhhhhh..eeeee.........hhhhhh..eeeee.............eeeee..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhh.....eeeeee.hhhhhhhhhhhhh...ee.........eee..........hhhhhhhhh....eeeee....hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4iy7 D  14 ALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSRTHNPTRFAYERCVAALEGGTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERALVNQS 401
                                    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  ||
                                                                                                                                                                                                                                                                                                                                                                                                                        396|
                                                                                                                                                                                                                                                                                                                                                                                                                         401
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4IY7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4IY7)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        Q5H4T8_XANOR | Q5H4T8: 3e6g 4ixs 4ixz 4iyo

(-) Related Entries Specified in the PDB File

4ixs SUBSTRATES COMPLEXED STRUCTURE
4ixz SUBSTRATES COMPLEXED STRUCTURE
4iyo