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(-) Description

Title :  CRYSTAL STRUCTURE OF CYSTATHIONINE GAMMA LYASE FROM XANTHOMONAS ORYZAE PV. ORYZAE (XOMETC) IN COMPLEX WITH E-SITE SERINE, A-SITE SERINE, A-SITE EXTERNAL ALDIMINE STRUCTURE WITH AMINOACRYLATE AND A-SITE IMINOPROPIONATE INTERMEDIATES
 
Authors :  H. P. T. Ngo, J. K. Kim, L. W. Kang
Date :  29 Jan 13  (Deposition) - 29 Jan 14  (Release) - 03 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Plp Dependent Enzyme, Lyase, Xocgl, Iminopropionate, Serine, 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
    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
 
Molecule 2 - CYSTATHIONINE GAMMA-LYASE-LIKE PROTEIN, LYS201A MODIFIED
    Chains: 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  (7, 16)

Asymmetric/Biological Unit (7, 16)
No.NameCountTypeFull Name
10JO1Ligand/Ion2-{[(E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE]AMINO}PROP-2-ENOICACID
2GOL3Ligand/IonGLYCEROL
3LLP3Mod. Amino Acid(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC ACID
4NAK2Ligand/IonAMINO-ACRYLATE
5PYR1Ligand/IonPYRUVIC ACID
6SER5Mod. Amino AcidSERINE
7SO41Ligand/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:240BINDING 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:675BINDING SITE FOR RESIDUE GOL A 402
03AC3SOFTWAREARG A:117 , HOH A:640 , HOH A:694 , PHE B:237 , VAL B:300 , ARG B:304BINDING SITE FOR RESIDUE SO4 A 403
04AC4SOFTWARESER A:87 , GLY A:88 , MET A:89 , TYR A:112 , ASN A:160 , ASP A:185 , PHE A:188 , 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 404
05AC5SOFTWAREGLU A:57 , TYR A:58 , ARG A:60 , THR A:61 , ASN A:240 , TYR B:112 , ARG B:117 , GLU B:338 , NAK B:402BINDING SITE FOR RESIDUE SER B 401
06AC6SOFTWARETYR A:58 , TYR B:112 , ASN B:160 , LLP B:210 , SER B:339 , LEU B:340 , THR B:354 , ARG B:374 , SER B:401BINDING SITE FOR RESIDUE NAK B 402
07AC7SOFTWAREGLN B:234 , PHE B:237 , LYS B:303 , ARG B:304 , HOH B:673 , HOH B:710BINDING SITE FOR RESIDUE PYR B 403
08AC8SOFTWARETYR C:112 , ARG C:117 , GLU C:338 , TYR D:58 , ARG D:60 , THR D:61 , ASN D:240BINDING SITE FOR RESIDUE SER C 401
09AC9SOFTWARETYR C:112 , ASN C:160 , LLP C:210 , SER C:339 , THR C:354 , ARG C:374 , TYR D:58BINDING SITE FOR RESIDUE NAK C 402
10BC1SOFTWAREALA A:18 , HOH A:813 , ALA C:267 , ASN C:271 , ILE C:379 , GLU C:380 , HOH C:568 , HOH C:580 , HOH C:597 , HOH C:603 , HOH C:726BINDING SITE FOR RESIDUE GOL C 403
11BC2SOFTWARETYR C:58 , ARG C:60 , THR C:61 , ASN C:240 , HOH C:745 , TYR D:112 , ARG D:117 , GLU D:338 , SER D:402 , HOH D:835BINDING SITE FOR RESIDUE SER D 401
12BC3SOFTWARETYR D:112 , ASN D:160 , LLP D:210 , SER D:339 , THR D:354 , ARG D:374 , SER D:401BINDING SITE FOR RESIDUE SER D 402
13BC4SOFTWAREPHE D:67 , GLU D:70 , ARG D:71 , HOH D:522 , HOH D:542 , HOH D:643 , HOH D:749 , HOH D:766BINDING SITE FOR RESIDUE GOL D 403

(-) SS Bonds  (0, 0)

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

(-) 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 4IYO)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IYO)

(-) 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 d4iyoa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh......................................hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhh..eeeee...hhhhhhhhh...eeeeeee..........hhhhhhhhhhhh..eeeee.........hhhhhh..eeeee.............eeeee..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhh.....eeeeee.hhhhhhhhhhhhh...ee.........eee..........hhhhhhhhh....eeeee....hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iyo 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 d4iyob_ 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
                 4iyo 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||
                                                                                                                                                                                                                              210-LLP                                                                                                                                                                                 394|
                                                                                                                                                                                                                                                                                                                                                                                                                       401


Chain C from PDB  Type:PROTEIN  Length:382
                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4iyoc_ C: automated matches                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh......................................hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhh..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
                 4iyo 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||
                                                                                                                                                                                                                              210-LLP                                                                                                                                                                                 394|
                                                                                                                                                                                                                                                                                                                                                                                                                       401


Chain D from PDB  Type:PROTEIN  Length:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4iyod_ 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
                 4iyo D  14 ALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSRTHNPTRFAYERCVAALEGGTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSATkYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERALVNQNSS 402
                                    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   || 
                                                                                                                                                                                                                              210-LLP                                                                                                                                                                                    397| 
                                                                                                                                                                                                                                                                                                                                                                                                                          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 4IYO)

(-) Pfam Domains  (0, 0)

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

(-) 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 4iy7

(-) Related Entries Specified in the PDB File

4ixs SUBSTRATE COMPLEXED STRUCTURE
4ixz SUBSTRATE COMPLEXED STRUCTURE
4iy7 DIFFERENT SUBSTRATE COMPLEXED STRUCTURE