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(-) Description

Title :  NATIVE STRUCTURE OF CYSTATHIONINE GAMMA LYASE (XOMETC) FROM XANTHOMONAS ORYZAE PV. ORYZAE AT PH 9.0
 
Authors :  H. P. T. Ngo, J. K. Kim, L. W. Kang
Date :  28 Jan 13  (Deposition) - 29 Jan 14  (Release) - 03 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Plp Dependent Enzyme, Lyase, Xocgl, Native, 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  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1BCT1Ligand/IonBICARBONATE ION
2BME3Ligand/IonBETA-MERCAPTOETHANOL
3GOL1Ligand/IonGLYCEROL
4LLP4Mod. Amino Acid(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:112 , ASN A:160 , LLP A:210 , SER A:339 , LEU A:340 , THR A:354 , ARG A:374 , HOH A:680BINDING SITE FOR RESIDUE BCT A 401
2AC2SOFTWARELEU A:193 , ARG A:266 , CYS A:269 , GLY A:308 , HOH A:553BINDING SITE FOR RESIDUE BME A 402
3AC3SOFTWARELEU B:193 , MET B:265 , ARG B:266 , CYS B:269 , GLY B:308 , PHE B:309 , HOH B:596BINDING SITE FOR RESIDUE BME B 401
4AC4SOFTWARELEU C:193 , ARG C:266 , CYS C:269 , GLY C:308 , HOH C:678BINDING SITE FOR RESIDUE BME C 401
5AC5SOFTWAREASP A:167 , ILE A:168 , ALA A:169 , ARG A:304 , GLN A:305 , ALA D:294 , SER D:295 , HIS D:296 , PRO D:297BINDING SITE FOR RESIDUE GOL D 401

(-) SS Bonds  (0, 0)

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

(-) 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 4IXZ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IXZ)

(-) 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:381
                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4ixza_ 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...hhhhhhhhhhhh..eeeee.............eeeee..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee........hhhhhhhhh.....eeeeee.hhhhhhhhhhhhh...ee.........eee..........hhhhhhhhh....eeeee....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ixz A  14 ALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSRTHNPTRFAYERCVAALEGGTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSATkYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERALV 394
                                    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                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:381
                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4ixzb_ 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
                 4ixz B  14 ALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSRTHNPTRFAYERCVAALEGGTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSATkYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERALV 394
                                    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                                                                                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:378
                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4ixzc_ C: automated matches                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhh......................................hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhh.eeeee...hhhhhhh.....eeeeeee..........hhhhhhhhhhhh..eeeee.........hhhhhh..eeeee.............eeeee..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee........hhhhhhhhh.....eeeeee.hhhhhhhhhhhhh...ee.........eee........hhhhhhhh....eeeee....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ixz C  14 ALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSRTHNPTRFAYERCVAALEGGTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSATkYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHPVARREQLGISDALVRLSVGIEDLGDLRGDLERALV 394
                                    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 ||    366       376       386        
                                                                                                                                                                                                                              210-LLP                                                                                                                                          355|                                   
                                                                                                                                                                                                                                                                                                                                                                                359                                   


Chain D from PDB  Type:PROTEIN  Length:378
                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4ixzd_ 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..........hhhhhhh....eeeee....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ixz D  14 ALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSRTHNPTRFAYERCVAALEGGTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSATkYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHAPVARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393
                                    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  ||   365       375       385        
                                                                                                                                                                                                                              210-LLP                                                                                                                                           356|                                  
                                                                                                                                                                                                                                                                                                                                                                                 359
   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 4IXZ)

(-) Pfam Domains  (0, 0)

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

(-) 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 4iy7 4iyo

(-) Related Entries Specified in the PDB File

4ixs NATIVE STRUCTURE AT DIFFERENT PH
4iy7
4iyo