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(-) Description

Title :  NATIVE STRUCTURE OF XOMETC AT PH 5.2
 
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 :  2.29
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Plp Dependent Enzyme, Lyase, Xometc, Cys-Met Metabolism Plp Dependent Enzyme, Cystathionine Gamma/Beta 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
    EC Number: 4.4.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: METB, XOO0778
    Organism Scientific: XANTHOMONAS ORYZAE PV. ORYZAE
    Organism Taxid: 291331
    Strain: KACC 10331/KXO85

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1CO31Ligand/IonCARBONATE ION
2GOL1Ligand/IonGLYCEROL
3LLP2Mod. Amino Acid(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC ACID
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1CO32Ligand/IonCARBONATE ION
2GOL2Ligand/IonGLYCEROL
3LLP4Mod. Amino Acid(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:267 , ASN A:271 , ILE A:379 , GLU A:380 , ASP A:381 , LEU A:382 , ARG B:266BINDING SITE FOR RESIDUE GOL A 401
2AC2SOFTWARETYR B:112 , ASN B:160 , LLP B:210 , GLU B:338 , SER B:339 , THR B:354 , ARG B:374BINDING SITE FOR RESIDUE CO3 B 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric 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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IXS)

(-) Sequences/Alignments

Asymmetric 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:361
                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4ixsa_ A: automated matches                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh...........................hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhhh.eeeee...hhhhhhh.....eeeeeee..........hhhhhhhhhhhh..eeeee.........hhhhhh..eeeee.............eeeee..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhh.....eeeeee.hhhhhhhhhhhhh...ee.........eee..............eeeee....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ixs A  14 ALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSRTHNPTRFAYERCVAALEGGTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSATkYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTEQLGISDALVRLSVGIEDLGDLRGDLERALV 394
                                    23        33        43   ||   64        74        84        94       104       114       124       134       144       154       164       174       184       194       204     | 214       224       234       244       254       264       274       284       294       304       314       324       334       344       354|      373       383       393 
                                                            47|                                                                                                                                                    210-LLP                                                                                                                                         354|                              
                                                             59                                                                                                                                                                                                                                                                                                     364                              


Chain B from PDB  Type:PROTEIN  Length:372
                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4ixsb_ 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...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
                 4ixs B  15 LSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPSRTHNPTRFAYERCVAALEGGTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSATkYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERALV 394
                                    24        34        44     || 62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392  
                                                              50|                                                                                                                                                    210-LLP                                                                                                                                                                                    
                                                               59
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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  4ixs
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  4.4.1.1
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 Related Entries

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

UniProtKB/TrEMBL
        Q5H4T8_XANOR | Q5H4T8: 3e6g 4ixz 4iy7 4iyo

(-) Related Entries Specified in the PDB File

3nnp SUPERCEDE THE OLD ENTRY 3NNP
4ixz
4iy7
4iyo