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(-) Description

Title :  THE CRYSTAL STRUCTURE OF Y333Q MUTANT PYRIDOXAL-DEPENDENT DECARBOXYLASE FROM SPHAEROBACTER THERMOPHILUS DSM 20745
 
Authors :  R. Wu, S. Clancy, A. Joachimiak, Midwest Center For Structural Gen (Mcsg)
Date :  07 Oct 14  (Deposition) - 12 Nov 14  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Lyase, Structural Genomics, Psi-Biology, Midwest Center For Structural Genomics, Mcsg, A/B/A Fold, Cytosolic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Wu, S. Clancy, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
The Crystal Structure Of Y333Q Mutant Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PYRIDOXAL-DEPENDENT DECARBOXYLASE
    Chains: A, B, C, D
    EC Number: 4.1.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: STHE_2364
    Mutation: YES
    Organism Scientific: SPHAEROBACTER THERMOPHILUS DSM 20745
    Organism Taxid: 479434
    Strain: DSM 20745 / S 6022

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2LLP4Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3NA3Ligand/IonSODIUM ION
4PMP3Ligand/Ion4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3NA-1Ligand/IonSODIUM ION
4PMP1Ligand/Ion4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3NA-1Ligand/IonSODIUM ION
4PMP2Ligand/Ion4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:150 , GLY A:151 , SER A:152 , HIS A:190 , GLY A:245 , THR A:247 , ASP A:272 , ALA A:274 , ASN A:301 , GLN A:303 , LLP A:304 , HOH A:620 , HOH A:741 , HOH A:841 , THR B:351BINDING SITE FOR RESIDUE PMP A 501
2AC2SOFTWAREHIS A:353 , HOH A:685 , HOH A:686 , HIS B:353 , HOH B:629BINDING SITE FOR RESIDUE NA A 502
3AC3SOFTWARELEU B:136 , PHE B:137 , ARG B:286 , GLU B:293BINDING SITE FOR RESIDUE GOL B 501
4AC4SOFTWARELEU B:374 , ASP B:377 , GLY B:378 , LEU B:381 , LEU B:454 , LEU B:455 , ASN B:456 , PRO B:457 , HOH B:648BINDING SITE FOR RESIDUE GOL B 503
5AC5SOFTWAREGLU A:171 , PRO A:172 , ARG B:180 , LEU B:202 , GLY B:203 , ALA B:205 , ALA B:206BINDING SITE FOR RESIDUE NA B 504
6AC6SOFTWAREGLY C:150 , GLY C:151 , SER C:152 , HIS C:190 , THR C:247 , ASP C:272 , ALA C:274 , ASN C:301 , GLN C:303 , LLP C:304 , HOH C:2217 , HOH C:2261 , THR D:351BINDING SITE FOR RESIDUE PMP C 2001
7AC7SOFTWARETHR C:351 , HOH C:2127 , GLY D:150 , GLY D:151 , SER D:152 , HIS D:190 , GLY D:245 , THR D:247 , ASP D:272 , ALA D:274 , ASN D:301 , GLN D:303 , LLP D:304 , HOH D:694BINDING SITE FOR RESIDUE PMP D 501
8AC8SOFTWARELEU D:136 , ARG D:286 , ALA D:290 , GLU D:293BINDING SITE FOR RESIDUE GOL D 502
9AC9SOFTWAREGLU C:171 , PRO C:172 , ARG D:180 , LEU D:202 , GLY D:203 , ALA D:205 , ALA D:206BINDING SITE FOR RESIDUE NA D 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Lys A:310 -Thr A:311
2Gly B:54 -Pro B:55
3Lys B:310 -Thr B:311
4Lys C:310 -Thr C:311
5Lys D:310 -Thr D:311

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RIZ)

(-) 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:470
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhhhhh............eeeeee....hhhhhhhhhh..hhh.eeee........hhhhhhhhhhhhhhh..eeeeeeee..........hhhhhhhhhhhh..eeeee..hhhhhhhh..hhhhhhhhhhh.eeeehhhhhh......eeeee...hhhhhh...............hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.......eeeeee.....hhhhhhhhhhhhhhhhhhhhh......ee..ee.eeee......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4riz A   3 SRFLPATAFIDPEGRNRNEVERLVQQVVDLILAKLTGAAERPPMPETPITIPEAAATEATLLQAIRDMVDGSMNPANPGYIGHMDPMPATMAILGDLVAAAVNNNMLSLEMSPSFSRLETLLLRAIAGLFGLGEQAGGVLTSGGSLANLQALAVARNVAFDSVEPGITGLAQRPVIFASEAAHTSLQKAAMLLGLGTAAVIPVRATADSRMDPEDLRARIDQARGAGQHPFCVVATAGTTTTGNIDPLAEIGAIAREHGLWFHVDAAYGGALVFSERHRWRLAGIEQADSITFNPQkWLYVAKTCAMVLFRDAGVLERAFRIPAPQMRATDGFINLGEIGVQGTRHADVVKLWLTLQHIGQQGYARLIDDGYRLAERVVEGVRQRPFLRLAGEIDTNIVCFRGEPDWLPAERWDDWNAALQALLLREGKIFLSLPVYRGGRWLRAVLLNPYTTDAVIDAMFKQIDRFAGR 477
                                    12        22        32        42      ||57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297      |307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477
                                                                         49|                                                                                                                                                                                                                                                      304-LLP                                                                                                                                                                         
                                                                          55                                                                                                                                                                                                                                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:475
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhhhhh............eeeeee....hhhhhhhhhh..hhh.eeee........hhhhhhhhhhhhhhh..eeeeeeee..........hhhhhhhhhhhh..eeeee..hhhhhhhh..hhhhhhhhhhh.eeeehhhhhh......eeeee...hhhhhh...............hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.......eeeeee.....hhhhhhhhhhhhhhhhhhhhh......ee..ee.eeee......hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4riz B  -1 NAMDSRFLPATAFIDPEGRNRNEVERLVQQVVDLILAKLTGAAERPPMPETGPITIPEAAATEATLLQAIRDMVDGSMNPANPGYIGHMDPMPATMAILGDLVAAAVNNNMLSLEMSPSFSRLETLLLRAIAGLFGLGEQAGGVLTSGGSLANLQALAVARNVAFDSVEPGITGLAQRPVIFASEAAHTSLQKAAMLLGLGTAAVIPVRATADSRMDPEDLRARIDQARGAGQHPFCVVATAGTTTTGNIDPLAEIGAIAREHGLWFHVDAAYGGALVFSERHRWRLAGIEQADSITFNPQkWLYVAKTCAMVLFRDAGVLERAFRIPAPQMRATDGFINLGEIGVQGTRHADVVKLWLTLQHIGQQGYARLIDDGYRLAERVVEGVRQRPFLRLAGEIDTNIVCFRGEPDWLPAERWDDWNAALQALLLREGKIFLSLPVYRGGRWLRAVLLNPYTTDAVIDAMFKQIDRFAGR 477
                                     8        18        28        38        48||      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       402       412       422       432       442       452       462       472     
                                                                             49|                                                                                                                                                                                                                                                       304-LLP                                                                                                                                                                         
                                                                              54                                                                                                                                                                                                                                                                                                                                                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:476
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhhhhh............eeeeee....hhhhhhhhhh..hhh.eeee........hhhhhhhhhhhhhhh..eeeeeeee..........hhhhhhhhhhhh..eeeee..hhhhhhhh..hhhhhhhhhhh.eeeehhhhhh......eeeee...hhhhhh...............hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.......eeeeee.....hhhhhhhhhhhhhhhhhhh........ee..ee.eeee......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4riz C   0 AMDSRFLPATAFIDPEGRNRNEVERLVQQVVDLILAKLTGAAERPPMPETLPGPITIPEAAATEATLLQAIRDMVDGSMNPANPGYIGHMDPMPATMAILGDLVAAAVNNNMLSLEMSPSFSRLETLLLRAIAGLFGLGEQAGGVLTSGGSLANLQALAVARNVAFDSVEPGITGLAQRPVIFASEAAHTSLQKAAMLLGLGTAAVIPVRATADSRMDPEDLRARIDQARGAGQHPFCVVATAGTTTTGNIDPLAEIGAIAREHGLWFHVDAAYGGALVFSERHRWRLAGIEQADSITFNPQkWLYVAKTCAMVLFRDAGVLERAFRIPAPQMRATDGFINLGEIGVQGTRHADVVKLWLTLQHIGQQGYARLIDDGYRLAERVVEGVRQRPFLRLAGEIDTNIVCFRGEPDWLPAERWDDWNAALQALLLREGKIFLSLPVYRGGRWLRAVLLNPYTTDAVIDAMFKQIDRFAGR 477
                                     9        19        29        39        49|       61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301  |    311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471      
                                                                            49|                                                                                                                                                                                                                                                         304-LLP                                                                                                                                                                         
                                                                             52                                                                                                                                                                                                                                                                                                                                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:472
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhhhhh............eeeeee....hhhhhhhhhh..hhh.eeee........hhhhhhhhhhhhhhh..eeeeeeee..........hhhhhhhhhhhh..eeeee..hhhhhhhh..hhhhhhhhhhh.eeeehhhhhh......eeeee...hhhhhh...............hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.......eeeeee.....hhhhhhhhhhhhhhhhhhhhh......ee..ee.eeee......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4riz D   5 FLPATAFIDPEGRNRNEVERLVQQVVDLILAKLTGAAERPPMPETVDLPGPITIPEAAATEATLLQAIRDMVDGSMNPANPGYIGHMDPMPATMAILGDLVAAAVNNNMLSLEMSPSFSRLETLLLRAIAGLFGLGEQAGGVLTSGGSLANLQALAVARNVAFDSVEPGITGLAQRPVIFASEAAHTSLQKAAMLLGLGTAAVIPVRATADSRMDPEDLRARIDQARGAGQHPFCVVATAGTTTTGNIDPLAEIGAIAREHGLWFHVDAAYGGALVFSERHRWRLAGIEQADSITFNPQkWLYVAKTCAMVLFRDAGVLERAFRIPAPQMRATDGFINLGEIGVQGTRHADVVKLWLTLQHIGQQGYARLIDDGYRLAERVVEGVRQRPFLRLAGEIDTNIVCFRGEPDWLPAERWDDWNAALQALLLREGKIFLSLPVYRGGRWLRAVLLNPYTTDAVIDAMFKQIDRFAG 476
                                    14        24        34        44        54        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       364       374       384       394       404       414       424       434       444       454       464       474  
                                                                                                                                                                                                                                                                                                                                     304-LLP
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 4RIZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

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        D1C7D8_SPHTD | D1C7D8: 4rit 4rj0 4rlg 4rm1

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