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(-) Description

Title :  THE CRYSTAL STRUCTURE OF Y333N 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 :  1.95
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Structural Genomics, Psi-Biology, Midwest Center For Structural Genomics, Mcsg, A/B/A Fold, Lyase, 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 Y333N Mutant Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PYRIDOXAL-DEPENDENT DECARBOXYLASE
    Chains: B, A, 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

 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, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2LLP4Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3PMP1Ligand/Ion4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
4PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3PMP-1Ligand/Ion4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
4PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 2 (4, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3PMP1Ligand/Ion4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
4PO41Ligand/IonPHOSPHATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:6 , PRO A:7 , ALA A:8 , ALA A:10 , PHE A:11 , TYR B:458BINDING SITE FOR RESIDUE GOL A 501
2AC2SOFTWARELEU A:136 , PHE A:137 , ARG A:286 , GLU A:293BINDING SITE FOR RESIDUE GOL A 502
3AC3SOFTWARELEU C:136 , PHE C:137 , ARG C:286 , GLU C:293BINDING SITE FOR RESIDUE PO4 C 501
4AC4SOFTWARETHR C:351 , MET D:91 , 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 , HOH D:2153 , HOH D:2169 , HOH D:2183BINDING SITE FOR RESIDUE PMP D 2001
5AC5SOFTWAREPHE D:137 , ARG D:286 , ALA D:290BINDING SITE FOR RESIDUE GOL D 2002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RJ0)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys B:310 -Thr B:311
2Lys A:310 -Thr A:311
3Lys C:310 -Thr C:311
4Lys D:310 -Thr D:311

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RJ0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RJ0)

(-) Exons   (0, 0)

(no "Exon" information available for 4RJ0)

(-) 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:467
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhhhhh............eeeeee....hhhhhhhhhh..hhh.eeee........hhhhhhhhhhhhhhh..eeeeeeee..........hhhhhhhhhhhh..eeeee..hhhhhhhh..hhhhhhhhhhh.eeee............eeeee...hhhhhh...............hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.......eeeeee.....hhhhhhhhhhhhhhhhhhhhh......ee..ee.eeee......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rj0 A   4 RFLPATAFIDPEGRNRNEVERLVQQVVDLILAKLTGAAERPPMPEPITIPEAAATEATLLQAIRDMVDGSMNPANPGYIGHMDPMPATMAILGDLVAAAVNNNMLSLEMSPSFSRLETLLLRAIAGLFGLGEQAGGVLTSGGSLANLQALAVARNVAFDSVEPGITGLAQRPVIFASEAAHTSLQKAAMLLGLGTAAVIPVRATADSRMDPEDLRARIDQARGAGQHPFCVVATAGTTTTGNIDPLAEIGAIAREHGLWFHVDAAYGGALVFSERHRWRLAGIEQADSITFNPQkWLYVAKTCAMVLFRDAGVLERAFRIPAPNMRATDGFINLGEIGVQGTRHADVVKLWLTLQHIGQQGYARLIDDGYRLAERVVEGVRQRPFLRLAGEIDTNIVCFRGEPDWLPAERWDDWNAALQALLLREGKIFLSLPVYRGGRWLRAVLLNPYTTDAVIDAMFKQIDRFAG 476
                                    13        23        33        43    ||  59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299    |  309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       
                                                                       48|                                                                                                                                                                                                                                                      304-LLP                                                                                                                                                                        
                                                                        55                                                                                                                                                                                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:471
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               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..eeeeee.hhhhhhhh..hhhhhhhhhhh.eeee............eeeee...hhhhhh...............hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.......eeeeee.....hhhhhhhhhhhhhhhhhhh........ee..ee.eeee......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rj0 B  -1 NAMDSRFLPATAFIDPEGRNRNEVERLVQQVVDLILAKLTGAAERPPMPEITIPEAAATEATLLQAIRDMVDGSMNPANPGYIGHMDPMPATMAILGDLVAAAVNNNMLSLEMSPSFSRLETLLLRAIAGLFGLGEQAGGVLTSGGSLANLQALAVARNVAFDSVEPGITGLAQRPVIFASEAAHTSLQKAAMLLGLGTAAVIPVRATADSRMDPEDLRARIDQARGAGQHPFCVVATAGTTTTGNIDPLAEIGAIAREHGLWFHVDAAYGGALVFSERHRWRLAGIEQADSITFNPQkWLYVAKTCAMVLFRDAGVLERAFRIPAPNMRATDGFINLGEIGVQGTRHADVVKLWLTLQHIGQQGYARLIDDGYRLAERVVEGVRQRPFLRLAGEIDTNIVCFRGEPDWLPAERWDDWNAALQALLLREGKIFLSLPVYRGGRWLRAVLLNPYTTDAVIDAMFKQIDRFAG 476
                                     8        18        28        38        48|       65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475 
                                                                            48|                                                                                                                                                                                                                                                     304-LLP                                                                                                                                                                        
                                                                             56                                                                                                                                                                                                                                                                                                                                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:463
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhh............eeeeee....hhhhhhhhhh..hhh.eeee........hhhhhhhhhhhhhhh..eeeeeeee..........hhhhhhhhhhhh..eeeeee.hhhhhhhh..hhhhhhhhhhh.eeeehhhhhh......eeeee...hhhhhhh........hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.......eeeeee.....hhhhhhhhhhhhhhhhhhh........ee..ee.eeee......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rj0 C   5 FLPATAFIDPEGRNRNEVERLVQQVVDLILAKLTGAAERPPMPETPGPITIPEAAATEATLLQAIRDMVDGSMNPANPGYIGHMDPMPATMAILGDLVAAAVNNNMLSLEMSPSFSRLETLLLRAIAGLFGLGEQAGGVLTSGGSLANLQALAVARNVAFDSVEPGITGLAQRPVIFASEAAHTSLQKAAMLLGLGTAAVIPVRATADSRMDPEDLRARIDQARGAGQHPFCVVATAGTTTTGNIDPLAEIGAIAREHGLWFHVDAAYGGALVFSERHRWRLAGIEQADSITFNPQkWLYVAKTCAMVLFRDAGVLERAFRIPAPGFINLGEIGVQGTRHADVVKLWLTLQHIGQQGYARLIDDGYRLAERVVEGVRQRPFLRLAGEIDTNIVCFRGEPDWLPAERWDDWNAALQALLLREGKIFLSLPVYRGGRWLRAVLLNPYTTDAVIDAMFKQIDRFAG 476
                                    14        24        34        44    ||  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    || 343       353       363       373       383       393       403       413       423       433       443       453       463       473   
                                                                       49|                                                                                                                                                                                                                                                        304-LLP                     332|                                                                                                                                         
                                                                        53                                                                                                                                                                                                                                                                                     339                                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:468
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhh............eeeeee....hhhhhhhhhh..hhh.eeee........hhhhhhhhhhhhhhh..eeeeeeee..........hhhhhhhhhhhh..eeeee..hhhhhhhh..hhhhhhhhhhh.eeeehhhhhh......eeeee...hhhhhh.......hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.......eeeeee.....hhhhhhhhhhhhhhhhhhh........ee..ee.eeee......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4rj0 D  -1 NAMDSRFLPATAFIDPEGRNRNEVERLVQQVVDLILAKLTGAAERPPMPETVPGPITIPEAAATEATLLQAIRDMVDGSMNPANPGYIGHMDPMPATMAILGDLVAAAVNNNMLSLEMSPSFSRLETLLLRAIAGLFGLGEQAGGVLTSGGSLANLQALAVARNVAFDSVEPGITGLAQRPVIFASEAAHTSLQKAAMLLGLGTAAVIPVRATADSRMDPEDLRARIDQARGAGQHPFCVVATAGTTTTGNIDPLAEIGAIAREHGLWFHVDAAYGGALVFSERHRWRLAGIEQADSITFNPQkWLYVAKTCAMVLFRDAGVLERAFRIPGFINLGEIGVQGTRHADVVKLWLTLQHIGQQGYARLIDDGYRLAERVVEGVRQRPFLRLAGEIDTNIVCFRGEPDWLPAERWDDWNAALQALLLREGKIFLSLPVYRGGRWLRAVLLNPYTTDAVIDAMFKQIDRFAG 476
                                     8        18        28        38        48 ||     60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300   |   310       320       330|      348       358       368       378       388       398       408       418       428       438       448       458       468        
                                                                              50|                                                                                                                                                                                                                                                        304-LLP                   330|                                                                                                                                         
                                                                               53                                                                                                                                                                                                                                                                                   339
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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  (0, 0)

(no "SCOP Domain" information available for 4RJ0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RJ0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RJ0)

(-) Gene Ontology  (5, 5)

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

(-) Related Entries Specified in the PDB File

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