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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 :  18 Oct 14  (Deposition) - 12 Nov 14  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
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 Y333Q 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, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GOL6Ligand/IonGLYCEROL
3LLP4Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
4PMP2Ligand/Ion4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL6Ligand/IonGLYCEROL
3LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
4PMP1Ligand/Ion4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL-1Ligand/IonGLYCEROL
3LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
4PMP1Ligand/Ion4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:351 , HOH A:668 , MET B:91 , GLY B:150 , GLY B:151 , SER B:152 , HIS B:190 , GLY B:245 , THR B:247 , ASP B:272 , ALA B:274 , ASN B:301 , GLN B:303 , LLP B:304 , HOH B:723 , HOH B:787BINDING SITE FOR RESIDUE PMP B 501
02AC2SOFTWARELEU B:136 , PHE B:137 , LEU B:289 , GLU B:293 , HOH B:887 , HOH B:924BINDING SITE FOR RESIDUE GOL B 502
03AC3SOFTWARELEU B:116 , GLU B:117 , ARG B:124 , HOH B:660BINDING SITE FOR RESIDUE GOL B 503
04AC4SOFTWAREALA B:188 , ALA B:189 , HIS B:190 , THR B:191 , THR B:247 , HOH B:711 , HOH B:835 , HOH B:906BINDING SITE FOR RESIDUE GOL B 504
05AC5SOFTWAREHIS A:353 , HOH A:621 , HOH A:714 , HIS B:353 , HOH B:648 , HOH B:740BINDING SITE FOR RESIDUE CL B 505
06AC6SOFTWAREARG A:409 , ALA A:417 , ASP A:421 , ARG A:445 , GLY A:447 , HOH A:661BINDING SITE FOR RESIDUE GOL A 501
07AC7SOFTWAREPHE A:137 , ARG A:286BINDING SITE FOR RESIDUE GOL A 502
08AC8SOFTWARESER A:186 , GLU A:187 , VAL A:207 , PRO A:209 , HOH A:940BINDING SITE FOR RESIDUE GOL A 503
09AC9SOFTWAREMET C:91 , GLY C:150 , GLY C:151 , SER C:152 , HIS C:190 , GLY C:245 , THR C:247 , ASP C:272 , ASN C:301 , GLN C:303 , LLP C:304 , HOH C:2116 , HOH C:2206 , HOH C:2302 , THR D:351BINDING SITE FOR RESIDUE PMP C 2000
10BC1SOFTWAREHIS C:353 , HOH C:2140 , HIS D:353 , HOH D:654 , HOH D:668BINDING SITE FOR RESIDUE CL D 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RM1)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Lys B:310 -Thr B:311
2Gly A:54 -Pro A:55
3Lys A:310 -Thr A: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 4RM1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RM1)

(-) Exons   (0, 0)

(no "Exon" information available for 4RM1)

(-) 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:474
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               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..eeeeee.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
                 4rm1 A  -1 NAMDSRFLPATAFIDPEGRNRNEVERLVQQVVDLILAKLTGAAERPPMPEGPITIPEAAATEATLLQAIRDMVDGSMNPANPGYIGHMDPMPATMAILGDLVAAAVNNNMLSLEMSPSFSRLETLLLRAIAGLFGLGEQAGGVLTSGGSLANLQALAVARNVAFDSVEPGITGLAQRPVIFASEAAHTSLQKAAMLLGLGTAAVIPVRATADSRMDPEDLRARIDQARGAGQHPFCVVATAGTTTTGNIDPLAEIGAIAREHGLWFHVDAAYGGALVFSERHRWRLAGIEQADSITFNPQkWLYVAKTCAMVLFRDAGVLERAFRIPAPQMRATDGFINLGEIGVQGTRHADVVKLWLTLQHIGQQGYARLIDDGYRLAERVVEGVRQRPFLRLAGEIDTNIVCFRGEPDWLPAERWDDWNAALQALLLREGKIFLSLPVYRGGRWLRAVLLNPYTTDAVIDAMFKQIDRFAGR 477
                                     8        18        28        38        48|       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       403       413       423       433       443       453       463       473    
                                                                            48|                                                                                                                                                                                                                                                       304-LLP                                                                                                                                                                         
                                                                             54                                                                                                                                                                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:473
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               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.....hhhhhhhhhhhhhhhhhhh........ee..ee.eeee......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rm1 B  -1 NAMDSRFLPATAFIDPEGRNRNEVERLVQQVVDLILAKLTGAAERPPMPETPITIPEAAATEATLLQAIRDMVDGSMNPANPGYIGHMDPMPATMAILGDLVAAAVNNNMLSLEMSPSFSRLETLLLRAIAGLFGLGEQAGGVLTSGGSLANLQALAVARNVAFDSVEPGITGLAQRPVIFASEAAHTSLQKAAMLLGLGTAAVIPVRATADSRMDPEDLRARIDQARGAGQHPFCVVATAGTTTTGNIDPLAEIGAIAREHGLWFHVDAAYGGALVFSERHRWRLAGIEQADSITFNPQkWLYVAKTCAMVLFRDAGVLERAFRIPAPQMRATDGFINLGEIGVQGTRHADVVKLWLTLQHIGQQGYARLIDDGYRLAERVVEGVRQRPFLRLAGEIDTNIVCFRGEPDWLPAERWDDWNAALQALLLREGKIFLSLPVYRGGRWLRAVLLNPYTTDAVIDAMFKQIDRFAG 476
                                     8        18        28        38        48||      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       403       413       423       433       443       453       463       473   
                                                                             49|                                                                                                                                                                                                                                                      304-LLP                                                                                                                                                                        
                                                                              55                                                                                                                                                                                                                                                                                                                                                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:476
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.....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
                 4rm1 C  -1 NAMDSRFLPATAFIDPEGRNRNEVERLVQQVVDLILAKLTGAAERPPMPETLPGPITIPEAAATEATLLQAIRDMVDGSMNPANPGYIGHMDPMPATMAILGDLVAAAVNNNMLSLEMSPSFSRLETLLLRAIAGLFGLGEQAGGVLTSGGSLANLQALAVARNVAFDSVEPGITGLAQRPVIFASEAAHTSLQKAAMLLGLGTAAVIPVRATADSRMDPEDLRARIDQARGAGQHPFCVVATAGTTTTGNIDPLAEIGAIAREHGLWFHVDAAYGGALVFSERHRWRLAGIEQADSITFNPQkWLYVAKTCAMVLFRDAGVLERAFRIPAPQMRADGFINLGEIGVQGTRHADVVKLWLTLQHIGQQGYARLIDDGYRLAERVVEGVRQRPFLRLAGEIDTNIVCFRGEPDWLPAERWDDWNAALQALLLREGKIFLSLPVYRGGRWLRAVLLNPYTTDAVIDAMFKQIDRFAGR 477
                                     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     ||341       351       361       371       381       391       401       411       421       431       441       451       461       471      
                                                                             49|                                                                                                                                                                                                                                                         304-LLP                         336|                                                                                                                                           
                                                                              52                                                                                                                                                                                                                                                                                          338                                                                                                                                           


Chain D 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.eeee............eeeee...hhhhhh...............hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.......eeeeee.....hhhhhhhhhhhhhhhhhhh........ee..ee.eeee......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rm1 D   5 FLPATAFIDPEGRNRNEVERLVQQVVDLILAKLTGAAERPPMPETVPGPITIPEAAATEATLLQAIRDMVDGSMNPANPGYIGHMDPMPATMAILGDLVAAAVNNNMLSLEMSPSFSRLETLLLRAIAGLFGLGEQAGGVLTSGGSLANLQALAVARNVAFDSVEPGITGLAQRPVIFASEAAHTSLQKAAMLLGLGTAAVIPVRATADSRMDPEDLRARIDQARGAGQHPFCVVATAGTTTTGNIDPLAEIGAIAREHGLWFHVDAAYGGALVFSERHRWRLAGIEQADSITFNPQkWLYVAKTCAMVLFRDAGVLERAFRIPAPQMRATDGFINLGEIGVQGTRHADVVKLWLTLQHIGQQGYARLIDDGYRLAERVVEGVRQRPFLRLAGEIDTNIVCFRGEPDWLPAERWDDWNAALQALLLREGKIFLSLPVYRGGRWLRAVLLNPYTTDAVIDAMFKQIDRFAG 476
                                    14        24        34        44     || 56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476
                                                                        50|                                                                                                                                                                                                                                                        304-LLP                                                                                                                                                                        
                                                                         53
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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 4RM1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RM1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RM1)

(-) Gene Ontology  (5, 5)

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

(-) Related Entries Specified in the PDB File

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