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(-) Description

Title :  THE YELLOW CRYSTAL STRUCTURE OF 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) - 22 Oct 14  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lyase, Mcsg, Structural Genomics, Psi-Biology, Midwest Center For Structural Genomics, A/B/A Fold, Decarboxylase, Cytosolic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Wu, S. Clancy, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
The Yellow Crystal Structure Of Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PYRIDOXAL-DEPENDENT DECARBOXYLASE
    Chains: B, A
    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
    Organism Scientific: SPHAEROBACTER THERMOPHILUS DSM 20745
    Organism Taxid: 479434
    Strain: DSM 20745

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 43)

Asymmetric/Biological Unit (5, 43)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2GOL11Ligand/IonGLYCEROL
3LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
4MSE24Mod. Amino AcidSELENOMETHIONINE
5TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG B:396 , LEU B:397BINDING SITE FOR RESIDUE CL B 501
02AC2SOFTWAREHIS A:353 , HOH A:643 , HOH A:686 , HOH B:616 , HOH B:661BINDING SITE FOR RESIDUE CL B 502
03AC3SOFTWARELEU A:6 , HOH A:791 , PRO B:457 , TYR B:458 , HOH B:729 , HOH B:750BINDING SITE FOR RESIDUE GOL B 503
04AC4SOFTWARELEU 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:628 , HOH B:750 , HOH B:787BINDING SITE FOR RESIDUE GOL B 504
05AC5SOFTWAREALA A:71 , MSE A:75 , TRP B:360 , HOH B:719BINDING SITE FOR RESIDUE GOL B 505
06AC6SOFTWAREARG B:409 , ALA B:417 , TRP B:420 , HOH B:708 , HOH B:886BINDING SITE FOR RESIDUE GOL B 506
07AC7SOFTWARETHR A:64 , ARG B:384 , GLU B:387 , GLY B:388 , GLN B:391 , ARG B:392 , ASP B:465 , PHE B:468 , HOH B:868BINDING SITE FOR RESIDUE GOL B 507
08AC8SOFTWARELEU B:136 , PHE B:137 , ARG B:286 , GLU B:293BINDING SITE FOR RESIDUE TRS B 508
09AC9SOFTWAREGLY B:266 , LEU B:267 , TRP B:268 , ASP B:296 , HOH B:871BINDING SITE FOR RESIDUE TRS B 509
10BC1SOFTWARELEU A:397BINDING SITE FOR RESIDUE CL A 501
11BC2SOFTWARETHR A:127 , GLY A:144 , GLY A:145 , ILE A:346 , HOH A:628 , HOH A:682 , HOH A:796 , HOH A:861BINDING SITE FOR RESIDUE GOL A 502
12BC3SOFTWAREARG A:124 , ARG A:131 , PHE A:340BINDING SITE FOR RESIDUE GOL A 503
13BC4SOFTWARETYR A:307 , LEU A:374 , ASP A:377 , GLY A:378 , LEU A:381 , LEU A:454 , LEU A:455 , ASN A:456 , PRO A:457 , HOH A:820 , HOH A:832BINDING SITE FOR RESIDUE GOL A 504
14BC5SOFTWAREARG A:384 , GLU A:387 , ASP A:465 , PHE A:468 , HOH A:864 , HOH A:865BINDING SITE FOR RESIDUE GOL A 505
15BC6SOFTWAREGLU A:117 , HOH A:826 , GLN B:428 , SER B:440 , LEU B:441BINDING SITE FOR RESIDUE GOL A 506
16BC7SOFTWAREGLY A:266 , LEU A:267 , ASP A:296 , HOH A:778 , HOH A:856BINDING SITE FOR RESIDUE GOL A 507
17BC8SOFTWARELEU A:136 , PHE A:137 , ARG A:286 , LEU A:289 , ALA A:290 , GLU A:293BINDING SITE FOR RESIDUE TRS A 508

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys B:310 -Thr B:311
2Lys A:310 -Thr A:311

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RIT)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:461
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh......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
                 4rit A   5 FLPATAFIDPEGRNRNEVERLVQQVVDLILAKLTGAAERPPmPEPGPITIPEAAATEATLLQAIRDmVDGSmNPANPGYIGHmDPmPATmAILGDLVAAAVNNNmLSLEmSPSFSRLETLLLRAIAGLFGLGEQAGGVLTSGGSLANLQALAVARNVAFDSVEPGITGLAQRPVIFASEAAHTSLQKAAmLLGLGTAAVIPVRATADSRmDPEDLRARIDQARGAGQHPFCVVATAGTTTTGNIDPLAEIGAIAREHGLWFHVDAAYGGALVFSERHRWRLAGIEQADSITFNPQkWLYVAKTCAmVLFRDAGVLERAFRIPAFINLGEIGVQGTRHADVVKLWLTLQHIGQQGYARLIDDGYRLAERVVEGVRQRPFLRLAGEIDTNIVCFRGEPDWLPAERWDDWNAALQALLLREGKIFLSLPVYRGGRWLRAVLLNPYTTDAVIDAmFKQIDRFAGR 477
                                    14        24        34        44 | ||   58        68      | 78 |      88  |  |  98       108    |  118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298     | 308     | 318       328  ||   346       356       366       376       386       396       406       416       426       436       446       456       466|      476 
                                                                    46-MSE                   75-MSE|         91-MSE  |            113-MSE|                                                                             198-MSE             218-MSE                                                                               304-LLP   314-MSE          331|                                                                                                                            467-MSE      
                                                                      48|                         80-MSE        94-MSE                 118-MSE                                                                                                                                                                                                               340                                                                                                                                         
                                                                       53                                           98-MSE                                                                                                                                                                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:469
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh.....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
                 4rit B   5 FLPATAFIDPEGRNRNEVERLVQQVVDLILAKLTGAAERPPmPETVDLPGPITIPEAAATEATLLQAIRDmVDGSmNPANPGYIGHmDPmPATmAILGDLVAAAVNNNmLSLEmSPSFSRLETLLLRAIAGLFGLGEQAGGVLTSGGSLANLQALAVARNVAFDSVEPGITGLAQRPVIFASEAAHTSLQKAAmLLGLGTAAVIPVRATADSRmDPEDLRARIDQARGAGQHPFCVVATAGTTTTGNIDPLAEIGAIAREHGLWFHVDAAYGGALVFSERHRWRLAGIEQADSITFNPQkWLYVAKTCAmVLFRDAGVLERAFRIPAGFINLGEIGVQGTRHADVVKLWLTLQHIGQQGYARLIDDGYRLAERVVEGVRQRPFLRLAGEIDTNIVCFRGEPDWLPAERWDDWNAALQALLLREGKIFLSLPVYRGGRWLRAVLLNPYTTDAVIDAmFKQIDRFAGRERG 480
                                    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      |341       351       361       371       381       391       401       411       421       431       441       451       461     | 471         
                                                                    46-MSE                       75-MSE|         91-MSE  |            113-MSE|                                                                             198-MSE             218-MSE                                                                               304-LLP   314-MSE          331|                                                                                                                             467-MSE         
                                                                                                      80-MSE        94-MSE                 118-MSE                                                                                                                                                                                                               339                                                                                                                                             
                                                                                                                        98-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 4RIT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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    Lys A:310 - Thr A:311   [ RasMol ]  
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        D1C7D8_SPHTD | D1C7D8: 4riz 4rj0 4rlg 4rm1

(-) Related Entries Specified in the PDB File

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