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(-) Description

Title :  CRYSTAL STRUCTURE OF DIHYDROPYRIMIDINASE FROM SINORHIZOBIUM MELILOTI
 
Authors :  J. A. Gavira, S. Martinez-Rodriguez
Date :  03 Jun 08  (Deposition) - 21 Apr 09  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Tim-Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Martinez-Rodriguez, A. I. Martinez-Gomez, J. M. Clemente-Jimenez, F. Rodriguez-Vico, J. M. Garcia-Ruiz, F. J. Las Heras-Vazquez, J. A. Gavira
Structure Of Dihydropyrimidinase From Sinorhizobium Melilot Cect4114: New Features In An Amidohydrolase Family Member
J. Struct. Biol. V. 169 200 2010
PubMed-ID: 19895890  |  Reference-DOI: 10.1016/J.JSB.2009.10.013
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIHYDROPYRIMIDINASE
    Chains: A, B
    EC Number: 3.5.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBSK
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DHP
    Organism Scientific: SINORHIZOBIUM MELILOTI
    Organism Taxid: 382
    Strain: CECT4114

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL4Ligand/IonGLYCEROL
3KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
4ZN4Ligand/IonZINC ION
Biological Unit 1 (3, 16)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2GOL8Ligand/IonGLYCEROL
3KCX4Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
4ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:180 , HIS A:236BINDING SITE FOR RESIDUE ZN A 501
02AC2SOFTWAREHIS A:56 , HIS A:58 , ASP A:313BINDING SITE FOR RESIDUE ZN A 502
03AC3SOFTWAREHIS B:180 , HIS B:236BINDING SITE FOR RESIDUE ZN B 501
04AC4SOFTWAREHIS B:56 , HIS B:58 , ASP B:313BINDING SITE FOR RESIDUE ZN B 502
05AC5SOFTWARETYR B:47 , MET B:358BINDING SITE FOR RESIDUE ACT B 503
06AC6SOFTWAREASN A:144 , GLY A:174 , ALA A:175 , LEU A:176 , ILE A:372 , PRO A:454 , PRO A:456 , SER A:459BINDING SITE FOR RESIDUE ACT A 503
07AC7SOFTWAREASP A:296 , TRP A:299 , ARG A:355 , GLY B:253BINDING SITE FOR RESIDUE GOL A 504
08AC8SOFTWAREALA A:303 , GLY A:354 , ARG A:355 , GLY B:253 , ARG B:255 , ALA B:461 , LEU B:462BINDING SITE FOR RESIDUE GOL A 505
09AC9SOFTWAREGLY A:253 , ARG A:255 , ALA A:461 , LEU A:462 , TRP A:465 , ALA B:303 , GLY B:354 , ARG B:355BINDING SITE FOR RESIDUE GOL A 506
10BC1SOFTWARELYS A:252 , GLY A:253 , ASP B:296 , TRP B:299 , ALA B:300 , ARG B:355BINDING SITE FOR RESIDUE GOL B 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DC8)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:286 -Pro A:287
2Tyr A:376 -Pro A:377
3Ser B:286 -Pro B:287
4Tyr B:376 -Pro B:377

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DC8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3DC8)

(-) Exons   (0, 0)

(no "Exon" information available for 3DC8)

(-) 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:483
 aligned with Q0PQZ5_RHIML | Q0PQZ5 from UniProtKB/TrEMBL  Length:484

    Alignment length:484
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            484 
                                    11        21        31        41        51        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       481  | 
         Q0PQZ5_RHIML     2 STVIKGGTIVTADLTYKADVKVEGGRIVEIGPNLSGAETLDATGCYVMPGGIDPHTHLEMPFMGTYSSDDFESGTRAALAGGTTMVVDFALPSPGQSLLEALTMWDNKSTRANCDYSFHMAITWWGEQVFNEMETIVKDKGINTFKHFMAYKGALMVDDDEMFSSFQRCAALGALPLVHAENGDVVAQLQAKLLAEGNSGPEAHAYSRPAEVEGEAANRAIMIADMAGCPVYIVHTSCEQAHEAIRRARAKGMRVFGEPLIQHLTLDETEYFDKDWDHAARRVMSPPFRNKLHQDSLWAGLASGSLQVVATDHCAFTTEQKRFGVGDFTRIPNGTGGLEDRMPMLWTYGVATGRITMNEFVAVTSTNIAKILNIYPKKGAILVGADADLVVWDPKRSKTISAKTQQSAIDYNVFEGKTVTGLPRFTLTRGVVSIEEGTVKTQEGHGEFVRRDPFPAVSTALSTWKEVTAPRAVQRSGIPASGV-   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eee....eee.eeeee..eeeeee......eeee....eeee.eeeeee....ee..ee...hhhhhhhhhhhh.eeeeeeee...-..hhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhh.hhhhhhhh.......hhhhhhhhhhhhhhh...eee......hhhhhhhhh.hhhhh........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhh................eeeeeeeeeee..................eeeeeeeeeee..eeeee..ee...............hhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dc8 A   2 STVIKGGTIVTADLTYKADVKVEGGRIVEIGPNLSGAETLDATGCYVMPGGIDPHTHLEMPFMGTYSSDDFESGTRAALAGGTTMVVDFALPS-GQSLLEALTMWDNKSTRANCDYSFHMAITWWGEQVFNEMETIVKDKGINTFkHFMAYKGALMVDDDEMFSSFQRCAALGALPLVHAENGDVVAQLQAKLLAEGNSGPEAHAYSRPAEVEGEAANRAIMIADMAGCPVYIVHTSCEQAHEAIRRARAKGMRVFGEPLIQHLTLDETEYFDKDWDHAARRVMSPPFRNKLHQDSLWAGLASGSLQVVATDHCAFTTEQKRFGVGDFTRIPNGTGGLEDRMPMLWTYGVATGRITMNEFVAVTSTNIAKILNIYPKKGAILVGADADLVVWDPKRSKTISAKTQQSAIDYNVFEGKTVTGLPRFTLTRGVVSIEEGTVKTQEGHGEFVRRDPFPAVSTALSTWKEVTAPRAVQRSGIPASGVH 485
                                    11        21        31        41        51        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       481    
                                                                                                                       94 |                                                147-KCX                                                                                                                                                                                                                                                                                                                                              
                                                                                                                         96                                                                                                                                                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:475
 aligned with Q0PQZ5_RHIML | Q0PQZ5 from UniProtKB/TrEMBL  Length:484

    Alignment length:476
                                    11        21        31        41        51        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      
         Q0PQZ5_RHIML     2 STVIKGGTIVTADLTYKADVKVEGGRIVEIGPNLSGAETLDATGCYVMPGGIDPHTHLEMPFMGTYSSDDFESGTRAALAGGTTMVVDFALPSPGQSLLEALTMWDNKSTRANCDYSFHMAITWWGEQVFNEMETIVKDKGINTFKHFMAYKGALMVDDDEMFSSFQRCAALGALPLVHAENGDVVAQLQAKLLAEGNSGPEAHAYSRPAEVEGEAANRAIMIADMAGCPVYIVHTSCEQAHEAIRRARAKGMRVFGEPLIQHLTLDETEYFDKDWDHAARRVMSPPFRNKLHQDSLWAGLASGSLQVVATDHCAFTTEQKRFGVGDFTRIPNGTGGLEDRMPMLWTYGVATGRITMNEFVAVTSTNIAKILNIYPKKGAILVGADADLVVWDPKRSKTISAKTQQSAIDYNVFEGKTVTGLPRFTLTRGVVSIEEGTVKTQEGHGEFVRRDPFPAVSTALSTWKEVTAPRAVQRS 477
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eee....eee.eeeee..eeeeee......eeee....eeee.eeeeee....ee..ee...hhhhhhhhhhhh.eeeeeeee...-..hhhhhhhhhhhhh.....eeeeeeee...hhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhh.hhhhhhhh.......hhhhhhhhhhhhhhh...eee......hhhhhhhhh.hhhhh........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhh................eeeeeeeeeee.hhhhh............eeeeeeeeeee..eeeee..ee...............hhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dc8 B   2 STVIKGGTIVTADLTYKADVKVEGGRIVEIGPNLSGAETLDATGCYVMPGGIDPHTHLEMPFMGTYSSDDFESGTRAALAGGTTMVVDFALPS-GQSLLEALTMWDNKSTRANCDYSFHMAITWWGEQVFNEMETIVKDKGINTFkHFMAYKGALMVDDDEMFSSFQRCAALGALPLVHAENGDVVAQLQAKLLAEGNSGPEAHAYSRPAEVEGEAANRAIMIADMAGCPVYIVHTSCEQAHEAIRRARAKGMRVFGEPLIQHLTLDETEYFDKDWDHAARRVMSPPFRNKLHQDSLWAGLASGSLQVVATDHCAFTTEQKRFGVGDFTRIPNGTGGLEDRMPMLWTYGVATGRITMNEFVAVTSTNIAKILNIYPKKGAILVGADADLVVWDPKRSKTISAKTQQSAIDYNVFEGKTVTGLPRFTLTRGVVSIEEGTVKTQEGHGEFVRRDPFPAVSTALSTWKEVTAPRAVQRS 477
                                    11        21        31        41        51        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      
                                                                                                                       94 |                                                147-KCX                                                                                                                                                                                                                                                                                                                                      
                                                                                                                         96
   Legend:   → Mismatch (orange background)
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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 3DC8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3DC8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DC8)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q0PQZ5_RHIML | Q0PQZ5)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016810    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds    Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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(-) Related Entries Specified in the PDB File

1k1d 1kcx 1yny