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(-) Description

Title :  CRYSTAL STRUCTURE OF DIHYDROPYRIMIDINASE FROM BREVIBACILLUS AGRI NCHU1002
 
Authors :  W. C. Wang, H. M. Wu
Date :  14 Jun 11  (Deposition) - 20 Jun 12  (Release) - 20 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Hydrolase, Zinc Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. C. Wang, H. M. Wu
Crystal Structure Of Dihydropyrimidinase From Brevibacillus Agri Nchu1002
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIHYDROPYRIMIDINASE
    Chains: A, B
    EC Number: 3.5.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-30
    Expression System Strain: NOVABLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PYDB
    Organism Scientific: BREVIBACILLUS AGRI
    Organism Taxid: 51101
    Strain: NCHU1002

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 16)
No.NameCountTypeFull Name
1ACT12Ligand/IonACETATE ION
2KCX4Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:247 , GLU A:254 , VAL A:299 , HOH A:1047BINDING SITE FOR RESIDUE ACT A 462
02AC2SOFTWAREKCX A:150 , HIS A:183 , HIS A:239 , ZN A:502 , HOH A:732 , HOH A:866BINDING SITE FOR RESIDUE ZN A 501
03AC3SOFTWAREGLY A:47 , TYR A:48 , HOH A:614BINDING SITE FOR RESIDUE ACT A 463
04AC4SOFTWAREHIS A:58 , HIS A:60 , KCX A:150 , ASP A:315 , ZN A:501BINDING SITE FOR RESIDUE ZN A 502
05AC5SOFTWARELYS A:277 , HOH A:938BINDING SITE FOR RESIDUE ACT A 464
06AC6SOFTWAREKCX B:150 , HIS B:183 , HIS B:239 , HOH B:500 , ZN B:504 , HOH B:586BINDING SITE FOR RESIDUE ZN B 503
07AC7SOFTWAREHIS B:58 , HIS B:60 , KCX B:150 , ASP B:315 , ZN B:503BINDING SITE FOR RESIDUE ZN B 504
08AC8SOFTWAREGLY B:47 , TYR B:48 , HOH B:775BINDING SITE FOR RESIDUE ACT B 462
09AC9SOFTWAREARG B:247 , GLU B:254BINDING SITE FOR RESIDUE ACT B 463
10BC1SOFTWAREGLU A:276 , HOH A:877 , GLY B:201 , HOH B:656 , HOH B:673BINDING SITE FOR RESIDUE ACT B 464

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:288 -Pro A:289
2Phe A:379 -Pro A:380
3Ser B:288 -Pro B:289
4Phe B:379 -Pro B:380

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3SFW)

(-) 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:461
 aligned with Q846U5_9BACL | Q846U5 from UniProtKB/TrEMBL  Length:461

    Alignment length:461
                                    10        20        30        40        50        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       340       350       360       370       380       390       400       410       420       430       440       450       460 
         Q846U5_9BACL     1 MKKWIRNGTVVTASDTYQADVLIDGEKVVAIGSDLQATDAEVIDATGYYLLPGGIDPHTHLDMPFGGTVTSDNFFTGTKAAAFGGTTSIVDFCLTSKGESLHSAIATWHEKARGKAVIDYGFHLMVSDANDHVLEELESVVNNEGITSLKVFMAYKNVLMADDETLFKTLIRAKELGALVQVHAENGDVLDYLTKQALAEGNTDPIYHAYTRPPEAEGEATGRAIALTALADAQLYVVHVSCADAVRRIAEAREKGWNVYGETCPQYLVLDITALEKPDFEGAKYVWSPPLREKWNQDVLWSALKNGILQTVGSDHCPFNFSGQKELGRRDFTKIPNGGPIIEDRMTILFSEGVRKGKISLNQFVDITSTKVAKLFGMFPQKGTIAVGSDADIVLFDPTVQRTISVETHHMNVDYNPFEGMQVHGDVISVLSRGAFVVRNKQFVGHAGAGRYVKRSTFARP 461
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eee....eee.eeeee..eeeeee........eeee....eeee.eeeeee....ee..ee...hhhhhhhhhhhh.eeeeeeee......hhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhh....eeeee.........hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh....hhhhhhh.hhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhh..hhhhhhh........hhhhhhhhhhhh....ee...........hhhhhh.hhhhh........hhhhhhhhhh......hhhhhhhhhhhhhhhhh................eeeeeeeeeee..................eeeeeeeeeee..eeeee..ee.................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sfw A   1 MKKWIRNGTVVTASDTYQADVLIDGEKVVAIGSDLQATDAEVIDATGYYLLPGGIDPHTHLDMPFGGTVTSDNFFTGTKAAAFGGTTSIVDFCLTSKGESLHSAIATWHEKARGKAVIDYGFHLMVSDANDHVLEELESVVNNEGITSLkVFMAYKNVLMADDETLFKTLIRAKELGALVQVHAENGDVLDYLTKQALAEGNTDPIYHAYTRPPEAEGEATGRAIALTALADAQLYVVHVSCADAVRRIAEAREKGWNVYGETCPQYLVLDITALEKPDFEGAKYVWSPPLREKWNQDVLWSALKNGILQTVGSDHCPFNFSGQKELGRRDFTKIPNGGPIIEDRMTILFSEGVRKGKISLNQFVDITSTKVAKLFGMFPQKGTIAVGSDADIVLFDPTVQRTISVETHHMNVDYNPFEGMQVHGDVISVLSRGAFVVRNKQFVGHAGAGRYVKRSTFARP 461
                                    10        20        30        40        50        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       340       350       360       370       380       390       400       410       420       430       440       450       460 
                                                                                                                                                                               150-KCX                                                                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:461
 aligned with Q846U5_9BACL | Q846U5 from UniProtKB/TrEMBL  Length:461

    Alignment length:461
                                    10        20        30        40        50        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       340       350       360       370       380       390       400       410       420       430       440       450       460 
         Q846U5_9BACL     1 MKKWIRNGTVVTASDTYQADVLIDGEKVVAIGSDLQATDAEVIDATGYYLLPGGIDPHTHLDMPFGGTVTSDNFFTGTKAAAFGGTTSIVDFCLTSKGESLHSAIATWHEKARGKAVIDYGFHLMVSDANDHVLEELESVVNNEGITSLKVFMAYKNVLMADDETLFKTLIRAKELGALVQVHAENGDVLDYLTKQALAEGNTDPIYHAYTRPPEAEGEATGRAIALTALADAQLYVVHVSCADAVRRIAEAREKGWNVYGETCPQYLVLDITALEKPDFEGAKYVWSPPLREKWNQDVLWSALKNGILQTVGSDHCPFNFSGQKELGRRDFTKIPNGGPIIEDRMTILFSEGVRKGKISLNQFVDITSTKVAKLFGMFPQKGTIAVGSDADIVLFDPTVQRTISVETHHMNVDYNPFEGMQVHGDVISVLSRGAFVVRNKQFVGHAGAGRYVKRSTFARP 461
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eee....eee.eeeee..eeeeee........eeee....eeee.eeeeee....ee..ee...hhhhhhhhhhhh.eeeeeeee......hhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhh....eeeee.........hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh.....hhhhhh.hhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhh..hhhhhhh........hhhhhhhhhhhh....ee...........hhhhhh.hhhhh........hhhhhhhhhh......hhhhhhhhhhhhhhhhh................eeeeeeeeeee..................eeeeeeeeeee..eeeee..ee.................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sfw B   1 MKKWIRNGTVVTASDTYQADVLIDGEKVVAIGSDLQATDAEVIDATGYYLLPGGIDPHTHLDMPFGGTVTSDNFFTGTKAAAFGGTTSIVDFCLTSKGESLHSAIATWHEKARGKAVIDYGFHLMVSDANDHVLEELESVVNNEGITSLkVFMAYKNVLMADDETLFKTLIRAKELGALVQVHAENGDVLDYLTKQALAEGNTDPIYHAYTRPPEAEGEATGRAIALTALADAQLYVVHVSCADAVRRIAEAREKGWNVYGETCPQYLVLDITALEKPDFEGAKYVWSPPLREKWNQDVLWSALKNGILQTVGSDHCPFNFSGQKELGRRDFTKIPNGGPIIEDRMTILFSEGVRKGKISLNQFVDITSTKVAKLFGMFPQKGTIAVGSDADIVLFDPTVQRTISVETHHMNVDYNPFEGMQVHGDVISVLSRGAFVVRNKQFVGHAGAGRYVKRSTFARP 461
                                    10        20        30        40        50        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       340       350       360       370       380       390       400       410       420       430       440       450       460 
                                                                                                                                                                               150-KCX
   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 3SFW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q846U5_9BACL | Q846U5)
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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