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(-) Description

Title :  CRYSTAL STRUCTURE OF CORDYCEPS MILITARIS IDCASE D323N MUTANT IN COMPLEX WITH 5-CARBOXYL-URACIL
 
Authors :  S. Xu, W. Li, J. Zhu, J. Ding
Date :  20 Jun 13  (Deposition) - 02 Oct 13  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pyrimidine Metabolism, Idcase, Decarboxylase, Uracil, Dna Decarboxylation, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Xu, W. Li, J. Zhu, R. Wang, Z. Li, G. L. Xu, J. Ding
Crystal Structures Of Isoorotate Decarboxylases Reveal A Novel Catalytic Mechanism Of 5-Carboxyl-Uracil Decarboxylation And Shed Light On The Search For Dna Decarboxylase.
Cell Res. V. 23 1296 2013
PubMed-ID: 23917530  |  Reference-DOI: 10.1038/CR.2013.107

(-) Compounds

Molecule 1 - URACIL-5-CARBOXYLATE DECARBOXYLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28SUMO
    Expression System Strain: BL21(DE3) CODON PLUS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CCM_01452
    Mutation: YES
    Organism Scientific: CORDYCEPS MILITARIS
    Organism Taxid: 983644
    Strain: CM01

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
15CU2Ligand/Ion2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMIDINE-5-CARBOXYLICACID
2P6G4Ligand/IonHEXAETHYLENE GLYCOL
3ZN2Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:12 , HIS A:14 , HIS A:195 , ASN A:323 , 5CU A:402BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREHIS A:12 , HIS A:14 , ARG A:68 , ASN A:98 , HIS A:195 , LEU A:218 , PHE A:222 , HIS A:251 , ASN A:323 , PHE A:326 , PHE A:327 , ZN A:401 , ARG B:262 , HOH B:503BINDING SITE FOR RESIDUE 5CU A 402
3AC3SOFTWARETYR A:234 , MET A:235 , GLY A:237 , ASP A:240 , LYS A:278 , ARG A:283 , HOH A:566 , HOH A:602 , GLU B:211BINDING SITE FOR RESIDUE P6G A 403
4AC4SOFTWAREASP A:102 , SER A:140 , SER A:167 , TYR A:198 , HOH A:661BINDING SITE FOR RESIDUE P6G A 404
5AC5SOFTWAREALA A:148 , ARG A:152 , HOH A:578 , HOH A:650 , HOH A:669 , ARG B:152BINDING SITE FOR RESIDUE P6G A 405
6AC6SOFTWAREHIS B:12 , HIS B:14 , HIS B:195 , ASN B:323 , 5CU B:402BINDING SITE FOR RESIDUE ZN B 401
7AC7SOFTWAREARG A:262 , HIS B:12 , HIS B:14 , ARG B:68 , ASN B:98 , HIS B:195 , LEU B:218 , PHE B:222 , HIS B:251 , ASN B:323 , PHE B:326 , ZN B:401 , HOH B:509BINDING SITE FOR RESIDUE 5CU B 402
8AC8SOFTWAREGLU A:211 , TYR B:234 , MET B:235 , GLY B:237 , ASP B:240 , LYS B:278 , HOH B:563BINDING SITE FOR RESIDUE P6G B 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Thr A:5 -Pro A:6
2Ile A:30 -Pro A:31
3Asn A:98 -Pro A:99
4His A:324 -Pro A:325
5Ile B:30 -Pro B:31
6Asn B:98 -Pro B:99
7His B:324 -Pro B:325

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LAM)

(-) 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:365
                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.hhhhhhhhhh.....eee........eee.hhhhhhhhhhhhhh.......ee.hhhhhhhhhhhhhhhhhh..eeeeee...........hhhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhhh..eeee......hhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhheeee....hhhhhhhhhhhhh...ee............hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lam A   5 TPVVVDIHTHMYPPSYIAMLEKRQTIPLVRTFPQADEPRLILLSSELAALDAALADPAAKLPGRPLSTHFASLAQKMHFMDTNGIRVSVISLANPWFDFLAPDEAPGIADAVNAEFSDMCAQHVGRLFFFAALPLSAPVDAVKASIERVKNLKYCRGIILGTSGLGKGLDDPHLLPVFEAVADAKLLVFLHPHYGLPNEVYGPRSEEYGHVLPLALGFPMETTIAVARMYMAGVFDHVRNLQMLLAHSGGTLPFLAGRIESCIVHDGHLVKTGKVPKDRRTIWTVLKEQIYLDAVIYSEVGLQAAIASSGADRLMFGTNHPFFPPIWDSSRLNAQAVIKAVGEGSSDAAAVMGLNAVRVLSLKAE 376
                                    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     
                                                                                                                                                                                                                                                                                                                                                               330|                                      
                                                                                                                                                                                                                                                                                                                                                                338                                      


Chain B from PDB  Type:PROTEIN  Length:367
                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.hhhhhhhhhhh....eee.......eee.hhhhhhhhhhhhh.......ee.hhhhhhhhhhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhhh..eeee......hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhheeee....hhhhhhhhhhhhh...ee..................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lam B   6 PVVVDIHTHMYPPSYIAMLEKRQTIPLVRTFPQAEPRLILLSSELAALDAALAPAAKLPGRPLSTHFASLAQKMHFMDTNGIRVSVISLANPWFDFLAPDEAPGIADAVNAEFSDMCAQHVGRLFFFAALPLSAPVDAVKASIERVKNLKYCRGIILGTSGLGKGLDDPHLLPVFEAVADAKLLVFLHPHYGLPNEVYGPRSEEYGHVLPLALGFPMETTIAVARMYMAGVFDHVRNLQMLLAHSGGTLPFLAGRIESCIVHDGHLVKTGKVPKDRRTIWTVLKEQIYLDAVIYSEVGLQAAIASSGADRLMFGTNHPFFPPIEEDVQGPWDSSRLNAQAVIKAVGEGSSDAAAVMGLNAVRVLSLK 374
                                    15        25        35   ||   46        56  ||    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       337       347       357       367       
                                                            39|                59|                                                                                                                                                                                                                                                                                                                         
                                                             41                 61
   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 4LAM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/TrEMBL
        G3J531_CORMM | G3J531: 4hk5 4hk6 4hk7 4lak 4lal 4lan 4lao

(-) Related Entries Specified in the PDB File

4lak 4lal 4lan 4lao