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(-) Description

Title :  CRYSTAL STRUCTURE OF CORDYCEPS MILITARIS IDCASE IN APO FORM
 
Authors :  S. Xu, J. Zhu, J. Ding
Date :  15 Oct 12  (Deposition) - 11 Sep 13  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Pyrimidine Metabolism, Dna Decarboxylation, Idcase, Decarboxylase, Uracil, 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, C, D
    EC Number: 4.1.1.66
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3) CODON PLUS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CCM_01452
    Organism Common: CATERPILLAR FUNGUS
    Organism Scientific: CORDYCEPS MILITARIS
    Organism Taxid: 73501
    Synonym: IDCASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1ZN5Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:12 , HIS A:14 , HIS A:195 , ASP A:323 , HOH A:503 , HOH A:603BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREHIS B:12 , HIS B:14 , HIS B:195 , ASP B:323 , HOH B:589 , HOH B:642BINDING SITE FOR RESIDUE ZN B 401
3AC3SOFTWAREHIS C:12 , HIS C:14 , HIS C:195 , ASP C:323 , HOH C:619 , HOH C:669BINDING SITE FOR RESIDUE ZN C 401
4AC4SOFTWAREHIS D:12 , HIS D:14 , HIS D:195 , ASP D:323 , HOH D:502 , HOH D:510BINDING SITE FOR RESIDUE ZN D 401
5AC5SOFTWAREHIS B:379 , HIS B:381 , HIS D:379 , HIS D:384 , HOH D:773BINDING SITE FOR RESIDUE ZN D 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HK5)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Ile A:30 -Pro A:31
2Asn A:98 -Pro A:99
3His A:324 -Pro A:325
4Ile B:30 -Pro B:31
5Asn B:98 -Pro B:99
6His B:324 -Pro B:325
7Ile C:30 -Pro C:31
8Asn C:98 -Pro C:99
9His C:324 -Pro C:325
10Ile D:30 -Pro D:31
11Asn D:98 -Pro D:99
12His D:324 -Pro D:325

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HK5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HK5)

(-) Exons   (0, 0)

(no "Exon" information available for 4HK5)

(-) 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:358
                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.hhhhhhhhhhh....eee...eee.hhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhhhh..eeeee.....hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhheeee....hhhhhhhhhhhhh...ee..................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hk5 A   6 PVVVDIHTHMYPPSYIAMLEKRQTIPLVRTFPRLILLSSELAALDAALLPGRPLSTHFASLAQKMHFMDTNGIRVSVISLANPWFDFLAPDEAPGIADAVNAEFSDMCAQHVGRLFFFAALPLSAPVDAVKASIERVKNLKYCRGIILGTSGLGKGLDDPHLLPVFEAVADAKLLVFLHPHYGLPNEVYGPRSEEYGHVLPLALGFPMETTIAVARMYMAGVFDHVRNLQMLLAHSGGTLPFLAGRIESCIVHDGHLVKTGKVPKDRRTIWTVLKEQIYLDAVIYSEVGLQAAIASSGADRLMFGTDHPFFPPIEEDVQGPWDSSRLNAQAVIKAVGEGSSDAAAVMGLNAVRVLSLK 374
                                    15        25        35||      50       |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        
                                                         36|              58|                                                                                                                                                                                                                                                                                                                     
                                                          42               65                                                                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:362
                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.hhhhhhhhhhh.......ee..hhhhhhhhhh...ee.hhhhhhhhhhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhhhh..eeeee.....hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhheeee....hhhhhhhhhhhhh...ee..................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hk5 B   6 PVVVDIHTHMYPPSYIAMLEKRQTIPLVPRLILLSSELAALDALPGRPLSTHFASLAQKMHFMDTNGIRVSVISLANPWFDFLAPDEAPGIADAVNAEFSDMCAQHVGRLFFFAALPLSAPVDAVKASIERVKNLKYCRGIILGTSGLGKGLDDPHLLPVFEAVADAKLLVFLHPHYGLPNEVYGPRSEEYGHVLPLALGFPMETTIAVARMYMAGVFDHVRNLQMLLAHSGGTLPFLAGRIESCIVHDGHLVKTGKVPKDRRTIWTVLKEQIYLDAVIYSEVGLQAAIASSGADRLMFGTDHPFFPPIEEDVQGPWDSSRLNAQAVIKAVGEGSSDAAAVMGLNAVRVLSLKAELEHHHHH 383
                                    15        25       |43        53  ||    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  
                                                      33|            56|                                                                                                                                                                                                                                                                                                                              
                                                       42             65                                                                                                                                                                                                                                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:370
                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.hhhhhhhhhhh....eee........eee.hhhhhhhhhhhhhh.......ee.hhhhhhhhhhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhhh..eeee......hhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhheeee....hhhhhhhhhhhhh...ee..................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hk5 C   5 TPVVVDIHTHMYPPSYIAMLEKRQTIPLVRTFPQADEPRLILLSSELAALDAALADPAAKLPGRPLSTHFASLAQKMHFMDTNGIRVSVISLANPWFDFLAPDEAPGIADAVNAEFSDMCAQHVGRLFFFAALPLSAPVDAVKASIERVKNLKYCRGIILGTSGLGKGLDDPHLLPVFEAVADAKLLVFLHPHYGLPNEVYGPRSEEYGHVLPLALGFPMETTIAVARMYMAGVFDHVRNLQMLLAHSGGTLPFLAGRIESCIVHDGHLVKTGKVPKDRRTIWTVLKEQIYLDAVIYSEVGLQAAIASSGADRLMFGTDHPFFPPIEEDVQGPWDSSRLNAQAVIKAVGEGSSDAAAVMGLNAVRVLSLK 374
                                    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       334       344       354       364       374


Chain D from PDB  Type:PROTEIN  Length:380
                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.hhhhhhhhhh.....eeeee..eeeeeee.hhhhhhhhhhhhhh.......ee.hhhhhhhhhhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhhh..eeee......hhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhheeee....hhhhhhhhhhhhh...ee..................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hk5 D   5 TPVVVDIHTHMYPPSYIAMLEKRQTIPLVRTFPQADEPRLILLSSELAALDAALADPAAKLPGRPLSTHFASLAQKMHFMDTNGIRVSVISLANPWFDFLAPDEAPGIADAVNAEFSDMCAQHVGRLFFFAALPLSAPVDAVKASIERVKNLKYCRGIILGTSGLGKGLDDPHLLPVFEAVADAKLLVFLHPHYGLPNEVYGPRSEEYGHVLPLALGFPMETTIAVARMYMAGVFDHVRNLQMLLAHSGGTLPFLAGRIESCIVHDGHLVKTGKVPKDRRTIWTVLKEQIYLDAVIYSEVGLQAAIASSGADRLMFGTDHPFFPPIEEDVQGPWDSSRLNAQAVIKAVGEGSSDAAAVMGLNAVRVLSLKAELEHHHHHH 384
                                    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       334       344       354       364       374       384
   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 4HK5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HK5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HK5)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

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  4.1.1.66
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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

(-) Related Entries Specified in the PDB File

4hjw 4hk6 4hk7