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(-) Description

Title :  CRYSTAL STRUCTURE OF CORDYCEPS MILITARIS IDCASE IN COMPLEX WITH 5-NITRO-URACIL
 
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 :  2.30
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

 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  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
15NU4Ligand/Ion5-NITROURACIL
2ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
15NU2Ligand/Ion5-NITROURACIL
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
15NU2Ligand/Ion5-NITROURACIL
2ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:12 , HIS A:14 , HIS A:195 , ASP A:323 , 5NU A:402BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREHIS A:14 , LEU A:46 , ARG A:68 , ASN A:98 , HIS A:195 , LEU A:218 , PHE A:222 , HIS A:251 , ASP A:323 , PHE A:326 , PHE A:327 , ZN A:401 , HOH A:501BINDING SITE FOR RESIDUE 5NU A 402
3AC3SOFTWAREHIS B:12 , HIS B:14 , HIS B:195 , ASP B:323 , 5NU B:402BINDING SITE FOR RESIDUE ZN B 401
4AC4SOFTWAREHIS B:12 , HIS B:14 , LEU B:46 , ARG B:68 , ASN B:98 , HIS B:195 , LEU B:218 , PHE B:222 , HIS B:251 , ASP B:323 , PHE B:326 , PHE B:327 , ZN B:401 , HOH B:508 , ARG D:262BINDING SITE FOR RESIDUE 5NU B 402
5AC5SOFTWAREHIS C:12 , HIS C:14 , HIS C:195 , ASP C:323 , 5NU C:402BINDING SITE FOR RESIDUE ZN C 401
6AC6SOFTWAREARG A:262 , HIS C:12 , HIS C:14 , LEU C:46 , ARG C:68 , ASN C:98 , HIS C:195 , LEU C:218 , PHE C:222 , HIS C:251 , ASP C:323 , PHE C:326 , PHE C:327 , ZN C:401BINDING SITE FOR RESIDUE 5NU C 402
7AC7SOFTWAREHIS D:12 , HIS D:14 , HIS D:195 , ASP D:323 , 5NU D:402BINDING SITE FOR RESIDUE ZN D 401
8AC8SOFTWAREARG B:262 , HIS D:12 , HIS D:14 , LEU D:46 , ARG D:68 , ASN D:98 , HIS D:195 , LEU D:218 , PHE D:222 , HIS D:251 , ASP D:323 , PHE D:326 , PHE D:327 , ZN D:401 , HOH D:523BINDING SITE FOR RESIDUE 5NU D 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HK6)

(-) 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 4HK6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HK6)

(-) Exons   (0, 0)

(no "Exon" information available for 4HK6)

(-) 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:369
                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.hhhhhhhhh......eeeee..eeeeeee.hhhhhhhhhhhhhh.......ee......hhhhhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhhh..eeee......hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhheeee....hhhhhhhhhhhhh...ee..................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hk6 A   6 PVVVDIHTHMYPPSYIAMLEKRQTIPLVRTFPQADEPRLILLSSELAALDAALADPAAKLPGRPLSTHFASLAQKMHFMDTNGIRVSVISLANPWFDFLAPDEAPGIADAVNAEFSDMCAQHVGRLFFFAALPLSAPVDAVKASIERVKNLKYCRGIILGTSGLGKGLDDPHLLPVFEAVADAKLLVFLHPHYGLPNEVYGPRSEEYGHVLPLALGFPMETTIAVARMYMAGVFDHVRNLQMLLAHSGGTLPFLAGRIESCIVHDGHLVKTGKVPKDRRTIWTVLKEQIYLDAVIYSEVGLQAAIASSGADRLMFGTDHPFFPPIEEDVQGPWDSSRLNAQAVIKAVGEGSSDAAAVMGLNAVRVLSLK 374
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365         


Chain B from PDB  Type:PROTEIN  Length:368
                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.hhhhhhhhhhh....eee........eee.hhhhhhhhhhhhhh.......ee......hhhhhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhhh..eeee......hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhheeee....hhhhhhhhhhhhh...ee..................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hk6 B   6 PVVVDIHTHMYPPSYIAMLEKRQTIPLVRTFPQADEPRLILLSSELAALDAALADPAAKLPGRPLSTHFASLAQKMHFMDTNGIRVSVISLANPWFDFLAPDEAPGIADAVNAEFSDMCAQHVGRLFFFAALPLSAPVDAVKASIERVKNLKYCRGIILGTSGLGKGLDDPHLLPVFEAVADAKLLVFLHPHYGLPNEVYGPRSEEYGHVLPLALGFPMETTIAVARMYMAGVFDHVRNLQMLLAHSGGTLPFLAGRIESCIVHDGHLVKTGKVPKDRRTIWTVLKEQIYLDAVIYSEVGLQAAIASSGADRLMFGTDHPFFPPIEEDVQGPWDSSRLNAQAVIKAVGEGSSDAAAVMGLNAVRVLSL 373
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365        


Chain C from PDB  Type:PROTEIN  Length:374
                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.hhhhhhhhhh.....eee........eee.hhhhhhhhhhhhhh.......ee.hhhhhhhhhhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhhh..eeee......hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhheeee....hhhhhhhhhhhhh...ee..................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hk6 C   6 PVVVDIHTHMYPPSYIAMLEKRQTIPLVRTFPQADEPRLILLSSELAALDAALADPAAKLPGRPLSTHFASLAQKMHFMDTNGIRVSVISLANPWFDFLAPDEAPGIADAVNAEFSDMCAQHVGRLFFFAALPLSAPVDAVKASIERVKNLKYCRGIILGTSGLGKGLDDPHLLPVFEAVADAKLLVFLHPHYGLPNEVYGPRSEEYGHVLPLALGFPMETTIAVARMYMAGVFDHVRNLQMLLAHSGGTLPFLAGRIESCIVHDGHLVKTGKVPKDRRTIWTVLKEQIYLDAVIYSEVGLQAAIASSGADRLMFGTDHPFFPPIEEDVQGPWDSSRLNAQAVIKAVGEGSSDAAAVMGLNAVRVLSLKAELEH 379
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375    


Chain D from PDB  Type:PROTEIN  Length:369
                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.hhhhhhhhhh.....eee........eee.hhhhhhhhhhhhhh.......ee.hhhhhhhhhhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhhh..eeee......hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhheeee....hhhhhhhhhhhhh...ee..................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hk6 D   6 PVVVDIHTHMYPPSYIAMLEKRQTIPLVRTFPQADEPRLILLSSELAALDAALADPAAKLPGRPLSTHFASLAQKMHFMDTNGIRVSVISLANPWFDFLAPDEAPGIADAVNAEFSDMCAQHVGRLFFFAALPLSAPVDAVKASIERVKNLKYCRGIILGTSGLGKGLDDPHLLPVFEAVADAKLLVFLHPHYGLPNEVYGPRSEEYGHVLPLALGFPMETTIAVARMYMAGVFDHVRNLQMLLAHSGGTLPFLAGRIESCIVHDGHLVKTGKVPKDRRTIWTVLKEQIYLDAVIYSEVGLQAAIASSGADRLMFGTDHPFFPPIEEDVQGPWDSSRLNAQAVIKAVGEGSSDAAAVMGLNAVRVLSLK 374
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365
   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 4HK6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HK6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HK6)

(-) Gene Ontology  (5, 5)

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  4hk6
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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: 4hk5 4hk7 4lak 4lal 4lam 4lan 4lao

(-) Related Entries Specified in the PDB File

4hjw 4hk5 4hk6