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(-) Description

Title :  CRYSTAL STRUCTURE OF CORDYCEPS MILITARIS IDCASE D323A 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. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
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, C, D
    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

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 19)

Asymmetric Unit (3, 19)
No.NameCountTypeFull Name
15CU4Ligand/Ion2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMIDINE-5-CARBOXYLICACID
2P6G11Ligand/IonHEXAETHYLENE GLYCOL
3ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
15CU2Ligand/Ion2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMIDINE-5-CARBOXYLICACID
2P6G5Ligand/IonHEXAETHYLENE GLYCOL
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
15CU2Ligand/Ion2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMIDINE-5-CARBOXYLICACID
2P6G6Ligand/IonHEXAETHYLENE GLYCOL
3ZN-1Ligand/IonZINC ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:12 , HIS A:14 , HIS A:195 , 5CU A:402BINDING SITE FOR RESIDUE ZN A 401
02AC2SOFTWAREHIS A:12 , HIS A:14 , ARG A:68 , ASN A:98 , HIS A:195 , LEU A:218 , PHE A:222 , HIS A:251 , PHE A:326 , PHE A:327 , ZN A:401 , ARG B:262 , HOH B:506BINDING SITE FOR RESIDUE 5CU A 402
03AC3SOFTWARELYS A:291 , ALA A:311BINDING SITE FOR RESIDUE P6G A 403
04AC4SOFTWAREARG A:152 , ARG C:152BINDING SITE FOR RESIDUE P6G A 404
05AC5SOFTWAREGLN A:38 , PRO A:61 , ASP A:144 , LYS A:147 , PRO A:180BINDING SITE FOR RESIDUE P6G A 405
06AC6SOFTWAREALA A:186 , LYS A:189 , LEU A:190 , ASN A:244 , GLN A:246 , HOH A:630 , GLY C:355 , SER C:357BINDING SITE FOR RESIDUE P6G A 406
07AC7SOFTWAREHIS B:12 , HIS B:14 , HIS B:195 , 5CU B:402BINDING SITE FOR RESIDUE ZN B 401
08AC8SOFTWAREARG A:262 , HOH A:519 , HIS B:12 , HIS B:14 , ARG B:68 , ASN B:98 , HIS B:195 , LEU B:218 , PHE B:222 , HIS B:251 , PHE B:326 , PHE B:327 , ZN B:401BINDING SITE FOR RESIDUE 5CU B 402
09AC9SOFTWAREARG A:208 , TYR B:234 , MET B:235 , ALA B:236 , GLY B:237 , ASP B:240 , LYS B:278 , HOH B:559BINDING SITE FOR RESIDUE P6G B 403
10BC1SOFTWAREHIS C:12 , HIS C:14 , HIS C:195 , 5CU C:402BINDING SITE FOR RESIDUE ZN C 401
11BC2SOFTWAREHIS C:12 , HIS C:14 , ARG C:68 , ASN C:98 , HIS C:195 , LEU C:218 , PHE C:222 , HIS C:251 , PHE C:326 , PHE C:327 , ZN C:401 , ARG D:262 , HOH D:503BINDING SITE FOR RESIDUE 5CU C 402
12BC3SOFTWARETRP C:287 , LYS C:291 , ALA C:311 , TYR D:301 , SER D:302 , GLU D:303 , LEU D:343 , LYS D:350BINDING SITE FOR RESIDUE P6G C 403
13BC4SOFTWARELYS C:189 , GLN C:246BINDING SITE FOR RESIDUE P6G C 404
14BC5SOFTWARETYR C:234 , MET C:235 , GLY C:237 , ASP C:240 , LYS C:278BINDING SITE FOR RESIDUE P6G C 405
15BC6SOFTWAREPRO C:37 , GLN C:38 , LYS C:147 , PRO C:180 , GLU C:183BINDING SITE FOR RESIDUE P6G C 406
16BC7SOFTWAREHIS D:12 , HIS D:14 , HIS D:195 , 5CU D:402BINDING SITE FOR RESIDUE ZN D 401
17BC8SOFTWAREARG C:262 , HIS D:12 , HIS D:14 , ARG D:68 , ASN D:98 , HIS D:195 , LEU D:218 , PHE D:222 , HIS D:251 , ALA D:323 , PHE D:326 , PHE D:327 , ZN D:401 , HOH D:508BINDING SITE FOR RESIDUE 5CU D 402
18BC9SOFTWARETRP D:287 , LYS D:291BINDING SITE FOR RESIDUE P6G D 403
19CC1SOFTWAREGLU C:211 , ASP C:282 , TYR D:234 , MET D:235 , ASP D:240 , LYS D:278BINDING SITE FOR RESIDUE P6G D 404

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (14, 14)

Asymmetric Unit
No.Residues
1Ile A:30 -Pro A:31
2Asn A:98 -Pro A:99
3His A:324 -Pro A:325
4Ile A:330 -Glu A:331
5Ile B:30 -Pro B:31
6Asn B:98 -Pro B:99
7His B:324 -Pro B:325
8Ile B:330 -Glu B:331
9Ile C:30 -Pro C:31
10Asn C:98 -Pro C:99
11His C:324 -Pro C:325
12Ile D:30 -Pro D:31
13Asn D:98 -Pro D:99
14His D:324 -Pro D:325

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LAL)

(-) 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:368
                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.hhhhhhhhhhh....eee........eee.hhhhhhhhhhhhhh.......ee.hhhhhhhhhhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhh....eeeee......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
                 4lal A   6 PVVVDIHTHMYPPSYIAMLEKRQTIPLVRTFPQADEPRLILLSSELAALDAALADPAAKLPGRPLSTHFASLAQKMHFMDTNGIRVSVISLANPWFDFLAPDEAPGIADAVNAEFSDMCAQHVGRLFFFAALPLSAPVDAVKASIERVKNLKYCRGIILGTSGLGKGLDDPHLLPVFEAVADAKLLVFLHPHYGLPNEVYGPRSEEYGHVLPLALGFPMETTIAVARMYMAGVFDHVRNLQMLLAHSGGTLPFLAGRIESCIVHDGHLVKTGKVPKDRRTIWTVLKEQIYLDAVIYSEVGLQAAIASSGADRLMFGTAHPFFPPIEEDVQGPWDSSRLNAQAVIKAVGEGSSDAAAVMGLNAVRVLSL 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 B 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.hhhhhhhhhhh.........ee.hhhhhhhhhhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhhh..eeee......hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhheeee....hhhhhhhhhhhhh...ee..................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lal B   6 PVVVDIHTHMYPPSYIAMLEKRQTIPLVRTFPQADEPRLILLSSELAALDAALDPAAKLPGRPLSTHFASLAQKMHFMDTNGIRVSVISLANPWFDFLAPDEAPGIADAVNAEFSDMCAQHVGRLFFFAALPLSAPVDAVKASIERVKNLKYCRGIILGTSGLGKGLDDPHLLPVFEAVADAKLLVFLHPHYGLPNEVYGPRSEEYGHVLPLALGFPMETTIAVARMYMAGVFDHVRNLQMLLAHSGGTLPFLAGRIESCIVHDGHLVKTGKVPKDRRTIWTVLKEQIYLDAVIYSEVGLQAAIASSGADRLMFGTAHPFFPPIEEDVQGPWDSSRLNAQAVIKAVGEGSSDAAAVMGLNAVRVLSLKA 375
                                    15        25        35        45        55  ||    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         
                                                                               58|                                                                                                                                                                                                                                                                                                                           
                                                                                60                                                                                                                                                                                                                                                                                                                           


Chain C 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......hhhhhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhhh..eeee......hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhheeee....hhhhhhhhhhhhh...ee..................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lal C   6 PVVVDIHTHMYPPSYIAMLEKRQTIPLVRTFPQADEPRLILLSSELAALDAALADPAAKLPGRPLSTHFASLAQKMHFMDTNGIRVSVISLANPWFDFLAPDEAPGIADAVNAEFSDMCAQHVGRLFFFAALPLSAPVDAVKASIERVKNLKYCRGIILGTSGLGKGLDDPHLLPVFEAVADAKLLVFLHPHYGLPNEVYGPRSEEYGHVLPLALGFPMETTIAVARMYMAGVFDHVRNLQMLLAHSGGTLPFLAGRIESCIVHDGHLVKTGKVPKDRRTIWTVLKEQIYLDAVIYSEVGLQAAIASSGADRLMFGTAHPFFPPIEEDVQGPWDSSRLNAQAVIKAVGEGSSDAAAVMGLNAVRVLSLK 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 D from PDB  Type:PROTEIN  Length:367
                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.hhhhhhhhhh.....eee........eee.hhhhhhhhhhh.........ee.hhhhhhhhhhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhhh..eeee......hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhheeee....hhhhhhhhhhhhh...ee.................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lal D   6 PVVVDIHTHMYPPSYIAMLEKRQTIPLVRTFPQADEPRLILLSSELAALDAALADPAKLPGRPLSTHFASLAQKMHFMDTNGIRVSVISLANPWFDFLAPDEAPGIADAVNAEFSDMCAQHVGRLFFFAALPLSAPVDAVKASIERVKNLKYCRGIILGTSGLGKGLDDPHLLPVFEAVADAKLLVFLHPHYGLPNEVYGPRSEEYGHVLPLALGFPMETTIAVARMYMAGVFDHVRNLQMLLAHSGGTLPFLAGRIESCIVHDGHLVKTGKVPKDRRTIWTVLKEQIYLDAVIYSEVGLQAAIASSGADRLMFGTAHPFFPPIEDVQGPWDSSRLNAQAVIKAVGEGSSDAAAVMGLNAVRVLSLK 374
                                    15        25        35        45        55     || 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    || 337       347       357       367       
                                                                                  61|                                                                                                                                                                                                                                                                         331|                                         
                                                                                   63                                                                                                                                                                                                                                                                          333
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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 4LAL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

4lak 4lam 4lan 4lao