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(-) Description

Title :  CRYSTAL STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM ARCHAEOGLOBUS FULGIDUS
 
Authors :  A. A. Fedorov, E. V. Fedorov, B. Desai, J. A. Gerlt, S. C. Almo
Date :  06 Oct 13  (Deposition) - 30 Oct 13  (Release) - 06 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C (1x),D (1x)
Biol. Unit 3:  A  (1x)
Biol. Unit 4:  B  (1x)
Biol. Unit 5:  C  (1x)
Biol. Unit 6:  D  (1x)
Keywords :  Tim Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Fedorov, E. V. Fedorov, B. Desai, J. A. Gerlt, S. C. Almo
Crystal Structure Of Orotidine 5'-Monophosphate Decarboxylase From Archaeoglobus Fulgidus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
    Chains: A, B, C, D
    EC Number: 4.1.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PYRF, AF_0929
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234
    Synonym: OMP DECARBOXYLASE, OMPDCASE, OMPDECASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   C (1x)D (1x)
Biological Unit 3 (1x): A   
Biological Unit 4 (1x):  B  
Biological Unit 5 (1x):   C 
Biological Unit 6 (1x):    D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
Biological Unit 6 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:51 , ASP A:77 , LYS A:79 , PRO A:186 , HOH A:401 , HOH A:459 , HOH A:460 , ASP B:82BINDING SITE FOR RESIDUE GOL A 301

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:117 -A:158
2B:117 -B:158
3C:117 -C:158
4D:117 -D:158

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4N2Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N2Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N2Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4N2Y)

(-) 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:209
                                                                                                                                                                                                                                                 
               SCOP domains d4n2ya_ A: automated matches                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhh.....eeeehhhhhhhhh.hhhhhhhh...eeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh..eeeee....hhhhhh.hhhhhhhhhhhhhhh...eee....hhhhhhhhhhhhh..eeeee....hhhhhhhh....eeeehhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n2y A  21 MKQLILALDVMDGEKAMEIAKKVAEHVDRIKVNYPLVLSAGVGIMKRLSEIKPVIADFKIADVPYTSSLIARIAFENSAESVIVHGFVGSDTLREVCRVAEEFGGKVYAVTELSSPGGEEFMSAVSLKIVEKAKEAGCHGLIAPSTRIERLREIRKAAGDMEILCPGIGAQKGSIEAVKYADGIIVGRGIYASGNPAEEARKLRRVLKI 229
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         


Chain B from PDB  Type:PROTEIN  Length:201
                                                                                                                                                                                                                                         
               SCOP domains d4n2yb_ B: automated matches                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhhh...eee....hhhhhhhhhhhhh..eeee.........eeeehhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n2y B  21 MKQLILALDVMDGEKAMEIAKKVAEHVDRIKVNYPLVLSAGVGIMKRLSEIKPVIADFKIADVPYTSSLIARIAFENSAESVIVHGFVGSDTLREVCRVAEEFGGKVYAVTELSSPGGEEFMSAVSLKIVEKAKEAGCHGLIAPSTRIERLREIRKAAGDMEILCPIEAVKYADGIIVGRGIYASGNPAEEARKLRRVLKI 229
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     ||198       208       218       228 
                                                                                                                                                                                               186|                                  
                                                                                                                                                                                                195                                  


Chain C from PDB  Type:PROTEIN  Length:201
                                                                                                                                                                                                                                         
               SCOP domains d4n2yc_ C: automated matches                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhhh...eee....hhhhhhhhhhhhh..eeee.........eeeehhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n2y C  21 MKQLILALDVMDGEKAMEIAKKVAEHVDRIKVNYPLVLSAGVGIMKRLSEIKPVIADFKIADVPYTSSLIARIAFENSAESVIVHGFVGSDTLREVCRVAEEFGGKVYAVTELSSPGGEEFMSAVSLKIVEKAKEAGCHGLIAPSTRIERLREIRKAAGDMEILCPIEAVKYADGIIVGRGIYASGNPAEEARKLRRVLKI 229
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     ||198       208       218       228 
                                                                                                                                                                                               186|                                  
                                                                                                                                                                                                195                                  


Chain D from PDB  Type:PROTEIN  Length:202
                                                                                                                                                                                                                                          
               SCOP domains d4n2yd_ D: automated matches                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhh.....eeeeehhhhhhhh.hhhhhhhh...eeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh..eeeee....hhhhhh.hhhhhhhhhhhhhhh...eee....hhhhhhhhhhhhh..eeee..hhhhhh..eeeehhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n2y D  21 MKQLILALDVMDGEKAMEIAKKVAEHVDRIKVNYPLVLSAGVGIMKRLSEIKPVIADFKIADVPYTSSLIARIAFENSAESVIVHGFVGSDTLREVCRVAEEFGGKVYAVTELSSPGGEEFMSAVSLKIVEKAKEAGCHGLIAPSTRIERLREIRKAAGDMEILCPSIEAVKYADGIIVGRGIYASGNPAEEARKLRRVLKI 229
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     ||197       207       217       227  
                                                                                                                                                                                               186|                                   
                                                                                                                                                                                                194
   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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N2Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N2Y)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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        PYRF_ARCFU | O29333: 4muz

(-) Related Entries Specified in the PDB File

4muz THE SAME PROTEIN COMPLEXED WITH BMP