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(-) Description

Title :  CRYSTAL STRUCTURE OF OROTIDINE MONOPHOSPHATE DECARBOXYLASE COMPLEX WITH XMP
 
Authors :  N. Wu, E. F. Pai
Date :  06 May 02  (Deposition) - 07 Aug 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tim Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Wu, E. F. Pai
Crystal Structures Of Inhibitor Complexes Reveal An Alternate Binding Mode In Orotidine-5'-Monophosphate Decarboxylase.
J. Biol. Chem. V. 277 28080 2002
PubMed-ID: 12011084  |  Reference-DOI: 10.1074/JBC.M202362200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE
    ChainsA, B
    EC Number4.1.1.23
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System Taxid562
    Organism ScientificMETHANOTHERMOBACTER THERMAUTOTROPHICUS STR. DELTA H
    Organism Taxid187420
    StrainDELTA H
    SynonymOMP DECARBOXYLASE, OMPDCASE, OMPDECASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1BU22Ligand/Ion1,3-BUTANEDIOL
2XMP2Ligand/IonXANTHOSINE-5'-MONOPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:70 , LYS A:72 , LEU A:123 , VAL A:155 , XMP A:2001 , HOH A:3015BINDING SITE FOR RESIDUE BU2 A 5001
2AC2SOFTWARELYS B:1042 , ASP B:1070 , LYS B:1072 , ILE B:1096 , VAL B:1155 , XMP B:2002BINDING SITE FOR RESIDUE BU2 B 5002
3AC3SOFTWAREALA A:18 , ASP A:20 , LYS A:42 , ASP A:70 , MET A:126 , SER A:127 , SER A:158 , PRO A:180 , GLY A:202 , ARG A:203 , HOH A:3009 , HOH A:3011 , HOH A:3012 , HOH A:3015 , HOH A:3085 , BU2 A:5001 , ILE B:1076 , HOH B:3066BINDING SITE FOR RESIDUE XMP A 2001
4AC4SOFTWAREILE A:76 , ALA B:1018 , ASP B:1020 , LYS B:1042 , ASP B:1070 , SER B:1127 , PRO B:1157 , SER B:1158 , PRO B:1180 , GLY B:1202 , ARG B:1203 , HOH B:3059 , HOH B:3112 , HOH B:3155 , HOH B:3159 , BU2 B:5002BINDING SITE FOR RESIDUE XMP B 2002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LOL)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp B:1188 -Pro B:1189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LOL)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OMPDECASEPS00156 Orotidine 5'-phosphate decarboxylase active site.PYRF_METTH67-80
 
  2A:67-80
B:1067-1080

(-) Exons   (0, 0)

(no "Exon" information available for 1LOL)

(-) 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:204
 aligned with PYRF_METTH | O26232 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:212
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  
          PYRF_METTH     11 VMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFRGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESI  222
               SCOP domains d1lola_ A: Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)                                                                                                                                              SCOP domains
               CATH domains 1lolA00 A:11-222 Aldolase class I                                                                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhh.eeeee...hhhhhhhhhhhhh....eeeeehhhhhhhh.hhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.eeeee..........hhhhhhhhhhhhhhhh...eee....hhhhhhhhhhhhh...eeeee.--------.hhhhh..eeeehhhhhh..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------OMPDECASE     ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lol A   11 VMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPG--------GETLRFADAIIVGRSIYLADNPAAAAAGIIESI  222
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180|      190       200       210       220  
                                                                                                                                                                                                    181      190                                

Chain B from PDB  Type:PROTEIN  Length:214
 aligned with PYRF_METTH | O26232 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:219
                                                                                                                                                                                                                                                   228 
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       | 
          PYRF_METTH     11 VMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFRGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESIKDLLNP-    -
               SCOP domains d1lolb_ B: Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)                                                                                                                                                     SCOP domains
               CATH domains 1lolB00 B:1011-1229 Aldolase class I                                                                                                                                                                                        CATH domains
           Pfam domains (1) --OMPdecase-1lolB01 B:1013-1218                                                                                                                                                                                 ----------- Pfam domains (1)
           Pfam domains (2) --OMPdecase-1lolB02 B:1013-1218                                                                                                                                                                                 ----------- Pfam domains (2)
         Sec.struct. author hhh.eeee....hhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.eeeee......hhhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhh...eeeee.-----....hhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------OMPDECASE     ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lol B 1011 VMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRPERLSRLREIIGQDSFLISPG-----GDPGETLRFADAIIVGRSIYLADNPAAAAAGIIESIKDLLIPE 1229
                                  1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180|     1190      1200      1210      1220         
                                                                                                                                                                                                   1181  1187                                          

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PYRF_METTH | O26232)
molecular function
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0004590    orotidine-5'-phosphate decarboxylase activity    Catalysis of the reaction: H(+) + orotidine 5'-phosphate = CO(2) + UMP.
biological process
    GO:0044205    'de novo' UMP biosynthetic process    The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD(+) or oxygen.
    GO:0006207    'de novo' pyrimidine nucleobase biosynthetic process    The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0006221    pyrimidine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PYRF_METTH | O262321dv7 1dvj 1kly 1klz 1km0 1km1 1km2 1km3 1km4 1km5 1km6 1loq 1lor 1los 1lp6 1x1z 2e6y 2zz1 2zz2 2zz3 2zz4 2zz5 2zz6 2zz7 3g18 3g1a 3g1d 3g1f 3g1h 3g1s 3g1v 3g1x 3g1y 3g22 3g24 3lht 3lhu 3lhv 3lhw 3lhy 3lhz 3li0 3li1 3lld 3llf 3ltp 3lts 3lty 3lv5 3lv6 3m1z 3m41 3m43 3m44 3m47 3m5x 3m5y 3m5z 3nq6 3nq7 3nqa 3nqc 3nqd 3nqe 3nqf 3nqg 3nqm 3p5y 3p5z 3p60 3p61 3pbu 3pbv 3pbw 3pby 3pc0 3qez 3qf0 3qmr 3qms 3qmt 3rlu 3rlv 3sec 3sgu 3siz 3sj3 3ssj 3sw6 3sy5 3thq 3v1p 3w07 3wjw 3wjx 3wjy 3wjz 3wk0 3wk1 3wk2 3wk3 4fx6 4fx8 4fxr 4gc4 4lc6 4lc8 4lw7 4nt0 4nuw 4nx5 4o11 4o8r

(-) Related Entries Specified in the PDB File

1loq OROTIDINE MONOPHOSPHATE DECARBOXYLASE COMPLEXED WITH UMP
1lor OROTIDINE MONOPHOSPHATE DECARBOXYLASE COMPLEXED WITH BMP
1los OROTIDINE MONOPHOSPHATE DECARBOXYLASE MUTANT DELTA R203A COMPLEXED WITH 6-AZAUMP
1lp6 OROTIDINE MONOPHOSPHATE DECARBOXYLASE COMPLEXED WITH CMP