Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF OROTATE PHOSPHORIBOSYLTRANSFERASE FROM AEROPYRUM PERNIX
 
Authors :  M. Kanagawa, S. Baba, S. Kuramitsu, S. Yokoyama, G. Kawai, G. Sampei, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  06 May 07  (Deposition) - 06 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Rossmann Fold, Glycosyltransferase, Magnesium, Pyrimidine Biosynthesis, Transferase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kanagawa, S. Baba, S. Kuramitsu, S. Yokoyama, G. Kawai, G. Sampei
Crystal Structure Of Orotate Phosphoribosyltransferase From Aeropyrum Pernix
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OROTATE PHOSPHORIBOSYLTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.4.2.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES IN DATABASE 10-186
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 56636
    Synonym: OPRT, OPRTASE

 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  (2, 18)

Asymmetric Unit (2, 18)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:20 , THR B:117 , THR B:118 , GLY B:119 , THR B:120 , SER B:121 , HOH B:267 , HOH B:650 , HOH B:656BINDING SITE FOR RESIDUE PO4 B 646
2AC2SOFTWARESER C:20 , THR C:117 , THR C:118 , GLY C:119 , THR C:120 , SER C:121 , HOH C:671 , HOH C:681 , HOH C:712 , HOH C:715 , HOH C:716BINDING SITE FOR RESIDUE PO4 C 647

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YZK)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala B:66 -Thr B:67
2Ala D:66 -Thr D:67

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YZK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YZK)

(-) Exons   (0, 0)

(no "Exon" information available for 2YZK)

(-) 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:177
 aligned with PYRE_AERPE | Q9Y9D8 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:177
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       
           PYRE_AERPE     9 VLAKVLKKRGAVLRGDFVLSSGRRSSVYIDMRRLLGDESSYSVALDLLLEVGGQDLARSSAVIGVATGGLPWAAMLALRLSKPLGYVRPERKGHGTLSQVEGDPPKGRVVVVDDVATTGTSIAKSIEVLRSNGYTVGTALVLVDRGEGAGELLARMGVRLVSVATLKTILEKLGWGG 185
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh..eeeeeee.....eeeeee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhh..eeee....................eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeee...hhhhhhhh...eeeeeeehhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yzk A   1 mLAKVLKKRGAVLRGDFVLSSGRRSSVYIDmRRLLGDESSYSVALDLLLEVGGQDLARSSAVIGVATGGLPWAAmLALRLSKPLGYVRPERKGHGTLSQVEGDPPKGRVVVVDDVATTGTSIAKSIEVLRSNGYTVGTALVLVDRGEGAGELLARmGVRLVSVATLKTILEKLGWGG 177
                            |       10        20        30|       40        50        60        70    |   80        90       100       110       120       130       140       150     | 160       170       
                            |                            31-MSE                                      75-MSE                                                                          156-MSE                 
                            1-MSE                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:167
 aligned with PYRE_AERPE | Q9Y9D8 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:175
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178     
           PYRE_AERPE     9 VLAKVLKKRGAVLRGDFVLSSGRRSSVYIDMRRLLGDESSYSVALDLLLEVGGQDLARSSAVIGVATGGLPWAAMLALRLSKPLGYVRPERKGHGTLSQVEGDPPKGRVVVVDDVATTGTSIAKSIEVLRSNGYTVGTALVLVDRGEGAGELLARMGVRLVSVATLKTILEKLGW 183
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh..eeeeeee.....eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhh..eeee..--------..........eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeee...hhhhhhhhh..eeeeeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yzk B   1 mLAKVLKKRGAVLRGDFVLSSGRRSSVYIDmRRLLGDESSYSVALDLLLEVGGQDLARSSAVIGVATGGLPWAAmLALRLSKPLGYVRP--------SQVEGDPPKGRVVVVDDVATTGTSIAKSIEVLRSNGYTVGTALVLVDRGEGAGELLARmGVRLVSVATLKTILEKLGW 175
                            |       10        20        30|       40        50        60        70    |   80        |-       100       110       120       130       140       150     | 160       170     
                            1-MSE                        31-MSE                                      75-MSE        89       98                                                       156-MSE               


Chain C from PDB  Type:PROTEIN  Length:166
 aligned with PYRE_AERPE | Q9Y9D8 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:175
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178     
           PYRE_AERPE     9 VLAKVLKKRGAVLRGDFVLSSGRRSSVYIDMRRLLGDESSYSVALDLLLEVGGQDLARSSAVIGVATGGLPWAAMLALRLSKPLGYVRPERKGHGTLSQVEGDPPKGRVVVVDDVATTGTSIAKSIEVLRSNGYTVGTALVLVDRGEGAGELLARMGVRLVSVATLKTILEKLGW 183
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh..eeeeeee.....eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhh..eeee.---------..........eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeee...hhhhhhhhh..eeeeeeehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yzk C   1 mLAKVLKKRGAVLRGDFVLSSGRRSSVYIDmRRLLGDESSYSVALDLLLEVGGQDLARSSAVIGVATGGLPWAAmLALRLSKPLGYVR---------SQVEGDPPKGRVVVVDDVATTGTSIAKSIEVLRSNGYTVGTALVLVDRGEGAGELLARmGVRLVSVATLKTILEKLGW 175
                            |       10        20        30|       40        50        60        70    |   80       | -       100       110       120       130       140       150     | 160       170     
                            1-MSE                        31-MSE                                      75-MSE       88        98                                                       156-MSE               


Chain D from PDB  Type:PROTEIN  Length:177
 aligned with PYRE_AERPE | Q9Y9D8 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:177
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       
           PYRE_AERPE     9 VLAKVLKKRGAVLRGDFVLSSGRRSSVYIDMRRLLGDESSYSVALDLLLEVGGQDLARSSAVIGVATGGLPWAAMLALRLSKPLGYVRPERKGHGTLSQVEGDPPKGRVVVVDDVATTGTSIAKSIEVLRSNGYTVGTALVLVDRGEGAGELLARMGVRLVSVATLKTILEKLGWGG 185
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------Pribosyltran-2yzkD01 D:25-143                                                                                          ---------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------Pribosyltran-2yzkD02 D:25-143                                                                                          ---------------------------------- Pfam domains (2)
           Pfam domains (3) ------------------------Pribosyltran-2yzkD03 D:25-143                                                                                          ---------------------------------- Pfam domains (3)
           Pfam domains (4) ------------------------Pribosyltran-2yzkD04 D:25-143                                                                                          ---------------------------------- Pfam domains (4)
         Sec.struct. author hhhhhhhhh..eeeeeee.....eeeeee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhh..eeee........ee..........eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeee...hhhhhhhh...eeeeeeehhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yzk D   1 mLAKVLKKRGAVLRGDFVLSSGRRSSVYIDmRRLLGDESSYSVALDLLLEVGGQDLARSSAVIGVATGGLPWAAmLALRLSKPLGYVRPERKGHGTLSQVEGDPPKGRVVVVDDVATTGTSIAKSIEVLRSNGYTVGTALVLVDRGEGAGELLARmGVRLVSVATLKTILEKLGWGG 177
                            |       10        20        30|       40        50        60        70    |   80        90       100       110       120       130       140       150     | 160       170       
                            1-MSE                        31-MSE                                      75-MSE                                                                          156-MSE
   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 2YZK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YZK)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: PRTase-like (59)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (PYRE_AERPE | Q9Y9D8)
molecular function
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0004588    orotate phosphoribosyltransferase activity    Catalysis of the reaction: orotidine 5'-phosphate + diphosphate = orotate + 5-phospho-alpha-D-ribose 1-diphosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
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:0009116    nucleoside metabolic process    The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
    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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala B:66 - Thr B:67   [ RasMol ]  
    Ala D:66 - Thr D:67   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2yzk
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PYRE_AERPE | Q9Y9D8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.4.2.10
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PYRE_AERPE | Q9Y9D8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2YZK)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2YZK)