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(-) Description

Title :  CRYSTAL STRUCTURE OF AMP NUCLEOSIDASE FROM BACTEROIDES THETAIOTAOMICRON VPI-5482
 
Authors :  N. R. Krishnamurthy, S. Swaminathan, S. K. Burley, New York Sgx Rese Center For Structural Genomics (Nysgxrc)
Date :  20 Dec 04  (Deposition) - 04 Jan 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  A,B,C  (2x)
Keywords :  Structural Genomics, Protein Structure Initiative, Psi, New York Sgx Research Center For Structural Genomics, Nysgxrc, T1840, Amp Nucleosidase, Bacteroides Thetaiotaomicron, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. R. Krishnamurthy, S. Swaminathan
Crystal Structure Of Amp Nucleosidase From Bacteroides Thetaiotaomicron
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - AMP NUCLEOSIDASE
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON
    Organism Taxid: 226186
    Strain: VPI-5482

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): ABC
Biological Unit 2 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 23)

Asymmetric Unit (1, 23)
No.NameCountTypeFull Name
1MSE23Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 23)
No.NameCountTypeFull Name
1MSE23Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 46)
No.NameCountTypeFull Name
1MSE46Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1YBF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YBF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YBF)

(-) Exons   (0, 0)

(no "Exon" information available for 1YBF)

(-) 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:240
 aligned with Q7MVU1_PORGI | Q7MVU1 from UniProtKB/TrEMBL  Length:258

    Alignment length:246
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242      
         Q7MVU1_PORGI     3 TKQEIVENWLPRYTQRQLIDFEPYILLTNFSHYLHVFAEHYGVPIVGEHTSMPNASAEGVTLINFGMGSANAATIMDLLWAIHPKAVIFLGKCGGLKLENALGDYLLPIAAIRGEGTSNDYLPEEVPSLPSFSVLRAISSAIQNKGKDYWTGTVYTTNRRVWEYDEKFKDYLRSTHASGVDMETATLMTVGFANKIPMGALLLISDRPMFPEGVKTEESDQLVTDNFAEEHLMLGIDALEIIRENK 248
               SCOP domains d1ybfa_ A: AMP nucleosidase                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.........eeeee.hhhhhhhhhhhhh.................eeeee...hhhhhhhhhhhh......eeeeeeee...........eeeeeeeee...hhhhh.........hhhhhhhhhhhhhh.....eeeeeee........hhhhhhhhhhh...eee.hhhhhhhhhhhh...eeeeeee...............------.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ybf A   5 TKQEIVENWLPRYTQRQLIDFEPYILLTNFSHYLHVFAEHYGVPIVGEHTSmPNASAEGVTLINFGmGSANAATImDLLWAIHPKAVIFLGKCGGLKLENALGDYLLPIAAIRGEGTSNDYLPEEVPSLPSFSVLRAISSAIQNKGKDYWTGTVYTTNRRVWEYDEKFKDYLRSTHASGVDmETATLmTVGFANKIPmGALLLISDRPmFPEGVKTEES------NFAEEHLmLGIDALEIIRENK 250
                                    14        24        34        44        54 |      64      | 74     |  84        94       104       114       124       134       144       154       164       174       184 |     194       204       214        |-     | 234  |    244      
                                                                              56-MSE         71-MSE   80-MSE                                                                                                   186-MSE |       202-MSE    213-MSE   223    230      |             
                                                                                                                                                                                                                     192-MSE                                      237-MSE         


Chain B from PDB  Type:PROTEIN  Length:228
 aligned with Q7MVU1_PORGI | Q7MVU1 from UniProtKB/TrEMBL  Length:258

    Alignment length:248
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242        
         Q7MVU1_PORGI     3 TKQEIVENWLPRYTQRQLIDFEPYILLTNFSHYLHVFAEHYGVPIVGEHTSMPNASAEGVTLINFGMGSANAATIMDLLWAIHPKAVIFLGKCGGLKLENALGDYLLPIAAIRGEGTSNDYLPEEVPSLPSFSVLRAISSAIQNKGKDYWTGTVYTTNRRVWEYDEKFKDYLRSTHASGVDMETATLMTVGFANKIPMGALLLISDRPMFPEGVKTEESDQLVTDNFAEEHLMLGIDALEIIRENKSS 250
               SCOP domains d1ybfb_ B: AMP nucleosidase                                                                                                                                                                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh.hhhhh..eeeee.hhhhhhhhhhhh............eeee..eeeee...hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh.........hhhhhhhhhhhhhh....eeeeeeeee.......hhhhhhhhhhh...eee.hhhhhhhhhhhh...eeeeeeee--------------------.hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ybf B   5 TKQEIVENWLPRYTQRQLIDFEPYILLTNFSHYLHVFAEHYGVPIVGEHTSmPNASAEGVTLINFGmGSANAATImDLLWAIHPKAVIFLGKCGGLKLENALGDYLLPIAAIRGEGTSNDYLPEEVPSLPSFSVLRAISSAIQNKGKDYWTGTVYTTNRRVWEYDEKFKDYLRSTHASGVDmETATLmTVGFANKIPmGALLLIS--------------------NFAEEHLmLGIDALEIIRENKSS 252
                                    14        24        34        44        54 |      64      | 74     |  84        94       104       114       124       134       144       154       164       174       184 |     194       204    |    -         -     | 234  |    244        
                                                                              56-MSE         71-MSE   80-MSE                                                                                                   186-MSE |       202-MSE209                  230      |               
                                                                                                                                                                                                                     192-MSE                                      237-MSE           


Chain C from PDB  Type:PROTEIN  Length:230
 aligned with Q7MVU1_PORGI | Q7MVU1 from UniProtKB/TrEMBL  Length:258

    Alignment length:247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       
         Q7MVU1_PORGI     2 KTKQEIVENWLPRYTQRQLIDFEPYILLTNFSHYLHVFAEHYGVPIVGEHTSMPNASAEGVTLINFGMGSANAATIMDLLWAIHPKAVIFLGKCGGLKLENALGDYLLPIAAIRGEGTSNDYLPEEVPSLPSFSVLRAISSAIQNKGKDYWTGTVYTTNRRVWEYDEKFKDYLRSTHASGVDMETATLMTVGFANKIPMGALLLISDRPMFPEGVKTEESDQLVTDNFAEEHLMLGIDALEIIRENK 248
               SCOP domains d1ybfc_ C: AMP nucleosidase                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------PNP_UDP_1-1ybfC01 C:27-240                                                                                                                                                                                            ---------- Pfam domains (1)
           Pfam domains (2) -----------------------PNP_UDP_1-1ybfC02 C:27-240                                                                                                                                                                                            ---------- Pfam domains (2)
           Pfam domains (3) -----------------------PNP_UDP_1-1ybfC03 C:27-240                                                                                                                                                                                            ---------- Pfam domains (3)
         Sec.struct. author .hhhhhhhhhhhhhhh.hhhhh..eeeee.hhhhhhhhhhhhh...........eeee..eeeee...hhhhhhhhhhhhhhh...eeeeeeeeee.----....eeeeeeeee..hhhhhh.........hhhhhhhhhhhhhh....eeeeeeee........hhhhhhhhhh....eee.hhhhhhhhhhhh...eeeeeeee.......-------------.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ybf C   4 KTKQEIVENWLPRYTQRQLIDFEPYILLTNFSHYLHVFAEHYGVPIVGEHTSmPNASAEGVTLINFGmGSANAATImDLLWAIHPKAVIFLGKCGGL----ALGDYLLPIAAIRGEGTSNDYLPEEVPSLPSFSVLRAISSAIQNKGKDYWTGTVYTTNRRVWEYDEKFKDYLRSTHASGVDmETATLmTVGFANKIPmGALLLISDRPmFPE-------------NFAEEHLmLGIDALEIIRENK 250
                                    13        23        33        43        53  |     63       |73      | 83        93      |  - |     113       123       133       143       153       163       173       183  |    193       203       213  |      -      |233   |   243       
                                                                               56-MSE         71-MSE   80-MSE             100  105                                                                              186-MSE |       202-MSE    213-MSE          230      |             
                                                                                                                                                                                                                      192-MSE                 216                  237-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  (1, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YBF)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: PUP (121)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q7MVU1_PORGI | Q7MVU1)
molecular function
    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.
biological process
    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).

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