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(-) Description

Title :  CRYSTAL STRUCTURE OF RUTC PROTEIN A MEMBER OF THE YJGF FAMILY FROM E.COLI
 
Authors :  A. A. Knapik, J. J. Petkowski, Z. Otwinowski, M. T. Cymborowski, D. R. Co M. Chruszcz, P. J. Porebski, E. Niedzialkowska, S. C. Almo, W. Minor, N Structural Genomics Research Consortium (Nysgrc)
Date :  14 Dec 11  (Deposition) - 04 Jan 12  (Release) - 12 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,F  (1x)
Biol. Unit 2:  B,D,E  (1x)
Keywords :  Structural Genomics, Psi-Biology, New York Structural Genomics Research Consortium, Nysgrc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Knapik, J. J. Petkowski, Z. Otwinowski, M. T. Cymborowski, D. R. Cooper, M. Chruszcz, W. M. Krajewska, W. Minor
Structure Of Escherichia Coli Rutc, A Member Of The Yjgf Family And Putative Aminoacrylate Peracid Reductase Of The Rut Operon.
Acta Crystallogr. , Sect. F V. 68 1294 2012
PubMed-ID: 23143235  |  Reference-DOI: 10.1107/S1744309112041796

(-) Compounds

Molecule 1 - AMINOACRYLATE PERACID REDUCTASE RUTC
    Chains: A, C, F, B, D, E
    EC Number: 1.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B MODIFIED FOR TEV CLEAVAGE
    Expression System Strain: BL21DE3RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: C1147, RUTC
    Organism Scientific: ESCHERICHIA COLI O6
    Organism Taxid: 217992
    Strain: XL-1 BLUE

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A C  F
Biological Unit 2 (1x):  B DE 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 11)

Asymmetric Unit (1, 11)
No.NameCountTypeFull Name
1MSE11Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3V4D)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3V4D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3V4D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3V4D)

(-) PROSITE Motifs  (1, 6)

Asymmetric Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UPF0076PS01094 Uncharacterized protein family UPF0076 signature.RUTC_ECOL6102-120
 
 
 
 
 		  6A:102-120
B:102-120
C:102-120
D:102-120
E:102-120
F:102-120
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UPF0076PS01094 Uncharacterized protein family UPF0076 signature.RUTC_ECOL6102-120
 
 
 
 
 		  3A:102-120
-
C:102-120
-
-
F:102-120
Biological Unit 2 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UPF0076PS01094 Uncharacterized protein family UPF0076 signature.RUTC_ECOL6102-120
 
 
 
 
 		  3-
B:102-120
-
D:102-120
E:102-120
-

(-) Exons   (0, 0)

(no "Exon" information available for 3V4D)

(-) 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:120
 aligned with RUTC_ECOL6 | P0AFQ6 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:126
                                    11        21        31        41        51        61        71        81        91       101       111       121      
           RUTC_ECOL6     2 PKSVIIPAGSSAPLAPFVPGTLADGVVYVSGTLAFDQHNNVLFADDPKAQTRHVLETIRKVIETAGGTMADVTFNSIFITDWKNYAAINEIYAEFFPGDKPARFCIQCGLVKPDALVEIATIAHIA 127
               SCOP domains d3v4da_ A      : automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee....------....eeee..eeeeeee.............hhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeee.hhhhhhhhhhhhhhhh.....eeeeee.........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------UPF0076            ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3v4d A   2 PKSVIIPAG------PFVPGTLADGVVYVSGTLAFDQHNNVLFADDPKAQTRHVLETIRKVIETAGGTmADVTFNSIFITDWKNYAAINEIYAEFFPGDKPARFCIQCGLVKPDALVEIATIAHIA 127
                                    |-     |  21        31        41        51        61        71        81        91       101       111       121      
                                   10     17                                                   70-MSE                                                     


Chain B from PDB  Type:PROTEIN  Length:125
 aligned with RUTC_ECOL6 | P0AFQ6 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:127
                             1                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       
           RUTC_ECOL6     - -MPKSVIIPAGSSAPLAPFVPGTLADGVVYVSGTLAFDQHNNVLFADDPKAQTRHVLETIRKVIETAGGTMADVTFNSIFITDWKNYAAINEIYAEFFPGDKPARFCIQCGLVKPDALVEIATIAHI 126
               SCOP domains d3v4db_ B: aut  omated matches                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.......--.....eeee..eeeeeee.............hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee.hhhhhhhhhhhhhhhh.....eeeeee.........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------UPF0076            ------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v4d B   0 HmPKSVIIPAGSSA--APFVPGTLADGVVYVSGTLAFDQHNNVLFADDPKAQTRHVLETIRKVIETAGGTmADVTFNSIFITDWKNYAAINEIYAEFFPGDKPARFCIQCGLVKPDALVEIATIAHI 126
                             |       9   |  | 19        29        39        49        59        69|       79        89        99       109       119       
                             1-MSE      13 16                                                    70-MSE                                                    


Chain C from PDB  Type:PROTEIN  Length:126
 aligned with RUTC_ECOL6 | P0AFQ6 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:130
                              1                                                                                                                               
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128
           RUTC_ECOL6     - --MPKSVIIPAGSSAPLAPFVPGTLADGVVYVSGTLAFDQHNNVLFADDPKAQTRHVLETIRKVIETAGGTMADVTFNSIFITDWKNYAAINEIYAEFFPGDKPARFCIQCGLVKPDALVEIATIAHIAK 128
               SCOP domains d3v4dc_ C: au    tomated matches                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.....----.....eeee..eeeeeee.............hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee.hhhhhhhhhhhhhhhh.....eeeeee.........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------UPF0076            -------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v4d C  -1 GHmPKSVIIPAGS----APFVPGTLADGVVYVSGTLAFDQHNNVLFADDPKAQTRHVLETIRKVIETAGGTmADVTFNSIFITDWKNYAAINEIYAEFFPGDKPARFCIQCGLVKPDALVEIATIAHIAK 128
                              |      8  |    |18        28        38        48        58        68 |      78        88        98       108       118       128
                              1-MSE    11   16                                                    70-MSE                                                      


Chain D from PDB  Type:PROTEIN  Length:130
 aligned with RUTC_ECOL6 | P0AFQ6 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:130
                              1                                                                                                                               
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128
           RUTC_ECOL6     - --MPKSVIIPAGSSAPLAPFVPGTLADGVVYVSGTLAFDQHNNVLFADDPKAQTRHVLETIRKVIETAGGTMADVTFNSIFITDWKNYAAINEIYAEFFPGDKPARFCIQCGLVKPDALVEIATIAHIAK 128
               SCOP domains d3v4dd_ D: automated matches                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..............eeee..eeeeeee.............hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee.hhhhhhhhhhhhhhhh.....eeeeee.........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------UPF0076            -------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v4d D  -1 GHmPKSVIIPAGSSAPLAPFVPGTLADGVVYVSGTLAFDQHNNVLFADDPKAQTRHVLETIRKVIETAGGTmADVTFNSIFITDWKNYAAINEIYAEFFPGDKPARFCIQCGLVKPDALVEIATIAHIAK 128
                              |      8        18        28        38        48        58        68 |      78        88        98       108       118       128
                              1-MSE                                                               70-MSE                                                      


Chain E from PDB  Type:PROTEIN  Length:125
 aligned with RUTC_ECOL6 | P0AFQ6 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:130
                              1                                                                                                                               
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128
           RUTC_ECOL6     - --MPKSVIIPAGSSAPLAPFVPGTLADGVVYVSGTLAFDQHNNVLFADDPKAQTRHVLETIRKVIETAGGTMADVTFNSIFITDWKNYAAINEIYAEFFPGDKPARFCIQCGLVKPDALVEIATIAHIAK 128
               SCOP domains d3v4de_ E: au     tomated matches                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.....-----....eeee..eeeeeee.............hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee.hhhhhhhhhhhhhhhh.....eeeeee.........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------UPF0076            -------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v4d E  -1 GHmPKSVIIPAGS-----PFVPGTLADGVVYVSGTLAFDQHNNVLFADDPKAQTRHVLETIRKVIETAGGTmADVTFNSIFITDWKNYAAINEIYAEFFPGDKPARFCIQCGLVKPDALVEIATIAHIAK 128
                              |      8  |     18        28        38        48        58        68 |      78        88        98       108       118       128
                              1-MSE    11    17                                                   70-MSE                                                      


Chain F from PDB  Type:PROTEIN  Length:133
 aligned with RUTC_ECOL6 | P0AFQ6 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:133
                                  1                                                                                                                              
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124   
           RUTC_ECOL6     - ------MPKSVIIPAGSSAPLAPFVPGTLADGVVYVSGTLAFDQHNNVLFADDPKAQTRHVLETIRKVIETAGGTMADVTFNSIFITDWKNYAAINEIYAEFFPGDKPARFCIQCGLVKPDALVEIATIAHIA 127
               SCOP domains d3v4df_ F: automated matches                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee..............eeee..eeeeeee...hhhhh.....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee.hhhhhhhhhhhhhhhh.....eeeeee.........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------UPF0076            ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v4d F  -5 LYFQGHmPKSVIIPAGSSAPLAPFVPGTLADGVVYVSGTLAFDQHNNVLFADDPKAQTRHVLETIRKVIETAGGTmADVTFNSIFITDWKNYAAINEIYAEFFPGDKPARFCIQCGLVKPDALVEIATIAHIA 127
                                  |  4        14        24        34        44        54        64     |  74        84        94       104       114       124   
                                  1-MSE                                                               70-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, 6)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V4D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V4D)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (RUTC_ECOL6 | P0AFQ6)
molecular function
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0019740    nitrogen utilization    A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary nitrogen source, usually ammonia, and then activates genes to scavenge the last traces of the primary nitrogen source and to transport and metabolize alternative nitrogen sources. The utilization process begins when the cell or organism detects nitrogen levels, includes the activation of genes whose products detect, transport or metabolize nitrogen-containing substances, and ends when nitrogen is incorporated into the cell or organism's metabolism.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006212    uracil catabolic process    The chemical reactions and pathways resulting in the breakdown of uracil, 2,4-dioxopyrimidine, one of the pyrimidine bases occurring in RNA, but not in DNA.

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