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(-) Description

Title :  CRYSTAL STRUCTURE OF 2'-DEOXYCYTIDINE 5'-TRIPHOSPHATE DEAMINASE FROM AGROBACTERIUM TUMEFACIENS
 
Authors :  R. Zhang, A. Dong, X. Xu, A. Savchenko, A. M. Edwards, A. Joachimiak, Mid Center For Structural Genomics (Mcsg)
Date :  13 Sep 07  (Deposition) - 02 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,X,Y
Biol. Unit 1:  A,B,C,D,X,Y  (1x)
Biol. Unit 2:  A,C,X  (1x)
Biol. Unit 3:  B,D,Y  (1x)
Keywords :  2'-Deoxycytidine 5'-Triphosphate Deaminase, Structural Genomics, Mcsg, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Zhang, A. Dong, X. Xu, H. Zheng, A. Savchenko, A. M. Edwards, A. Joachimiak
The Crystal Structure Of 2'-Deoxycytidine 5'-Triphosphate Deaminase From Agrobacterium Tumefaciens.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 2'-DEOXYCYTIDINE 5'-TRIPHOSPHATE DEAMINASE
    Atcc: 33970
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PDM68
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: DCD, AGR_C_764, ATU0434
    Organism Scientific: AGROBACTERIUM TUMEFACIENS STR.
    Organism Taxid: 176299
    Strain: C58
    Synonym: AGR_C_764P
 
Molecule 2 - SYNTHETIC PEPTIDE 1
    Chains: X
    Engineered: YES
    Other Details: SYNTHETIC PEPTIDE
    Synthetic: YES
 
Molecule 3 - SYNTHETIC PEPTIDE 2
    Chains: Y
    Engineered: YES
    Other Details: SYNTHETIC PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDXY
Biological Unit 1 (1x): ABCDXY
Biological Unit 2 (1x): A C X 
Biological Unit 3 (1x):  B D Y

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2R9Q)

(-) Sites  (0, 0)

(no "Site" information available for 2R9Q)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R9Q)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu B:194 -Asn B:195
2Ala X:1003 -Cys X:1004

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R9Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R9Q)

(-) Exons   (0, 0)

(no "Exon" information available for 2R9Q)

(-) 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:327
 aligned with A9CKA1_AGRFC | A9CKA1 from UniProtKB/TrEMBL  Length:370

    Alignment length:338
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337        
        A9CKA1_AGRFC      8 RTTGILADGAIRALFAGDKLKSEADLDVDQVQPASLDLRLGSKAYRVRASFMPGPGTRVIDKLNRFSLHEVDLSQGAVLETGCVYIVPLMESLALPADMSASANPKSSTGRLDIFTRVMTDNAQEFDKIPAGYTGPLYLEISPRTFPIVVRRGSRLSQIRFRIGHALLNESEVLKLHETETLVASENPNVTGGGIALSIDLKGFGENGLIGYRGKHHTAVVDVDKKAQHDVLDFWEPLFARGRAELILDPDEFYILVSREAVHVPPLYAAEMTPFDPLVGEFRVHYAGFFDPGFGHAQAGGTGSRAVLEVRSHEVPFILEHGQIVGRLVYEHMLEKPE  345
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2r9qA01 A:9-173  [code=2.70.40.10, no name defined]                                                                                                                  2r9qA02 A:174-346     [cod  e=2.70.40.10, no name defined]                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.hhhhhhhhhhh..eee.............eeee...eeeee..........hhhhhhhhh-.eeee....eee....eeeeeeeeeee....eeeeeeehhhhhh..eeeeeee.......ee....eeeeeeeeee....eee....eeeeeeeee.....hhhhhhhhhhhh....---....--.eeee..........eeeeee......ee..hhhhhhhhh.eeeee.....eeee.....eeeeeeeee.....eeeeeee.hhhh..eeee...ee......-----..eeeeeeeee....eeee...eeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2r9q A    9 RTTGILADGAIRALFAGDKLKSEADLDVDQVQPASLDLRLGSKAYRVRASFMPGPGTRVIDKLNRF-LHEVDLSQGAVLETGCVYIVPLMESLALPADMSASANPKSSTGRLDIFTRVMTDNAQEFDKIPAGYTGPLYLEISPRTFPIVVRRGSRLSQIRFRIGHALLNESEVLKLHETETLVA---PNVT--GIALSIDLKGFGENGLIGYRGKHHTAVVDVDKKAQHDVLDFWEPLFARGRAELILDPDEFYILVSREAVHVPPLYAAEMTPFDPLVGEFRVHYAGFFDPGFGH-----TGSRAVLEVRSHEVPFILEHGQIVGRLVYEHMLEKPE  346
                                    18        28        38        48        58        68     | |78        88        98       108       118       128       138       148       158       168       178       188   |   198|  |   208       218       228       238       248       258       268       278       288       298     |   - |     318       328       338        
                                                                                            74 |                                                                                                                 192 196  |  |                                                                                                   304   310                                    
                                                                                              76                                                                                                                        199  |                                                                                                                                                
                                                                                                                                                                                                                           202                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:342
 aligned with A9CKA1_AGRFC | A9CKA1 from UniProtKB/TrEMBL  Length:370

    Alignment length:346
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347      
        A9CKA1_AGRFC      8 RTTGILADGAIRALFAGDKLKSEADLDVDQVQPASLDLRLGSKAYRVRASFMPGPGTRVIDKLNRFSLHEVDLSQGAVLETGCVYIVPLMESLALPADMSASANPKSSTGRLDIFTRVMTDNAQEFDKIPAGYTGPLYLEISPRTFPIVVRRGSRLSQIRFRIGHALLNESEVLKLHETETLVASENPNVTGGGIALSIDLKGFGENGLIGYRGKHHTAVVDVDKKAQHDVLDFWEPLFARGRAELILDPDEFYILVSREAVHVPPLYAAEMTPFDPLVGEFRVHYAGFFDPGFGHAQAGGTGSRAVLEVRSHEVPFILEHGQIVGRLVYEHMLEKPEGLYGTGLG  353
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2r9qB01 B:9-173  [code=2.70.40.10, no name defined]                                                                                                                  2r9qB02 B:174-354  [code=2  .70.40.10, no name defined]                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.hhhhhhhhhhh..ee.........ee..eeeee...eeeee..........hhhhhhhh.-.eeee....eee....eeeeeeeeeee....eeeeeeehhhhhhh.eeeeeee.......ee....eeeeeeeeee....eee....eeeeeeeee.....hhhhhhhhhhhh...........--.eeee..........eeeeee......ee..hhhhhhhhh.eeeee.....eeee.....eeeeeeeee.....eeeeeee.hhhh..eeee...ee........-....eeeeeeeee....eeee...eeeeeeeee.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2r9q B    9 RTTGILADGAIRALFAGDKLKSEADLDVDQVQPASLDLRLGSKAYRVRASFMPGPGTRVIDKLNRF-LHEVDLSQGAVLETGCVYIVPLMESLALPADMSASANPKSSTGRLDIFTRVMTDNAQEFDKIPAGYTGPLYLEISPRTFPIVVRRGSRLSQIRFRIGHALLNESEVLKLHETETLVASENPNVT--GIALSIDLKGFGENGLIGYRGKHHTAVVDVDKKAQHDVLDFWEPLFARGRAELILDPDEFYILVSREAVHVPPLYAAEMTPFDPLVGEFRVHYAGFFDPGFGHAQ-GGTGSRAVLEVRSHEVPFILEHGQIVGRLVYEHMLEKPEGLYGTGLG  354
                                    18        28        38        48        58        68     | |78        88        98       108       118       128       138       148       158       168       178       188       198|  |   208       218       228       238       248       258       268       278       288       298       308       318       328       338       348      
                                                                                            74 |                                                                                                                        199  |                                                                                                     306 |                                              
                                                                                              76                                                                                                                           202                                                                                                       308                                              


Chain C from PDB  Type:PROTEIN  Length:331
 aligned with A9CKA1_AGRFC | A9CKA1 from UniProtKB/TrEMBL  Length:370

    Alignment length:338
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337        
        A9CKA1_AGRFC      8 RTTGILADGAIRALFAGDKLKSEADLDVDQVQPASLDLRLGSKAYRVRASFMPGPGTRVIDKLNRFSLHEVDLSQGAVLETGCVYIVPLMESLALPADMSASANPKSSTGRLDIFTRVMTDNAQEFDKIPAGYTGPLYLEISPRTFPIVVRRGSRLSQIRFRIGHALLNESEVLKLHETETLVASENPNVTGGGIALSIDLKGFGENGLIGYRGKHHTAVVDVDKKAQHDVLDFWEPLFARGRAELILDPDEFYILVSREAVHVPPLYAAEMTPFDPLVGEFRVHYAGFFDPGFGHAQAGGTGSRAVLEVRSHEVPFILEHGQIVGRLVYEHMLEKPE  345
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2r9qC01 C:9-173  [code=2.70.40.10, no name defined]                                                                                                                  2r9qC02 C:174-346  [ code=  2.70.40.10, no name defined]                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.hhhhhhhhhhh..eee.............eeee...eeeee..........hhhhhhh.--..eee....eee....eeeeeeeeeee....eeeeeeehhhhhhh.eeeeeee.......ee....eeeeeeeeee....eee....eeeeeeeee.....hhhhhhhhhhhh.....-.....--.eeee..........eeeeee......ee.......hhhh.eeeeee....eeee.....eeeeeeeee.....eeeeeee.hhhh..eeee...ee........--...eeeeeeeee....eeee...eeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2r9q C    9 RTTGILADGAIRALFAGDKLKSEADLDVDQVQPASLDLRLGSKAYRVRASFMPGPGTRVIDKLNR--LHEVDLSQGAVLETGCVYIVPLMESLALPADMSASANPKSSTGRLDIFTRVMTDNAQEFDKIPAGYTGPLYLEISPRTFPIVVRRGSRLSQIRFRIGHALLNESEVLKLHETETLVAS-NPNVT--GIALSIDLKGFGENGLIGYRGKHHTAVVDVDKKAQHDVLDFWEPLFARGRAELILDPDEFYILVSREAVHVPPLYAAEMTPFDPLVGEFRVHYAGFFDPGFGHAQ--GTGSRAVLEVRSHEVPFILEHGQIVGRLVYEHMLEKPE  346
                                    18        28        38        48        58        68    |  |78        88        98       108       118       128       138       148       158       168       178       188    | |198|  |   208       218       228       238       248       258       268       278       288       298       | -|      318       328       338        
                                                                                           73 76                                                                                                                  193 | 199  |                                                                                                     306  |                                     
                                                                                                                                                                                                                    195    202                                                                                                        309                                     


Chain D from PDB  Type:PROTEIN  Length:330
 aligned with A9CKA1_AGRFC | A9CKA1 from UniProtKB/TrEMBL  Length:370

    Alignment length:334
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337    
        A9CKA1_AGRFC      8 RTTGILADGAIRALFAGDKLKSEADLDVDQVQPASLDLRLGSKAYRVRASFMPGPGTRVIDKLNRFSLHEVDLSQGAVLETGCVYIVPLMESLALPADMSASANPKSSTGRLDIFTRVMTDNAQEFDKIPAGYTGPLYLEISPRTFPIVVRRGSRLSQIRFRIGHALLNESEVLKLHETETLVASENPNVTGGGIALSIDLKGFGENGLIGYRGKHHTAVVDVDKKAQHDVLDFWEPLFARGRAELILDPDEFYILVSREAVHVPPLYAAEMTPFDPLVGEFRVHYAGFFDPGFGHAQAGGTGSRAVLEVRSHEVPFILEHGQIVGRLVYEHML  341
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2r9qD01 D:9-173  [code=2.70.40.10, no name defined]                                                                                                                  2r9qD02 D:174-342   [code=  2.70.40.10, no name defined]                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.hhhhhhhhhhh..eee........ee..eeeee...eeeee..........hhhhhhhhh-.eeee....eee....eeeeeeeeeee....eeeeeeehhhhhhh.eeeeeee.......ee....eeeeeeeeee....eee....eeeeeeeee.....hhhhhhhhhhhh....-......--.eeee..........eeeeee......ee.......hhhh.eeeee.....eeee.....eeeeeeeee.....eeeeeee.hhhh..eeee...ee.............eeeeeeeee....eeee...eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2r9q D    9 RTTGILADGAIRALFAGDKLKSEADLDVDQVQPASLDLRLGSKAYRVRASFMPGPGTRVIDKLNRF-LHEVDLSQGAVLETGCVYIVPLMESLALPADMSASANPKSSTGRLDIFTRVMTDNAQEFDKIPAGYTGPLYLEISPRTFPIVVRRGSRLSQIRFRIGHALLNESEVLKLHETETLVA-ENPNVT--GIALSIDLKGFGENGLIGYRGKHHTAVVDVDKKAQHDVLDFWEPLFARGRAELILDPDEFYILVSREAVHVPPLYAAEMTPFDPLVGEFRVHYAGFFDPGFGHAQAGGTGSRAVLEVRSHEVPFILEHGQIVGRLVYEHML  342
                                    18        28        38        48        58        68     | |78        88        98       108       118       128       138       148       158       168       178       188   | | 198|  |   208       218       228       238       248       258       268       278       288       298       308       318       328       338    
                                                                                            74 |                                                                                                                 192 |  199  |                                                                                                                                            
                                                                                              76                                                                                                                   194     202                                                                                                                                            


Chain X from PDB  Type:PROTEIN  Length:7
                                        
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author .....ee Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                2r9q X 1000 SNPACVA 1006


Chain Y from PDB  Type:PROTEIN  Length:9
                                          
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                2r9q Y 1017 VEVPLAGAV 1025
   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 2R9Q)

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2R9Q)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (A9CKA1_AGRFC | A9CKA1)
molecular function
    GO:0008829    dCTP deaminase activity    Catalysis of the reaction: dCTP + H2O = dUTP + NH3.
biological process
    GO:0009394    2'-deoxyribonucleotide metabolic process    The chemical reactions and pathways involving a 2'-deoxyribonucleotide, a compound consisting of 2'-deoxyribonucleoside (a base linked to a 2'-deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

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    Ala X:1003 - Cys X:1004   [ RasMol ]  
    Glu B:194 - Asn B:195   [ RasMol ]  
 
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