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(-) Description

Title :  CRYSTAL STRUCTURE OF DCMP DEAMINASE FROM THE CYANOPHAGE S-TIM5 IN COMPLEX WITH DTMP AND DTTP.
 
Authors :  A. Marx, A. Alian
Date :  03 Apr 14  (Deposition) - 26 Nov 14  (Release) - 14 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Deoxycytidylate Deaminase, Dcmp Deaminase, Cytidine Deaminase, S-Tim5 Cyanophage, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Marx, A. Alian
The First Crystal Structure Of A Dttp-Bound Deoxycytidylate Deaminase Validates And Details The Allosteric-Inhibitor Binding Site.
J. Biol. Chem. V. 290 682 2015
PubMed-ID: 25404739  |  Reference-DOI: 10.1074/JBC.M114.617720

(-) Compounds

Molecule 1 - DEOXYCYTIDYLATE DEAMINASE
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: CYANOPHAGE S-TIM5
    Organism Taxid: 1137745

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 27)

Asymmetric/Biological Unit (5, 27)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2MG6Ligand/IonMAGNESIUM ION
3TMP6Ligand/IonTHYMIDINE-5'-PHOSPHATE
4TTP6Ligand/IonTHYMIDINE-5'-TRIPHOSPHATE
5ZN6Ligand/IonZINC ION

(-) Sites  (27, 27)

Asymmetric Unit (27, 27)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:67 , CYS A:95 , CYS A:98 , TMP A:204 , HOH A:304binding site for residue ZN A 201
02AC2SOFTWAREASN A:52 , TTP A:203 , HOH A:301 , HOH A:305binding site for residue MG A 202
03AC3SOFTWAREHIS A:40 , GLY A:41 , TRP A:42 , GLY A:44 , THR A:45 , SER A:47 , GLY A:48 , ASN A:52 , ASN A:71 , LYS A:75 , MG A:202 , HOH A:301 , LYS B:2 , GLY B:35 , GLN D:104binding site for residue TTP A 203
04AC4SOFTWARECYS A:22 , ARG A:24 , MET A:25 , VAL A:27 , ASN A:43 , THR A:61 , HIS A:67 , ALA A:68 , GLU A:69 , CYS A:95 , TYR A:116 , ZN A:201 , HOH A:303 , HOH A:304binding site for residue TMP A 204
05AC5SOFTWAREMET A:76 , SER A:79 , GLU A:81 , MET D:76 , SER D:79 , GLU D:81binding site for residue CL A 205
06AC6SOFTWAREHIS B:67 , CYS B:95 , CYS B:98 , TMP B:203 , HOH B:305binding site for residue ZN B 201
07AC7SOFTWAREPRO B:46 , ASN B:52 , TTP B:204 , HOH B:306binding site for residue MG B 202
08AC8SOFTWARECYS B:22 , ARG B:24 , VAL B:27 , ASN B:43 , THR B:61 , VAL B:65 , HIS B:67 , ALA B:68 , GLU B:69 , CYS B:95 , TYR B:116 , ARG B:117 , ZN B:201 , HOH B:303 , HOH B:305binding site for residue TMP B 203
09AC9SOFTWARELYS A:2 , GLY A:35 , HIS B:40 , GLY B:41 , TRP B:42 , GLY B:44 , THR B:45 , SER B:47 , GLY B:48 , ASN B:52 , ASN B:71 , LYS B:75 , MG B:202 , GLN C:104binding site for residue TTP B 204
10AD1SOFTWAREMET B:76 , SER B:79 , GLU B:81 , MET C:76 , SER C:79 , GLU C:81binding site for residue CL B 205
11AD2SOFTWAREHIS C:67 , CYS C:95 , CYS C:98 , TMP C:204 , HOH C:307binding site for residue ZN C 201
12AD3SOFTWAREASN C:52 , TTP C:203binding site for residue MG C 202
13AD4SOFTWAREGLN B:104 , HIS C:40 , GLY C:41 , TRP C:42 , GLY C:44 , THR C:45 , SER C:47 , GLY C:48 , ASN C:52 , ASN C:71 , MG C:202binding site for residue TTP C 203
14AD5SOFTWAREARG C:24 , VAL C:27 , ASN C:43 , THR C:61 , HIS C:67 , ALA C:68 , GLU C:69 , SER C:93 , CYS C:95 , TYR C:116 , ZN C:201 , HOH C:304 , HOH C:307binding site for residue TMP C 204
15AD6SOFTWAREHIS D:67 , CYS D:95 , CYS D:98 , TMP D:204 , HOH D:304binding site for residue ZN D 201
16AD7SOFTWAREASN D:52 , TTP D:203 , HOH D:305binding site for residue MG D 202
17AD8SOFTWAREHIS D:40 , GLY D:41 , TRP D:42 , GLY D:44 , THR D:45 , SER D:47 , GLY D:48 , ASN D:52 , ASN D:71 , MG D:202 , HOH D:305 , LYS E:2binding site for residue TTP D 203
18AD9SOFTWARECYS D:22 , ARG D:24 , MET D:25 , VAL D:27 , ASN D:43 , THR D:61 , HIS D:67 , ALA D:68 , GLU D:69 , CYS D:95 , TYR D:116 , ZN D:201 , HOH D:304 , HOH D:306binding site for residue TMP D 204
19AE1SOFTWAREHIS E:67 , CYS E:95 , CYS E:98 , HOH E:303binding site for residue ZN E 201
20AE2SOFTWAREPRO E:46 , ASN E:52 , TTP E:203 , HOH E:302binding site for residue MG E 202
21AE3SOFTWARELYS D:2 , HIS E:40 , GLY E:41 , TRP E:42 , GLY E:44 , THR E:45 , SER E:47 , GLY E:48 , ASN E:52 , ASN E:71 , MG E:202 , GLN F:104binding site for residue TTP E 203
22AE4SOFTWAREARG E:24 , VAL E:27 , ASN E:43 , THR E:61 , HIS E:67 , ALA E:68 , GLU E:69 , SER E:93 , PRO E:94 , CYS E:95 , TYR E:116 , HOH E:303 , HOH E:304 , HOH E:305binding site for residue TMP E 204
23AE5SOFTWAREMET E:76 , SER E:79 , GLU E:81 , MET F:76 , SER F:79 , GLU F:81binding site for residue CL E 205
24AE6SOFTWAREHIS F:67 , CYS F:95 , CYS F:98 , TMP F:204 , HOH F:306binding site for residue ZN F 201
25AE7SOFTWAREASN F:52 , TTP F:203 , HOH F:301binding site for residue MG F 202
26AE8SOFTWARELYS C:2 , MET D:1 , GLN E:104 , HIS F:40 , GLY F:41 , TRP F:42 , GLY F:44 , THR F:45 , SER F:47 , GLY F:48 , ASN F:52 , ASN F:71 , MG F:202 , HOH F:301binding site for residue TTP F 203
27AE9SOFTWARECYS F:22 , ARG F:24 , VAL F:27 , ASN F:43 , THR F:61 , HIS F:67 , ALA F:68 , GLU F:69 , CYS F:95 , TYR F:116 , ZN F:201 , HOH F:304 , HOH F:306binding site for residue TMP F 204

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:54
2B:22 -B:54
3C:22 -C:54
4D:22 -D:54
5E:22 -E:54
6F:22 -F:54

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4P9D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P9D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P9D)

(-) Exons   (0, 0)

(no "Exon" information available for 4P9D)

(-) 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:135
                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.........eeeee....eeeeee........................hhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhhh..eeeeee....hhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p9d A   1 MKPEIKEAYMKTAELFSQVSNCKRMKVGAIVVKNGSILAHGWNGTPSGFHTNCCELEDGSTNPFVLHAEQNALVKMAKSSESIDGSELFCTHSPCPDCSKMIAQAGVKKVYYRNEYRITDGIDVLQQLGVEVEKM 135
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     


Chain B from PDB  Type:PROTEIN  Length:135
                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.........eeeeee..eeeeeee........................hhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhh...eeeeee....hhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p9d B   1 MKPEIKEAYMKTAELFSQVSNCKRMKVGAIVVKNGSILAHGWNGTPSGFHTNCCELEDGSTNPFVLHAEQNALVKMAKSSESIDGSELFCTHSPCPDCSKMIAQAGVKKVYYRNEYRITDGIDVLQQLGVEVEKM 135
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     


Chain C from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh.......eeeeee..eeeeeee........................hhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhh...eeeeee....hhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p9d C   0 HMKPEIKEAYMKTAELFSQVSNCKRMKVGAIVVKNGSILAHGWNGTPSGFHTNCCELEDGSTNPFVLHAEQNALVKMAKSSESIDGSELFCTHSPCPDCSKMIAQAGVKKVYYRNEYRITDGIDVLQQLGVEVEKM 135
                                     9        19        29        39        49        59        69        79        89        99       109       119       129      


Chain D from PDB  Type:PROTEIN  Length:135
                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.........eeeeee..eeeeeee........................hhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhh...eeeeee....hhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p9d D   1 MKPEIKEAYMKTAELFSQVSNCKRMKVGAIVVKNGSILAHGWNGTPSGFHTNCCELEDGSTNPFVLHAEQNALVKMAKSSESIDGSELFCTHSPCPDCSKMIAQAGVKKVYYRNEYRITDGIDVLQQLGVEVEKM 135
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     


Chain E from PDB  Type:PROTEIN  Length:135
                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.........eeeeee..eeeeeee........................hhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhh...eeeeee.....hhhhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p9d E   1 MKPEIKEAYMKTAELFSQVSNCKRMKVGAIVVKNGSILAHGWNGTPSGFHTNCCELEDGSTNPFVLHAEQNALVKMAKSSESIDGSELFCTHSPCPDCSKMIAQAGVKKVYYRNEYRITDGIDVLQQLGVEVEKM 135
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     


Chain F from PDB  Type:PROTEIN  Length:135
                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.........eeeeee..eeeeeee........................hhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhh...eeeeee....hhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p9d F   1 MKPEIKEAYMKTAELFSQVSNCKRMKVGAIVVKNGSILAHGWNGTPSGFHTNCCELEDGSTNPFVLHAEQNALVKMAKSSESIDGSELFCTHSPCPDCSKMIAQAGVKKVYYRNEYRITDGIDVLQQLGVEVEKM 135
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4P9D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P9D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P9D)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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        H6WFU3_9CAUD | H6WFU3: 4p9c 4p9e

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4p9c 4p9e