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(-) Description

Title :  DCTP DEAMINASE-DUTPASE FROM BACILLUS HALODURANS
 
Authors :  C. Oehlenschlaeger, M. Loevgreen, M. Willemoes, P. Harris
Date :  08 Jan 15  (Deposition) - 18 Mar 15  (Release) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,E  (1x)
Biol. Unit 2:  B,D,F  (1x)
Keywords :  Bifunctional, Ttp Binding, Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. B. Oehlenschlger, M. N. Lvgreen, E. Reinauer, E. Lehtinen, M. L. Pind, P. Harris, J. Martinussen, M. Willemoes
Bacillus Halodurans Strain C125 Encodes And Synthesizes Enzymes From Both Known Pathways To Form Dump Directly From Cytosine Deoxyribonucleotides.
Appl. Environ. Microbiol. V. 81 3395 2015
PubMed-ID: 25746996  |  Reference-DOI: 10.1128/AEM.00268-15

(-) Compounds

Molecule 1 - DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE
    Chains: A, C, E, B, D, F
    EC Number: 3.5.4.13
    Engineered: YES
    Expression System: BACILLUS HALODURANS C-125
    Expression System Taxid: 272558
    Gene: DCD, BH0368
    Organism Scientific: BACILLUS HALODURANS C-125
    Organism Taxid: 272558
    Synonym: DCTP DEAMINASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1MG6Ligand/IonMAGNESIUM ION
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
3TTP6Ligand/IonTHYMIDINE-5'-TRIPHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
3TTP3Ligand/IonTHYMIDINE-5'-TRIPHOSPHATE
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
3TTP3Ligand/IonTHYMIDINE-5'-TRIPHOSPHATE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:110 , GLY A:112 , ASP A:115 , PHE A:118 , ILE A:122 , THR A:123 , TYR A:157 , GLY A:159 , LYS A:160 , TYR A:161 , GLN A:164 , HOH A:312 , HOH A:325 , HOH A:333 , ARG E:98 , SER E:99 , SER E:100 , ARG E:103 , GLN E:144 , MG E:201 , HOH E:319 , HOH E:320 , HOH E:330binding site for residue TTP A 201
02AC2SOFTWAREHOH A:313 , HOH A:314 , TTP C:201 , HOH C:308binding site for residue MG A 202
03AC3SOFTWAREPRO A:88 , ASN A:89 , HIS A:90 , HOH A:307 , HOH A:310binding site for residue PEG A 203
04AC4SOFTWAREARG A:98 , SER A:99 , SER A:100 , ARG A:103 , GLN A:144 , MG A:202 , HOH A:313 , HOH A:314 , HOH A:321 , ASN C:110 , GLY C:112 , VAL C:114 , ASP C:115 , PHE C:118 , ILE C:122 , THR C:123 , TYR C:157 , GLY C:159 , LYS C:160 , TYR C:161 , GLN C:164 , HOH C:308 , HOH C:315 , HOH C:329binding site for residue TTP C 201
05AC5SOFTWAREHOH C:309 , TTP E:202 , HOH E:321 , HOH E:322binding site for residue MG C 202
06AC6SOFTWARETTP A:201 , HOH A:312 , HOH E:319 , HOH E:320binding site for residue MG E 201
07AC7SOFTWAREARG C:98 , SER C:99 , SER C:100 , ARG C:103 , GLN C:144 , MG C:202 , HOH C:309 , HOH C:311 , VAL E:95 , ASN E:110 , GLY E:112 , ASP E:115 , PHE E:118 , ILE E:122 , THR E:123 , TYR E:157 , GLY E:159 , LYS E:160 , TYR E:161 , GLN E:164 , HOH E:321 , HOH E:322 , HOH E:324binding site for residue TTP E 202
08AC8SOFTWAREASN B:110 , GLY B:112 , ASP B:115 , PHE B:118 , ILE B:122 , THR B:123 , TYR B:157 , GLY B:159 , LYS B:160 , TYR B:161 , GLN B:164 , HOH B:357 , ARG F:98 , SER F:99 , SER F:100 , ARG F:103 , GLN F:144 , MG F:201 , HOH F:306 , HOH F:307 , HOH F:316 , HOH F:318binding site for residue TTP B 201
09AC9SOFTWAREHOH B:317 , HOH B:318 , TTP D:201 , HOH D:318binding site for residue MG B 202
10AD1SOFTWAREARG B:98 , SER B:99 , SER B:100 , ARG B:103 , GLN B:144 , MG B:202 , HOH B:317 , HOH B:318 , HOH B:345 , ASN D:110 , GLY D:112 , ASP D:115 , PHE D:118 , ILE D:122 , THR D:123 , TYR D:157 , GLY D:159 , LYS D:160 , TYR D:161 , GLN D:164 , HOH D:318 , HOH D:320 , HOH D:333 , HOH D:354binding site for residue TTP D 201
11AD2SOFTWAREHOH D:319 , HOH D:356 , TTP F:202 , HOH F:308binding site for residue MG D 202
12AD3SOFTWARETTP B:201 , HOH B:316 , HOH F:306 , HOH F:307binding site for residue MG F 201
13AD4SOFTWAREARG D:98 , SER D:99 , SER D:100 , ARG D:103 , GLN D:144 , MG D:202 , HOH D:319 , HOH D:356 , ASN F:110 , ASP F:115 , PHE F:118 , ILE F:122 , THR F:123 , TYR F:157 , GLY F:159 , LYS F:160 , TYR F:161 , GLN F:164 , HOH F:308 , HOH F:320 , HOH F:332binding site for residue TTP F 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XJC)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Thr A:20 -Pro A:21
2Thr C:20 -Pro C:21
3Thr E:20 -Pro E:21
4Thr B:20 -Pro B:21
5Thr D:20 -Pro D:21
6Thr F:20 -Pro F:21

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XJC)

(-) 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
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhhh...eee..hhhhh....eeee...eeeee...............eeeee....eeee....eeeeeeeeeee....eeeeeeehhhhhh..eee...eee....eeeeeeeeee.....eeee...eeeeeeeeeee...................hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xjc A   1 MILSGKTISEKLTEKELEITPLTEEQIQPASVDLRLGPHFVTIDDSKEAVISFERPIRYREWTTSDETIVLPPHTFLLATTMETVKLPNHLTAFVEGRSSVGRLGLFIQNAGWVDPGFNGQITLELFNANRLPIELPIGRRICQLVFAEVTGEVAPYQGKYLFQKGATMSEIYKDAF 177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       


Chain B from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhhh...eee..hhh.ee..eeeee...eeeee.......ee......eeeee....eeee....eeeeeeeeeee....eeeeeeehhhhhh..eee...eee....eeeeeeeeee.....eeee...eeeeeeeeeee...................hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xjc B   1 MILSGKTISEKLTEKELEITPLTEEQIQPASVDLRLGPHFVTIDDSKEAVISFERPIRYREWTTSDETIVLPPHTFLLATTMETVKLPNHLTAFVEGRSSVGRLGLFIQNAGWVDPGFNGQITLELFNANRLPIELPIGRRICQLVFAEVTGEVAPYQGKYLFQKGATMSEIYKDAF 177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       


Chain C from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhhh...eee..hhhhh....eeee...eeeee...............eeeee....eeee....eeeeeeeeeee....eeeeeeehhhhhh..eee...eee....eeeeeeeeee.....eeee...eeeeeeeeeee...................hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xjc C   1 MILSGKTISEKLTEKELEITPLTEEQIQPASVDLRLGPHFVTIDDSKEAVISFERPIRYREWTTSDETIVLPPHTFLLATTMETVKLPNHLTAFVEGRSSVGRLGLFIQNAGWVDPGFNGQITLELFNANRLPIELPIGRRICQLVFAEVTGEVAPYQGKYLFQKGATMSEIYKDAF 177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       


Chain D from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhhh...eee..hhh.ee..eeeee...eeeee...............eeeee....eeee....eeeeeeeeeee....eeeeeeehhhhhh..eee...eee....eeeeeeeeee.....eeee...eeeeeeeeeee...................hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xjc D   1 MILSGKTISEKLTEKELEITPLTEEQIQPASVDLRLGPHFVTIDDSKEAVISFERPIRYREWTTSDETIVLPPHTFLLATTMETVKLPNHLTAFVEGRSSVGRLGLFIQNAGWVDPGFNGQITLELFNANRLPIELPIGRRICQLVFAEVTGEVAPYQGKYLFQKGATMSEIYKDAF 177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       


Chain E from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhhh...eee..hhh.ee..eeeee...eeeee...............eeeee....eeee....eeeeeeeeeee....eeeeeeehhhhhh..eee...eee....eeeeeeeeee.....eeee...eeeeeeeeeee...................hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xjc E   1 MILSGKTISEKLTEKELEITPLTEEQIQPASVDLRLGPHFVTIDDSKEAVISFERPIRYREWTTSDETIVLPPHTFLLATTMETVKLPNHLTAFVEGRSSVGRLGLFIQNAGWVDPGFNGQITLELFNANRLPIELPIGRRICQLVFAEVTGEVAPYQGKYLFQKGATMSEIYKDAF 177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       


Chain F from PDB  Type:PROTEIN  Length:169
                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhhh...eee..hhhhh....eeee...eeee............eeee....eeee....eeeeeeeeeee....eeeeeeehhhhhh..eee...eee....eeeeeeeeee.....eeee...eeeeeeeeeee....................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xjc F   1 MILSGKTISEKLTEKELEITPLTEEQIQPASVDLRLGPHFVTIAVISFERPIRYREWTTSDETIVLPPHTFLLATTMETVKLPNHLTAFVEGRSSVGRLGLFIQNAGWVDPGFNGQITLELFNANRLPIELPIGRRICQLVFAEVTGEVAPYQGKYLFQKGATMSEIYK 174
                                    10        20        30        40  ||    55        65        75        85        95       105       115       125       135       145       155       165         
                                                                     43|                                                                                                                             
                                                                      49
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  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 4XJC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

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