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(-) Description

Title :  STRUCTURE OF 5-CHLOROURACIL MODIFIED A:U BASE PAIRS
 
Authors :  A. Patra, M. Egli
Date :  02 Nov 12  (Deposition) - 19 Dec 12  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  5-Chloro-2'-Deoxyuridine, W-C Base Pair, Wobble Base Pair, Double Helix, Watson-Crick Base Pairing Pattern, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Patra, J. Harp, P. S. Pallan, L. Zhao, M. Abramov, P. Herdewijn, M. Egli
Structure, Stability And Function Of 5-Chlorouracil Modifie A:U And G:U Base Pairs.
Nucleic Acids Res. V. 41 2689 2013
PubMed-ID: 23275540  |  Reference-DOI: 10.1093/NAR/GKS1316

(-) Compounds

Molecule 1 - RIBONUCLEASE H
    Chains: A, B
    EC Number: 3.1.26.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: RNHA, BH0863
    Mutation: YES
    Organism Scientific: BACILLUS HALODURANS
    Organism Taxid: 272558
    Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125
    Synonym: RNASE H
 
Molecule 2 - DNA (5'-D(*CP*GP*CP*GP*AP*AP*(UCL)P*(UCL)P*CP*GP*CP*G)-3')
    Chains: C, D, E, F
    Engineered: YES
    Other Details: DICKERSON DODECAMER DNA, CLU7/8
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A CD  
Biological Unit 2 (1x):  B  EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GOL2Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION
4UCL8Mod. Nucleotide5-CHLORO-2'-DEOXYURIDINE 5'-(DIHYDROGEN PHOSPHATE)
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4UCL4Mod. Nucleotide5-CHLORO-2'-DEOXYURIDINE 5'-(DIHYDROGEN PHOSPHATE)
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4UCL4Mod. Nucleotide5-CHLORO-2'-DEOXYURIDINE 5'-(DIHYDROGEN PHOSPHATE)

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:71 , GLU A:109 , ASN A:132 , HOH A:340 , HOH A:378 , HOH A:385 , HOH B:339BINDING SITE FOR RESIDUE MG A 201
2AC2SOFTWAREGLY A:76 , ASN A:77 , PRO A:78 , HOH A:406 , THR B:176 , PRO B:177 , ILE B:178 , HOH B:351 , HOH B:409BINDING SITE FOR RESIDUE GOL B 201
3AC3SOFTWARETHR A:135 , DG C:2 , HOH C:103 , DG D:22 , DC D:23 , DG D:24 , HOH D:201 , HOH D:202 , HOH D:203 , HOH D:208 , HOH D:212BINDING SITE FOR RESIDUE GOL D 101
4AC4SOFTWARELYS A:141 , DG E:2 , DC E:3 , HOH E:205 , HOH E:218 , HOH E:220 , DC F:21 , DG F:22 , HOH F:206BINDING SITE FOR RESIDUE EDO E 101
5AC5SOFTWAREDG E:2 , HOH E:205 , HOH E:212 , HOH E:213 , HOH E:216 , HOH E:217BINDING SITE FOR RESIDUE MG E 102
6AC6SOFTWARELYS A:143 , THR A:173 , TYR A:174 , DG F:24 , HOH F:203BINDING SITE FOR RESIDUE EDO F 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:77 -Pro A:78
2Asn B:77 -Pro B:78

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HUG)

(-) 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:134
                                                                                                                                                                      
               SCOP domains d4huga_ A: BH0863-like Ribonuclease H                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeee...eeeeeeeee.....eeeeeeeeeeehhhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhh............hhhhhhhhhhhhhhhhhh.....eee.hhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hug A  61 EEIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADYG 194
                                    70        80        90       100       110       120       130       140       150       160       170       180       190    


Chain B from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains d4hugb_ B: BH0863-like Ribonuclease H                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeee...eeeeeeeee.....eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh.....eee.hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hug B  61 EEIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKA 191
                                    70        80        90       100       110       120       130       140       150       160       170       180       190 


Chain C from PDB  Type:DNA  Length:12
                                            
                 4hug C   1 CGCGAAxxCGCG  12
                                  ||10  
                                  7-UCL 
                                   8-UCL


Chain D from PDB  Type:DNA  Length:12
                                            
                 4hug D  13 CGCGAAxxCGCG  24
                                  ||22  
                                 19-UCL 
                                  20-UCL


Chain E from PDB  Type:DNA  Length:8
                                        
                 4hug E   1 CGCGAAxx   8
                                  ||
                                  7-UCL
                                   8-UCL


Chain F from PDB  Type:DNA  Length:9
                                         
                 4hug F  16 GAAxxCGCG  24
                               ||    
                               ||    
                              19-UCL 
                               20-UCL
   Legend:   → Mismatch (orange background)
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    → 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, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RNH1_BACHD | Q9KEI9: 1zbf 1zbi 1zbl 2g8f 2g8h 2g8i 2g8k 2g8u 2g8v 2g8w 2r7y 3d0p 3ey1 3i8d 3twh 3uld 4htu 4hue 4huf 4opj 4opk 5swm 5us2 5usa 5use 5usg 5w7n 5w7o

(-) Related Entries Specified in the PDB File

4htu STRUCTURE OF 5-CHLOROURACIL MODIFIED A:U BASE PAIR
4hue
4huf