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(-) Description

Title :  CRYSTALLOGRAPHIC STRUCTURE OF HHV-1 URACIL-DNA GLYCOSYLASE COMPLEXED WITH THE BACILLUS PHAGE PZA INHIBITOR PROTEIN P56
 
Authors :  A. R. Cole, O. Sapir, K. Ryzhenkova, G. Baltulionis, P. Hornyak, R. Savv
Date :  11 Jun 13  (Deposition) - 07 Aug 13  (Release) - 23 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.16
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B,E,F  (1x)
Biol. Unit 4:  B  (1x)
Biol. Unit 5:  C,D  (1x)
Biol. Unit 6:  E,F  (1x)
Keywords :  Udg Inhibition, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. R. Cole, S. Ofer, K. Ryzhenkova, G. Baltulionis, P. Hornyak, R. Savv
Architecturally Diverse Proteins Converge On An Analogous Mechanism To Inactivate Uracil-Dna Glycosylase.
Nucleic Acids Res. V. 41 8760 2013
PubMed-ID: 23892286  |  Reference-DOI: 10.1093/NAR/GKT633

(-) Compounds

Molecule 1 - URACIL-DNA GLYCOSYLASE
    Chains: A, B
    EC Number: 3.2.2.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 96-334
    Gene: UL2
    Organism Scientific: HERPES SIMPLEX VIRUS TYPE 1
    Organism Taxid: 10299
    Strain: STRAIN 17
    Synonym: UDG, UNG
 
Molecule 2 - EARLY PROTEIN GP1B
    Chains: C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: 1B
    Organism Scientific: BACILLUS PHAGE PZA
    Organism Taxid: 10757

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A CD  
Biological Unit 2 (1x): A     
Biological Unit 3 (1x):  B  EF
Biological Unit 4 (1x):  B    
Biological Unit 5 (1x):   CD  
Biological Unit 6 (1x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 15)

Asymmetric Unit (1, 15)
No.NameCountTypeFull Name
1ACT15Ligand/IonACETATE ION
Biological Unit 1 (1, 9)
No.NameCountTypeFull Name
1ACT9Ligand/IonACETATE ION
Biological Unit 2 (1, 7)
No.NameCountTypeFull Name
1ACT7Ligand/IonACETATE ION
Biological Unit 3 (1, 6)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
Biological Unit 5 (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
Biological Unit 6 (1, 4)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:87 , ASP A:88 , HOH A:411 , ASP C:35 , VAL C:38 , HOH C:208BINDING SITE FOR RESIDUE ACT A 301
02AC2SOFTWAREPRO A:200 , ARG A:201 , VAL A:202 , HIS A:203 , TYR A:231BINDING SITE FOR RESIDUE ACT A 302
03AC3SOFTWARELYS A:216 , HOH A:410 , TYR D:40 , THR D:43 , ILE D:47BINDING SITE FOR RESIDUE ACT A 303
04AC4SOFTWAREARG A:174 , ALA A:177 , ILE A:196 , HOH A:440BINDING SITE FOR RESIDUE ACT A 304
05AC5SOFTWAREVAL A:25 , TYR A:52 , ASN A:53 , HOH A:551BINDING SITE FOR RESIDUE ACT A 305
06AC6SOFTWARESER D:32 , LEU D:33 , SER D:34BINDING SITE FOR RESIDUE ACT A 306
07AC7SOFTWARETYR A:124 , ALA A:127 , ILE A:240 , ASP A:241 , TRP A:242 , SER A:243BINDING SITE FOR RESIDUE ACT A 307
08AC8SOFTWARETYR B:124 , ALA B:127 , ASP B:241 , TRP B:242 , SER B:243BINDING SITE FOR RESIDUE ACT B 301
09AC9SOFTWAREGLN B:87 , ASP B:88 , HOH B:453 , ASP E:35 , VAL E:38BINDING SITE FOR RESIDUE ACT B 302
10BC1SOFTWAREARG A:73 , TYR A:74 , ARG A:140 , ASP C:53 , LYS C:54 , ILE D:48 , LYS D:49 , ACT D:101BINDING SITE FOR RESIDUE ACT C 101
11BC2SOFTWAREARG A:73 , TYR A:74 , ACT C:101 , GLN D:23BINDING SITE FOR RESIDUE ACT D 101
12BC3SOFTWAREARG B:230 , GLN E:23 , TYR E:25BINDING SITE FOR RESIDUE ACT E 101
13BC4SOFTWAREHIS A:47 , GLY D:30 , ASP F:18 , LYS F:22 , GLN F:23 , TYR F:24BINDING SITE FOR RESIDUE ACT F 101
14BC5SOFTWARELYS B:216 , HOH B:401 , TYR F:40 , THR F:43 , ILE F:47BINDING SITE FOR RESIDUE ACT F 102
15BC6SOFTWAREPRO A:38 , ASN A:42 , ARG A:175 , TYR F:27 , LYS F:29BINDING SITE FOR RESIDUE ACT F 103

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4L5N)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:62 -Pro A:63
2Leu B:62 -Pro B:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4L5N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4L5N)

(-) Exons   (0, 0)

(no "Exon" information available for 4L5N)

(-) 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:229
                                                                                                                                                                                                                                                                     
               SCOP domains d4l5na_ A: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee.hhhhhhhhhh..hhhhh.eeeee.......................hhhhhhhhhhhhhhh..........hhhhhhh.eeeee....ee..........hhhhhhhhhhhhhhhhh...eeeeehhhhhhhh.......eeeee.........hhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l5n A  16 PLDWTTFRRVFLIDDAWRPLMEPELANPLTAHLLAEYNRRCQTEEVLPPREDVFSWTRYCTPDEVRVVIIGQDPYHHPGQAHGLAFSVRANVPPPPSLRNVLAAVKNCYPEARMSGHGCLEKWARDGVLLLNTTLTVKRGAAASHSRIGWDRFVGGVIRRLAARRPGLVFMLWGTHAQNAIRPDPRVHCVLKFSHPSPLSKVPFGTCQHFLVANRYLETRSISPIDWSV 244
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235         


Chain B from PDB  Type:PROTEIN  Length:227
                                                                                                                                                                                                                                                                   
               SCOP domains d4l5nb_ B: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee......hhhhh........eeeee.......................hhhhhhhhhhhhhhh..........hhhhhhh.eeeee....ee..........hhhhhhhhhhhhhhhhh...eeeeehhhhhhhh.......eeeee.........hhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l5n B  18 DWTTFRRVFLIDDAWRPLMEPELANPLTAHLLAEYNRRCQTEEVLPPREDVFSWTRYCTPDEVRVVIIGQDPYHHPGQAHGLAFSVRANVPPPPSLRNVLAAVKNCYPEARMSGHGCLEKWARDGVLLLNTTLTVKRGAAASHSRIGWDRFVGGVIRRLAARRPGLVFMLWGTHAQNAIRPDPRVHCVLKFSHPSPLSKVPFGTCQHFLVANRYLETRSISPIDWSV 244
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       


Chain C from PDB  Type:PROTEIN  Length:50
                                                                                  
               SCOP domains -------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.....eeeeeeeeehhhhhhhhhhhh..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                 4l5n C   7 LDSYDVTMLLQDDNGKQYYEYHKGLSLSDFEVLYGNTVDEIIKLRVDKIS  56
                                    16        26        36        46        56


Chain D from PDB  Type:PROTEIN  Length:49
                                                                                 
               SCOP domains ------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.....eeeeeeeeehhhhhhhhhhh...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------- Transcript
                 4l5n D   7 LDSYDVTMLLQDDNGKQYYEYHKGLSLSDFEVLYGNTVDEIIKLRVDKI  55
                                    16        26        36        46         


Chain E from PDB  Type:PROTEIN  Length:47
                                                                               
               SCOP domains ----------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....eeeeeeeeehhhhhhhhhhh...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                 4l5n E   9 SYDVTMLLQDDNGKQYYEYHKGLSLSDFEVLYGNTVDEIIKLRVDKI  55
                                    18        28        38        48       


Chain F from PDB  Type:PROTEIN  Length:48
                                                                                
               SCOP domains ------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee.....eeeeeeeeehhhhhhhhhhh...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------ Transcript
                 4l5n F   8 DSYDVTMLLQDDNGKQYYEYHKGLSLSDFEVLYGNTVDEIIKLRVDKI  55
                                    17        27        37        47
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4L5N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4L5N)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        UNG_HHV11 | P10186: 1lau 1udg 1udh 1udi 2c53 2c56 5ays

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