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(-) Description

Title :  CRYSTAL STRUCTURE OF PACI-DNA ENZYME PRODUCT COMPLEX
 
Authors :  B. W. Shen, B. L. Stoddard
Date :  16 Mar 10  (Deposition) - 21 Apr 10  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Hnh Restriction Endonuclease, Beta-Beta-Alpha-Metal Active Site, 8 Base-Pair Rare Cutter, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. W. Shen, D. F. Heiter, S. H. Chan, H. Wang, S. Y. Xu, R. D. Morgan, G. G. Wilson, B. L. Stoddard
Unusual Target Site Disruption By The Rare-Cutting Hnh Restriction Endonuclease Paci.
Structure V. 18 734 2010
PubMed-ID: 20541511  |  Reference-DOI: 10.1016/J.STR.2010.03.009

(-) Compounds

Molecule 1 - RESTRICTION ENDONUCLEASE PACI
    Chains: A
    Engineered: YES
    Expression System: PSEUDOMONAS ALCALIGENES
    Expression System Plasmid: PVS1
    Expression System Strain: NEB 585
    Expression System Taxid: 43263
    Expression System Vector Type: PLASMID
    Gene: PACIR
    Organism Scientific: PSEUDOMONAS ALCALIGENES
    Organism Taxid: 43263
    Strain: NEB 585
 
Molecule 2 - DNA (5'-D(*GP*AP*GP*GP*CP*TP*TP*AP*AP*T)-3')
    Chains: B
    Engineered: YES
    Other Details: TOP STRAND PRODUCT OF PACI
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*TP*AP*AP*GP*CP*CP*TP*C)-3')
    Chains: C
    Engineered: YES
    Other Details: BOTTOM STRAND OF PACI PRODUCT
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 16)

Asymmetric Unit (6, 16)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MG1Ligand/IonMAGNESIUM ION
3NA9Ligand/IonSODIUM ION
4PT1Ligand/IonPLATINUM (II) ION
5SO42Ligand/IonSULFATE ION
6ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MG-1Ligand/IonMAGNESIUM ION
3NA-1Ligand/IonSODIUM ION
4PT-1Ligand/IonPLATINUM (II) ION
5SO44Ligand/IonSULFATE ION
6ZN-1Ligand/IonZINC ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:63 , CYS A:66 , CYS A:109 , CYS A:112BINDING SITE FOR RESIDUE ZN A 143
02AC2SOFTWARECYS A:4 , CYS A:7 , CYS A:24 , CYS A:27BINDING SITE FOR RESIDUE ZN A 144
03AC3SOFTWAREASP A:92 , ASN A:113 , HOH A:157 , HOH A:160 , DT B:10 , HOH C:7BINDING SITE FOR RESIDUE MG A 145
04AC4SOFTWAREMET A:23 , MET A:28 , DG C:14 , HOH C:102BINDING SITE FOR RESIDUE PT A 146
05AC5SOFTWAREHIS A:77 , HOH A:244BINDING SITE FOR RESIDUE NA A 147
06AC6SOFTWAREHOH A:162 , HOH C:5 , DA C:12 , HOH C:36BINDING SITE FOR RESIDUE NA C 6
07AC7SOFTWAREHOH A:171 , DA B:8BINDING SITE FOR RESIDUE NA B 11
08AC8SOFTWAREGLN A:60 , HIS A:62 , SO4 A:156 , HOH A:213 , HOH A:219BINDING SITE FOR RESIDUE NA A 148
09AC9SOFTWAREHOH A:211BINDING SITE FOR RESIDUE NA A 149
10BC1SOFTWAREALA A:12 , THR A:50 , HOH A:198 , HOH A:225BINDING SITE FOR RESIDUE NA A 150
11BC2SOFTWAREHIS A:85 , HOH A:237 , HOH A:245 , HOH A:246BINDING SITE FOR RESIDUE NA A 151
12BC3SOFTWAREHOH A:221 , HOH A:231BINDING SITE FOR RESIDUE NA A 152
13BC4SOFTWAREVAL A:127 , GLU A:130 , HOH A:202BINDING SITE FOR RESIDUE NA A 153
14BC5SOFTWAREILE A:119 , SER A:121 , ARG A:139 , HOH A:172BINDING SITE FOR RESIDUE EDO A 154
15BC6SOFTWAREHOH A:213 , HOH A:216 , HOH A:238BINDING SITE FOR RESIDUE SO4 A 155
16BC7SOFTWAREMET A:1 , TRP A:54 , TYR A:55 , GLN A:60 , ARG A:61 , NA A:148BINDING SITE FOR RESIDUE SO4 A 156

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M7K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3M7K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M7K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3M7K)

(-) Exons   (0, 0)

(no "Exon" information available for 3M7K)

(-) 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:142
 aligned with D5MNX7_PSEAC | D5MNX7 from UniProtKB/TrEMBL  Length:142

    Alignment length:142
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  
         D5MNX7_PSEAC     1 MTQCPRCQRNLAADEFYAGSSKMCKGCMTWQNLSYNANKEGHANTFTKATFLAWYGLSAQRHCGYCGISEAGFTSLHRTNPRGYHIQCLGVDRSDSFEGYSPQNARLACFICNRIKSNIFSASEMDVLGEAISKAWHGRGIA 142
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eehhhhh.......hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.......hhhhhhh..............eeee...........eeeehhhhhhhhh...hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m7k A   1 MTQCPRCQRNLAADEFYAGSSKMCKGCMTWQNLSYNANKEGHANTFTKATFLAWYGLSAQRHCGYCGISEAGFTSLHRTNPRGYHIQCLGVDRSDSFEGYSPQNARLACFICNRIKSNIFSASEMDVLGEAISKAWHGRGIA 142
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  


Chain B from PDB  Type:DNA  Length:10
                                          
                 3m7k B   1 GAGGCTTAAT  10
                                    10


Chain C from PDB  Type:DNA  Length:8
                                        
                 3m7k C  11 TAAGCCTC  18
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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 3M7K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M7K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3M7K)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A   (D5MNX7_PSEAC | D5MNX7)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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        D5MNX7_PSEAC | D5MNX7: 3ldy

(-) Related Entries Specified in the PDB File

3ldy THE SAME PROTEIN-DNA COMPLEX, UNCLEAVED