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(-) Description

Title :  1.6A RESOLUTION STRUCTURE OF ARCHAEOGLOBUS FULGIDUS HJC, A HOLLIDAY JUNCTION RESOLVASE FROM AN ARCHAEAL HYPERTHERMOPHILE
 
Authors :  C. Carolis, C. Koehler, C. Sauter, J. Basquin, D. Suck, I. Toeroe
Date :  17 Mar 09  (Deposition) - 24 Mar 09  (Release) - 24 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Type Ii Restriction Endonuclease, Hydrolase, Dna Binding Protein, Holliday Junction Resolvase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Carolis, C. Koehler, C. Sauter, J. Basquin, D. Suck, I. Toeroe
1. 6 A Resolution Structure Of Archaeoglobus Fulgidus Hjc, A Holliday Junction Resolvase From An Archaeal Hyperthermophile
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HJC
    Atcc: 49558
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector: PETM12
    Fragment: RESIDUES 2-136
    Mutation: YES
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234
    Other Details: GERMAN COLLECTION OF MICROORGANISMS (DSM)
    Strain: 4304

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2NH45Ligand/IonAMMONIUM ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2NH42Ligand/IonAMMONIUM ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2NH43Ligand/IonAMMONIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU B:62 , SER B:63 , GLU B:66 , HOH B:2071BINDING SITE FOR RESIDUE NH4 B1130
02AC2SOFTWAREASP C:110 , GLU C:111BINDING SITE FOR RESIDUE NH4 C1126
03AC3SOFTWARELYS D:53 , MET D:54 , ARG D:55 , ACT D:1130BINDING SITE FOR RESIDUE NH4 D1128
04AC4SOFTWAREACT A:1130 , HOH A:2026 , HOH A:2151 , HOH A:2153BINDING SITE FOR RESIDUE NH4 A1132
05AC5SOFTWARELYS C:56 , GLU C:57 , ACT C:1128BINDING SITE FOR RESIDUE NH4 C1127
06AC6SOFTWAREARG A:45 , PHE A:128 , NH4 A:1132 , HOH A:2149BINDING SITE FOR RESIDUE ACT A1130
07AC7SOFTWARELYS C:105 , ALA D:64 , ARG D:102 , GLU D:104 , LYS D:105 , HOH D:2127 , HOH D:2150BINDING SITE FOR RESIDUE ACT D1129
08AC8SOFTWAREGLU A:111 , TYR A:114 , PRO A:115 , GLU B:57 , LEU B:58 , LEU B:87 , HOH B:2134 , HOH B:2135BINDING SITE FOR RESIDUE ACT B1131
09AC9SOFTWARELYS D:53 , ARG D:55 , NH4 D:1128 , HOH D:2051BINDING SITE FOR RESIDUE ACT D1130
10BC1SOFTWAREALA A:91 , TRP A:92 , ARG A:93 , GLU A:119 , HOH A:2112 , GLU B:111BINDING SITE FOR RESIDUE ACT A1131
11BC2SOFTWAREARG C:55 , LYS C:56 , NH4 C:1127 , HOH C:2088BINDING SITE FOR RESIDUE ACT C1128

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WCW)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:58 -Pro A:59
2Leu B:58 -Pro B:59
3Leu C:58 -Pro C:59
4Leu D:58 -Pro D:59

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WCW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WCW)

(-) Exons   (0, 0)

(no "Exon" information available for 2WCW)

(-) 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:126
 aligned with HJC_ARCFU | O28314 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:126
                                    13        23        33        43        53        63        73        83        93       103       113       123      
            HJC_ARCFU     4 KGTRFERDLLVELWKAGFAAIRVAGSGVSPFPCPDIVAGNGRTYLAIEVKMRKELPLYLSADEVEQLVTFARGFGAEAYVALKLPRKKWRFFPVQMLERTEKNFKIDESVYPLGLEIAEVAGKFFQ 129
               SCOP domains d2wcwa_ A: automated matches                                                                                                   SCOP domains
               CATH domains 2wcwA00 A:4-129  [code=3.40.1350.10, no name defined]                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh..eeee.............eeee....eeeeeeee.....eeeehhhhhhhhhhhhhhh.eeeeeee......eeee.hhhee...eeee...hhhhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wcw A   4 KGTRFERDLLVELWKAGFAAIRVAGAGVSPFPCPDIVAGNGRTYLAIEVKMRKELPLYLSADEVEQLVTFARGFGAEAYVALKLPRAAWRFFPVQMLERTEKNFKIDESVYPLGLEIAEVAGKFFQ 129
                                    13        23        33        43        53        63        73        83        93       103       113       123      


Chain B from PDB  Type:PROTEIN  Length:122
 aligned with HJC_ARCFU | O28314 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:127
                                    12        22        32        42        52        62        72        82        92       102       112       122       
            HJC_ARCFU     3 SKGTRFERDLLVELWKAGFAAIRVAGSGVSPFPCPDIVAGNGRTYLAIEVKMRKELPLYLSADEVEQLVTFARGFGAEAYVALKLPRKKWRFFPVQMLERTEKNFKIDESVYPLGLEIAEVAGKFFQ 129
               SCOP domains d2wcwb_ B: automated match     es                                                                                               SCOP domains
               CATH domains 2wcwB00 B:3-129  [code=3.4     0.1350.10, no name defined]                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh..eeee...-----.....eeee....eeeeeeee.....eeeehhhhhhhhhhhhhhh.eeeeeee......eeee.hhhee...eeee...hhhhh.hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wcw B   3 SKGTRFERDLLVELWKAGFAAIRVAG-----FPCPDIVAGNGRTYLAIEVKMRKELPLYLSADEVEQLVTFARGFGAEAYVALKLPRAAWRFFPVQMLERTEKNFKIDESVYPLGLEIAEVAGKFFQ 129
                                    12        22     |   - |      42        52        62        72        82        92       102       112       122       
                                                    28    34                                                                                               


Chain C from PDB  Type:PROTEIN  Length:121
 aligned with HJC_ARCFU | O28314 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:121
                                    14        24        34        44        54        64        74        84        94       104       114       124 
            HJC_ARCFU     5 GTRFERDLLVELWKAGFAAIRVAGSGVSPFPCPDIVAGNGRTYLAIEVKMRKELPLYLSADEVEQLVTFARGFGAEAYVALKLPRKKWRFFPVQMLERTEKNFKIDESVYPLGLEIAEVAG 125
               SCOP domains d2wcwc_ C: automated matches                                                                                              SCOP domains
               CATH domains 2wcwC00 C:5-125  [code=3.40.1350.10, no name defined]                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh..eeee.............eeee....eeeeeeee.....eeehhhhhhhhhhhhhhhh.eeeeeee......eeee.hhhee....eee...hhhhh.hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wcw C   5 GTRFERDLLVELWKAGFAAIRVAGAGVSPFPCPDIVAGNGRTYLAIEVKMRKELPLYLSADEVEQLVTFARGFGAEAYVALKLPRAAWRFFPVQMLERTEKNFKIDESVYPLGLEIAEVAG 125
                                    14        24        34        44        54        64        74        84        94       104       114       124 


Chain D from PDB  Type:PROTEIN  Length:125
 aligned with HJC_ARCFU | O28314 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:125
                                    12        22        32        42        52        62        72        82        92       102       112       122     
            HJC_ARCFU     3 SKGTRFERDLLVELWKAGFAAIRVAGSGVSPFPCPDIVAGNGRTYLAIEVKMRKELPLYLSADEVEQLVTFARGFGAEAYVALKLPRKKWRFFPVQMLERTEKNFKIDESVYPLGLEIAEVAGKF 127
               SCOP domains d2wcwd_ D: automated matches                                                                                                  SCOP domains
               CATH domains 2wcwD00 D:3-127  [code=3.40.1350.10, no name defined]                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh..eeee.............eeee....eeeeeeee.....eeehhhhhhhhhhhhhhhh.eeeeeee......eeee.hhhee....eee...hhhhh.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wcw D   3 SKGTRFERDLLVELWKAGFAAIRVAGAGVSPFPCPDIVAGNGRTYLAIEVKMRKELPLYLSADEVEQLVTFARGFGAEAYVALKLPRAAWRFFPVQMLERTEKNFKIDESVYPLGLEIAEVAGKF 127
                                    12        22        32        42        52        62        72        82        92       102       112       122
   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, 4)

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

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2WCW)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (HJC_ARCFU | O28314)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008821    crossover junction endodeoxyribonuclease activity    Catalysis of the endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction).
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
biological process
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HJC_ARCFU | O28314: 2wcz 2wiw 2wiz 2wj0

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2WCW)