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(-) Description

Title :  CRYSTAL STRUCTURE OF LAMBDA EXONUCLEASE IN COMPLEX WITH DNA AND CA2+
 
Authors :  J. Zhang, C. E. Bell
Date :  04 Nov 14  (Deposition) - 19 Nov 14  (Release) - 10 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.38
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Exonuclease, Type Ii Restriction Endonuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Zhang, X. Pan, C. E. Bell
Crystal Structure Of Lambda Exonuclease In Complex With Dna And Ca(2+).
Biochemistry V. 53 7415 2014
PubMed-ID: 25370446  |  Reference-DOI: 10.1021/BI501155Q

(-) Compounds

Molecule 1 - EXONUCLEASE
    Chains: A, B, C
    EC Number: 3.1.11.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (AI)
    Expression System Taxid: 511693
    Gene: EXO, RED-ALPHA, REDX
    Organism Scientific: ENTEROBACTERIA PHAGE LAMBDA
    Organism Taxid: 10710
 
Molecule 2 - DNA (5'-D(*TP*T*TP*CP*GP*GP*TP*AP*CP*AP*GP*TP*AP*G)-3')
    Chains: D
    Engineered: YES
    Organism Scientific: SYNTHETIC
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*AP*GP*CP*TP*AP*CP*TP*GP*TP*AP*CP*CP*GP*A)-3')
    Chains: E
    Engineered: YES
    Organism Scientific: SYNTHETIC
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:119 , GLU A:129binding site for residue CA A 301
2AC2SOFTWAREARG A:28 , THR A:33 , ALA A:34 , SER A:35 , ALA A:115 , CYS A:116 , SER A:117 , HOH A:440binding site for residue PO4 A 302
3AC3SOFTWAREASP B:119 , GLU B:129 , LEU B:130 , DG E:2 , HOH E:103binding site for residue CA B 301
4AC4SOFTWAREARG C:28 , THR C:33 , ALA C:34 , SER C:35 , ALA C:115 , CYS C:116 , SER C:117 , GLN C:157binding site for residue PO4 C 301
5AC5SOFTWAREASP C:119 , GLU C:129 , HOH C:463binding site for residue CA C 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:19 -Gly A:20

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WUZ)

(-) Sequences/Alignments

Asymmetric/Biological 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:226
                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.hhhhh...hhhhhhh....ee..hhhhhhh........hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh..ee....ee......eee...eee....eeeee...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..eeeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wuz A   1 MTPDIILQRTGIDVRAVEQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDMKMSYFHTLLAEVCTGVAPEVNAKALAWGKQYENDARTLFEFTSGVNVTESPIIYRDESMRTACSPDGLCSDGNGLELKCPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKNAWYFANYDPRMKREGLHYVVIERDEKYMASFDEIVPEFIEKMDEALAEIGFVFGEQWR 226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      


Chain B from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.........hhhhhhhhh..ee...hhhhhh........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh..ee....ee......eee...eee....eeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wuz B   1 MTPDIILQRTGIDVRAVEQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDMKMSYFHTLLAEVCTGVAPEVNAKALAWGKQYENDARTLFEFTSGVNVTESPIIYRDESMRTACSPDGLCSDGNGLELKCPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKNAWYFANYDPRMKREGLHYVVIERDEKYMASFDEIVPEFIEKMDEALAEIGFVFGEQWR 226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      


Chain C from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.hhhhh...hhhhhhhhh..ee.hhhhhh..........hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh..ee....ee......eee...eee....eeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wuz C   2 TPDIILQRTGIDVRAVEQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDMKMSYFHTLLAEVCTGVAPEVNAKALAWGKQYENDARTLFEFTSGVNVTESPIIYRDESMRTACSPDGLCSDGNGLELKCPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKNAWYFANYDPRMKREGLHYVVIERDEKYMASFDEIVPEFIEKMDEALAEIGFVFGEQWR 226
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221     


Chain D from PDB  Type:DNA  Length:12
                                            
                 4wuz D   1 TCGGTACAGTAG  12
                                    10  


Chain E from PDB  Type:DNA  Length:14
                                              
                 4wuz E   1 AGCTACTGTACCGA  14
                                    10
   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  (0, 0)

(no "SCOP Domain" information available for 4WUZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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    Gln A:19 - Gly A:20   [ RasMol ]  
 

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 Related Entries

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        EXO_LAMBD | P03697: 1avq 3slp 3sm4

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