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(-) Description

Title :  CRYSTAL STRUCTURE OF OPEN BACILLUS FRAGMENT DNA POLYMERASE BOUND TO DNA AND DTTP
 
Authors :  E. Y. Wu
Date :  25 Feb 15  (Deposition) - 22 Jul 15  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Protein-Dna Complex, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. R. Miller, L. S. Beese, C. A. Parish, E. Y. Wu
The Closing Mechanism Of Dna Polymerase I At Atomic Resolution.
Structure V. 23 1609 2015
PubMed-ID: 26211612  |  Reference-DOI: 10.1016/J.STR.2015.06.016

(-) Compounds

Molecule 1 - DNA POLYMERASE
    Chains: A, D
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
 
Molecule 2 - PRIMER DNA
    Chains: B, E
    Engineered: YES
    Fragment: PRIMER DNA OLIGONUCLEOTIDE
    Mutation: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - TEMPLATE DNA
    Chains: C, F
    Engineered: YES
    Fragment: TEMPLATE DNA OLIGONUCLEOTIDE
    Mutation: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric Unit (5, 8)
No.NameCountTypeFull Name
12DT2Mod. Nucleotide3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
2CME2Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
3SO41Ligand/IonSULFATE ION
4SUC2Ligand/IonSUCROSE
5TTP1Ligand/IonTHYMIDINE-5'-TRIPHOSPHATE
Biological Unit 1 (4, 4)
No.NameCountTypeFull Name
12DT1Mod. Nucleotide3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
2CME1Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
3SO4-1Ligand/IonSULFATE ION
4SUC1Ligand/IonSUCROSE
5TTP1Ligand/IonTHYMIDINE-5'-TRIPHOSPHATE
Biological Unit 2 (4, 4)
No.NameCountTypeFull Name
12DT1Mod. Nucleotide3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
2CME1Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
3SO41Ligand/IonSULFATE ION
4SUC1Ligand/IonSUCROSE
5TTP-1Ligand/IonTHYMIDINE-5'-TRIPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:656 , HIS A:682 , ARG A:702 , LYS A:706 , TYR A:710 , TYR A:714 , ASP A:830 , HOH A:1121 , HOH A:1149 , HOH A:1161 , HOH A:1177 , HOH A:1179 , HOH A:1184 , HOH A:1187 , HOH A:1192 , HOH A:1261 , HOH A:1420 , HOH A:1518 , 2DT B:101 , DG C:5binding site for residue TTP A 901
2AC2SOFTWAREGLU A:325 , TYR A:327 , ASP A:372 , ARG A:375 , ASP A:408 , ILE A:605 , ASN A:607 , HOH A:1374 , HOH A:1392 , HOH A:1397 , HOH A:1443 , HOH A:1502 , HOH A:1514 , HOH A:1526binding site for residue SUC A 902
3AC3SOFTWAREGLU D:325 , TYR D:327 , ASP D:372 , ARG D:375 , LEU D:395 , ASP D:408 , ILE D:605 , ASN D:607 , HOH D:1445 , HOH D:1452 , HOH D:1470 , HOH D:1479 , HOH D:1533 , HOH D:1583 , HOH D:1595binding site for residue SUC D 901
4AC4SOFTWARELYS D:298 , MET D:299 , ALA D:300 , ARG D:343 , ARG D:677 , HOH D:1054binding site for residue SO4 D 902
5AC5SOFTWAREARG A:615 , ILE A:628 , ARG A:629 , VAL A:828 , HIS A:829 , ASP A:830 , TTP A:901 , HOH A:1429 , DC B:28 , HOH B:325 , HOH B:331 , DA C:6 , DG C:7binding site for residue 2DT B 101
6AC6SOFTWAREARG D:615 , GLN D:624 , ASN D:625 , ILE D:626 , PRO D:627 , ILE D:628 , ARG D:629 , VAL D:828 , HIS D:829 , ASP D:830 , HOH D:1266 , HOH D:1597 , DG E:27 , HOH E:205 , HOH E:210 , HOH E:226 , HOH E:227 , HOH E:228 , HOH E:231 , DA F:6 , DG F:7binding site for Di-nucleotide 2DT E 101 and DC E 28

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Glu A:620 -Pro A:621
2Gly D:430 -Lys D:431
3Gly D:432 -Ala D:433
4Ala D:433 -Lys D:434
5Glu D:620 -Pro D:621

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YFU)

(-) 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:579
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....hhhhh..eeeeeee............eeeeee..eeeeehhhhhh.hhhhhhhhh....eeee.hhhhhhhhhhhh......eeeehhhhhhhhhhhhh..hhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh........ee..ee..hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee..eee.........eee..........hhhhhhhhh.ee.....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.....eee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...eeeeeee..hhhhhhhhhhhhhhhh........eeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yfu A 298 KMAFTLADRVTEEMLADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELcGVSFDLLLAAYLLDPAQGVDDVAAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSPKQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPATKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEVTPNMRRQAKAVNYGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVKRYMENIVQEAKQKGYVTTLLHRRRYLPDITSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARLKEERLQAHLLLQVHDELILEAPKEEMERLCRLVPEVMEQAVTLRVPLKVDYHYGSTWYDAK 876
                                   307       317       327       337       347       357       367       377       387|      397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867         
                                                                                                                    388-CME                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:DNA  Length:9
                                         
                 4yfu B  21 CATGATGCt 101
                                   ||
                                  28|
                                  101-2DT


Chain C from PDB  Type:DNA  Length:11
                                           
                 4yfu C   4 CGAGCATCATG  14
                                    13 


Chain D from PDB  Type:PROTEIN  Length:580
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...hhhhh..eeeeeee............eeeeee..eeeeehhhhhh.hhhhhhhhhh...eeee.hhhhhhhhhhh.......eeeehhhhhhhhhhhhh..hhhhhhhh.......hhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh........ee..ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee..eee.........eee..........hhhhhhhhh.ee.....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.....eee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...eeeeeee..hhhhhhhhhhhhhhh.........eeeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yfu D 297 KKMAFTLADRVTEEMLADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELcGVSFDLLLAAYLLDPAQGVDDVAAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSPKQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPATKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEVTPNMRRQAKAVNYGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVKRYMENIVQEAKQKGYVTTLLHRRRYLPDITSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARLKEERLQAHLLLQVHDELILEAPKEEMERLCRLVPEVMEQAVTLRVPLKVDYHYGSTWYDAK 876
                                   306       316       326       336       346       356       366       376       386 |     396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876
                                                                                                                     388-CME                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    


Chain E from PDB  Type:DNA  Length:9
                                         
                 4yfu E  21 CATGATGCt 101
                                   ||
                                  28|
                                  101-2DT


Chain F from PDB  Type:DNA  Length:14
                                              
                 4yfu F   1 GAGCGAGCATCATG  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 4YFU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

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  4yfu
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  2.7.7.7
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        E1C9K5_GEOSE | E1C9K5: 2xo7 2xy5 2xy6 2xy7 2y1i 2y1j 4b9l 4b9m 4b9n 4b9s 4b9t 4b9u 4b9v 4dsi 4dsj 4dsk 4dsl 4dwi 4uqg

(-) Related Entries Specified in the PDB File

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