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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC ALPHA SUBUNIT OF E. COLI REPLICATIVE DNA POLYMERASE III
 
Authors :  M. H. Lamers, R. E. Georgescu, S. G. Lee, M. O'Donnell, J. Kuriyan
Date :  18 Jul 06  (Deposition) - 19 Sep 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Dna Polymerase Iii, Dna Replication, Nucleotidyltransferase, Pol Beta, Php, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. H. Lamers, R. E. Georgescu, S. G. Lee, M. O'Donnell, J. Kuriyan
Crystal Structure Of The Catalytic Alpha Subunit Of E. Coli Replicative Dna Polymerase Iii.
Cell(Cambridge, Mass. ) V. 126 881 2006
PubMed-ID: 16959568  |  Reference-DOI: 10.1016/J.CELL.2006.07.028

(-) Compounds

Molecule 1 - DNA POLYMERASE III ALPHA SUBUNIT
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: NOVAGEN PET3D
    Expression System Strain: BL21 (DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC FRAGMENT (RESIDUES 1-917)
    Gene: DNAE
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 33)

Asymmetric/Biological Unit (2, 33)
No.NameCountTypeFull Name
1MSE30Mod. Amino AcidSELENOMETHIONINE
2PO43Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:10 , HIS A:83 , GLY A:133 , ARG A:135 , MSE A:136 , ILE A:171 , ARG A:175 , ASP A:201 , HOH A:936BINDING SITE FOR RESIDUE PO4 A 918
2AC2SOFTWARELYS A:52 , ASP A:542 , SER A:544 , PO4 A:920BINDING SITE FOR RESIDUE PO4 A 919
3AC3SOFTWARETHR A:432 , PHE A:433 , ASP A:542 , PO4 A:919 , HOH A:1016BINDING SITE FOR RESIDUE PO4 A 920

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:580 -Glu A:581
2Tyr A:663 -Pro A:664
3Gly A:735 -Ile A:736

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2HQA)

(-) 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:910
 aligned with DPO3A_ECOLI | P10443 from UniProtKB/Swiss-Prot  Length:1160

    Alignment length:910
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911
          DPO3A_ECOLI     2 SEPRFVHLRVHSDYSMIDGLAKTAPLVKKAAALGMPALAITDFTNLCGLVKFYGAGHGAGIKPIVGADFNVQCDLLGDELTHLTVLAANNTGYQNLTLLISKAYQRGYGAAGPIIDRDWLIELNEGLILLSGGRMGDVGRSLLRGNSALVDECVAFYEEHFPDRYFLELIRTGRPDEESYLHAAVELAEARGLPVVATNDVRFIDSSDFDAHEIRVAIHDGFTLDDPKRPRNYSPQQYMRSEEEMCELFADIPEALANTVEIAKRCNVTVRLGEYFLPQFPTGDMSTEDYLVKRAKEGLEERLAFLFPDEEERLKRRPEYDERLETELQVINQMGFPGYFLIVMEFIQWSKDNGVPVGPGRGSGAGSLVAYALKITDLDPLEFDLLFERFLNPERVSMPDFDVDFCMEKRDQVIEHVADMYGRDAVSQIITFGTMAAKAVIRDVGRVLGHPYGFVDRISKLIPPDPGMTLAKAFEAEPQLPEIYEADEEVKALIDMARKLEGVTRNAGKHAGGVVIAPTKITDFAPLYCDEEGKHPVTQFDKSDVEYAGLVKFDFLGLRTLTIINWALEMINKRRAKNGEPPLDIAAIPLDDKKSFDMLQRSETTAVFQLESRGMKDLIKRLQPDCFEDMIALVALFRPGPLQSGMVDNFIDRKHGREEISYPDVQWQHESLKPVLEPTYGIILYQEQVMQIAQVLSGYTLGGADMLRRAMGKKKPEEMAKQRSVFAEGAEKNGINAELAMKIFDLVEKFAGYGFNKSHSAAYALVSYQTLWLKAHYPAEFMAAVMTADMDNTEKVVGLVDECWRMGLKILPPDINSGLYHFHVNDDGEIVYGIGAIKGVGEGPIEAIIEARNKGGYFRELFDLCARTDTKKLNRRVLEKLIMSGAFDRLGPHRAALMNSLGDALKAADQ 911
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhh.....hhhhhhhhhhhh...eeee.......hhhhhhhhhhhhh.eeeeeeeeeeehhhhh...eeeeeee.hhhhhhhhhhhhhhhhhh........ee.hhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhh...................hhhhhhhhh..hhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhh..............................eehhhhhhhhhhhhhhhhh...eeee..eee.hhhhhhhhhhhhh..hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.....eeee...hhhhh..ee........ee..hhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhh..........hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...ee...........ee.....ee.hhhhh...hhhhhhhhhhhhhhhh...hhhhhhhhh.....hhhhhhhhhh.........hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hqa A   2 SEPRFVHLRVHSDYSmIDGLAKTAPLVKKAAALGmPALAITDFTNLCGLVKFYGAGHGAGIKPIVGADFNVQCDLLGDELTHLTVLAANNTGYQNLTLLISKAYQRGYGAAGPIIDRDWLIELNEGLILLSGGRmGDVGRSLLRGNSALVDECVAFYEEHFPDRYFLELIRTGRPDEESYLHAAVELAEARGLPVVATNDVRFIDSSDFDAHEIRVAIHDGFTLDDPKRPRNYSPQQYmRSEEEmCELFADIPEALANTVEIAKRCNVTVRLGEYFLPQFPTGDmSTEDYLVKRAKEGLEERLAFLFPDEEERLKRRPEYDERLETELQVINQmGFPGYFLIVmEFIQWSKDNGVPVGPGRGSGAGSLVAYALKITDLDPLEFDLLFERFLNPERVSmPDFDVDFCmEKRDQVIEHVADmYGRDAVSQIITFGTmAAKAVIRDVGRVLGHPYGFVDRISKLIPPDPGmTLAKAFEAEPQLPEIYEADEEVKALIDmARKLEGVTRNAGKHAGGVVIAPTKITDFAPLYCDEEGKHPVTQFDKSDVEYAGLVKFDFLGLRTLTIINWALEmINKRRAKNGEPPLDIAAIPLDDKKSFDmLQRSETTAVFQLESRGmKDLIKRLQPDCFEDmIALVALFRPGPLQSGmVDNFIDRKHGREEISYPDVQWQHESLKPVLEPTYGIILYQEQVmQIAQVLSGYTLGGADmLRRAmGKKKPEEmAKQRSVFAEGAEKNGINAELAmKIFDLVEKFAGYGFNKSHSAAYALVSYQTLWLKAHYPAEFmAAVmTADmDNTEKVVGLVDECWRmGLKILPPDINSGLYHFHVNDDGEIVYGIGAIKGVGEGPIEAIIEARNKGGYFRELFDLCARTDTKKLNRRVLEKLImSGAFDRLGPHRAALmNSLGDALKAADQ 911
                                    11     |  21        31    |   41        51        61        71        81        91       101       111       121       131    |  141       151       161       171       181       191       201       211       221       231       241    |  251       261       271       281    |  291       301       311       321       331   |   341   |   351       361       371       381       391       401      |411       421       431    |  441       451       461       471       481       491     | 501       511       521       531       541       551       561       571       581       591       601       611    |  621       631       641     | 651       661       671       681       691       701     | 711|      721       731       741|      751       761       771       781 |   | 791       801     | 811       821       831       841       851       861       871       881  |    891       901       911
                                          17-MSE             36-MSE                                                                                             136-MSE                                                                                                 240-MSE |                                     286-MSE                                          335-MSE   345-MSE                                               399-MSE  408-MSE      421-MSE        436-MSE                          469-MSE                     497-MSE                                                                   571-MSE                     599-MSE          616-MSE        631-MSE         647-MSE                                     691-MSE         707-MSE|     720-MSE               742-MSE                                  783-MSE   |             807-MSE                                                                      884-MSE        899-MSE        
                                                                                                                                                                                                                                                                              246-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                                                           712-MSE                                                                    787-MSE                                                                                                                        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               791-MSE
   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 2HQA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2HQA)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DPO3A_ECOLI | P10443)
molecular function
    GO:0008408    3'-5' exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
cellular component
    GO:0044776    DNA polymerase III, core complex    The DNA polymerase III core complex consists of the alpha,epsilon and theta subunits and is carries out the polymerase and the 3'-5' exonuclease proofreading activities.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DPO3A_ECOLI | P10443: 2hnh 4gx8 4gx9 4jom 5fku 5fkv 5fkw 5m1s

(-) Related Entries Specified in the PDB File

2hnh SAME STRUCTURE WITH DOMAIN MOVEMENT.