DNA Polymerase I

PDB ID:   1KLN

Number of Polypeptide Chains in the Protein:   3

Chain Designation:  

Chain 1: B; Chain 2: C; Chain 3: A

Gene Names:  

polA, resA, b3863, JW3835

PDB Deposition Title:  

DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7) MUTANT/DNA COMPLEX

Primary Citation Title:  

Structure of DNA polymerase I Klenow fragment bound to duplex DNA

Citation Authors:  

Beese, L.S., Derbyshire, V., Steitz, T.A.

Citation Journal:  

(1993) Science 260: 352-355

Related PDB Entries:  

2KZZ, 1D8Y, 1D9D, 1D9F, 1QSL

 


Information for Chain A;  UniprotKB Accession Number:  P00582

Primary Structure

Length of the Chain (from Uniprot P00582):  928

FASTA Sequence for the chain (from Uniprot P00582):

MVQIPQNPLILVDGSSYLYRAYHAFPPLTNSAGEPTGAMYGVLNMLRSLIMQYKPTHAAV
VFDAKGKTFRDELFEHYKSHRPPMPDDLRAQIEPLHAMVKAMGLPLLAVSGVEADDVIGT
LAREAEKAGRPVLISTGDKDMAQLVTPNITLINTMTNTILGPEEVVNKYGVPPELIIDFL
ALMGDSSDNIPGVPGVGEKTAQALLQGLGGLDTLYAEPEKIAGLSFRGAKTMAAKLEQNK
EVAYLSYQLATIKTDVELELTCEQLEVQQPAAEELLGLFKKYEFKRWTADVEAGKWLQAK
GAKPAAKPQETSVADEAPEVTATVISYDNYVTILDEETLKAWIAKLEKAPVFAFDTETDS
LDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERALELLKPLLEDEKALKVGQN
LKYDRGILANYGIELRGIAFDTMLESYILNSVAGRHDMDSLAERWLKHKTITFEEIAGKG
KNQLTFNQIALEEAGRYAAEDADVTLQLHLKMWPDLQKHKGPLNVFENIEMPLVPVLSRI
ERNGVKIDPKVLHNHSEELTLRLAELEKKAHEIAGEEFNLSSTKQLQTILFEKQGIKPLK
KTPGGAPSTSEEVLEELALDYPLPKVILEYRGLAKLKSTYTDKLPLMINPKTGRVHTSYH
QAVTATGRLSSTDPNLQNIPVRNEEGRRIRQAFIAPEDYVIVSADYSQIELRIMAHLSRD
KGLLTAFAEGKDIHRATAAEVFGLPLETVTSEQRRSAKAINFGLIYGMSAFGLARQLNIP
RKEAQKYMDLYFERYPGVLEYMERTRAQAKEQGYVETLDGRRLYLPDIKSSNGARRAAAE
RAAINAPMQGTAADIIKRAMIAVDAWLQAEQPRVRMIMQVHDELVFEVHKDDVDAVAKQI
HQLMENCTRLDVPLLVEVGSGENWDQAH

Secondary Structures (DSSP defined; from RCSB PDB)

Helical Structures:  Number of Helices:  29;  Percentage of Residues:  50

Beta Strands:  Number of Strands:  20;  Percentage of Residues:  13

Secondary Structure Map:

 

Tertiary Structure

Number of Domains Along Chain A:  4

CATH Domain IDs:  1klnA01, 1klnA02, 1klnA03, 1klnA04

CATH Classes:  A01: Alpha Beta, A02: Mainly Alpha, A03: Alpha Beta, A04: Mainly Alpha

CATH Architectures:  A01: 2-Layer Sandwich, A02: Up-down Bundle, A03: 2-Layer Sandwich, A04: Orthogonal Bundle

CATH Topologies:  A01: Nucleotidyltransferase; domain 5, A02: Taq DNA Polymerase; Chain T, domain 4, A03: Alpha-Beta Plaits, A04: DNA polymerase; domain 1

Topological Diagrams:
, , ,

 

 

Function and Ligand Binding Site

Excerpt from Abstract:

Not Applicable

Description of Function from Uniprot:

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).

Selected Molecular Function GO Terms:

GO ID: 0003676, Name: Nucleic acid binding, Definition: Interacting selectively and non-covalently with any nucleic acid.

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GO ID: 0003677, Name: DNA binding, Definition: Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

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GO ID: 0003887, Name: DNA-directed DNA polymerase activity, Definition: 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.

EC Number:   EC 2.7.7.7

EC Description:   

Transferases that transfers phosphorous-containing groups. Nucleotidyltransferases.

Major Organic Ligand:   DNA

Ligand Binding Residues:

Thr 356, Glu 357, Thr 358, Leu 361, Gln 419, Asn 420, Lys 422, Tyr 423, Met 443, Arg 455, Asp 457, Met 458, Phe 473, Tyr 497, Asn 579, Leu 580, Ser 582, Thr 609, Ser 610, Glu 611, Arg 631, Lys 635, Ser 658, Tyr 659, His 660, Thr 672, Asn 675, Asn 678, Asp 827

Ligand Binding Site: