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(-) Description

Title :  CRYSTAL STRUCTURES OF THE N-TERMINAL FRAGMENT FROM MOLONEY MURINE LEUKEMIA VIRUS REVERSE TRANSCRIPTASE COMPLEXED WITH NUCLEIC ACID: FUNCTIONAL IMPLICATIONS FOR TEMPLATE-PRIMER BINDING TO THE FINGERS DOMAIN
 
Authors :  S. Najmudin, M. Cote, D. Sun, S. Yohannan, S. P. Montano, J. Gu, M. M. Geor
Date :  18 Mar 99  (Deposition) - 02 Apr 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protein-Dna Complex, Polymerase, Reverse Transcriptase, Moloney Murine Leukemia Virus, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Najmudin, M. L. Cote, D. Sun, S. Yohannan, S. P. Montano, J. Gu, M. M. Georgiadis
Crystal Structures Of An N-Terminal Fragment From Moloney Murine Leukemia Virus Reverse Transcriptase Complexed With Nucleic Acid: Functional Implications For Template-Primer Binding To The Fingers Domain.
J. Mol. Biol. V. 296 613 2000
PubMed-ID: 10669612  |  Reference-DOI: 10.1006/JMBI.1999.3477
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*CP*AP*TP*GP*CP*AP*TP*G)-3')
    ChainsC, D
    EngineeredYES
    SyntheticYES
 
Molecule 2 - REVERSE TRANSCRIPTASE
    ChainsA, B
    EC Number2.7.7.49
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPRT 107-3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL FRAGMENT COMPRISING FINGERS AND PALM DOMAINS
    GeneMMLV-RT
    Organism ScientificMOLONEY MURINE LEUKEMIA VIRUS
    Organism Taxid11801
    SynonymRT

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1QAJ)

(-) Sites  (0, 0)

(no "Site" information available for 1QAJ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QAJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QAJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QAJ)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RT_POLPS50878 Reverse transcriptase (RT) catalytic domain profile.POL_MLVMS741-932
 
  2A:82-273
B:82-273

(-) Exons   (0, 0)

(no "Exon" information available for 1QAJ)

(-) 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:259
 aligned with POL_MLVMS | P03355 from UniProtKB/Swiss-Prot  Length:1738

    Alignment length:295
                                   652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932     
            POL_MLVMS   643 GSGAQVMGPMGQPLQVLTLNIEDEHRLHETSKEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNSPTLFDEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGNLGYRASAKKAQICQKQVKYLGYLLKEGQR 937
               SCOP domains d1                         qaj           a_ A: MMLV reverse transcriptase                                                                                                                                                                                                                               SCOP domains
               CATH domains -----------------------------------------1qajA02                   -1qajA01 A:52-121,A:166-187                                            ---1qajA02                           -------1qajA01               1qajA02 A:25-50,A:125-158,A:188-273  [code=3.30.70.270, no name defined]              ----- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ..-------------------------hhh-----------hhhhh.....................................hh..................eeee.......-hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhh......eeeeee...hhhhh.....hhhhhheeeeehhhheeeeeee........hhhhhhhhhhhhhhhhhhhhh...eeeee..eeeeee.hhhhhhhhhhhhhhhhhhhh........eeee..eee..eee..... Sec.struct. author (1)
     Sec.struct. author (2) ------------------------------------------------------------------------------------------------------------------eeeee------eeeee--------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------RT_POL  PDB: A:82-273 UniProt: 741-932                                                                                                                                                          ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qaj A  20 GS-------------------------HMT-----------WLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNSPTLFDEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGNLGYRASAKKAQICQKQVKYLGYLLKEGQR 278
                             |       -         -       |24         - |      33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273     
                             |                        22 |          25                                                                                                                                                                                                                                                             
                            21                          24                                                                                                                                                                                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:257
 aligned with POL_MLVMS | P03355 from UniProtKB/Swiss-Prot  Length:1738

    Alignment length:257
                                   690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       
            POL_MLVMS   681 GSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNSPTLFDEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGNLGYRASAKKAQICQKQVKYLGYLLKEGQR 937
               SCOP domains d1qajb_ B: MMLV reverse transcriptase                                                                                                                                                                                                                             SCOP domains
               CATH domains ---1qajB02                   -1qajB01 B:52-121,B:166-187                                            ---1qajB02                           -------1qajB01               1qajB02 B:25-50,B:125-158,B:188-273  [code=3.30.70.270, no name defined]              ----- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------RVT_1-1qajB01 B:101-273                                                                                                                                                      ----- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------RVT_1-1qajB02 B:101-273                                                                                                                                                      ----- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhh..............................hhhhhhhhhhhhhhhh..eeee.......eee..........eee.hhhhhh..........hhhhhhh.......eeeeee..hhhhhh..hhhhhhhhhee..........eeee........hhhhhhhhhhhhhhhhhhhhh...eeeee..eeeeee.hhhhhhhhhhhhhhhhhhhh........eeee..eee..eee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------RT_POL  PDB: B:82-273 UniProt: 741-932                                                                                                                                                          ----- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qaj B  22 HMTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNSPTLFDEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGNLGYRASAKKAQICQKQVKYLGYLLKEGQR 278
                                    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       

Chain C from PDB  Type:DNA  Length:8
                                        
                 1qaj C   1 CATGCATG   8

Chain D from PDB  Type:DNA  Length:8
                                        
                 1qaj D   1 CATGCATG   8

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: RdRP (210)

(-) Gene Ontology  (36, 36)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (POL_MLVMS | P03355)
molecular function
    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:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004523    RNA-DNA hybrid ribonuclease activity    Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
    GO:0003964    RNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    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: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: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.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0039660    structural constituent of virion    The action of a molecule that contributes to the structural integrity of a virion.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
    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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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:0015074    DNA integration    The process in which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome.
    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. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0006278    RNA-dependent DNA biosynthetic process    A DNA biosynthetic process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strand.
    GO:0075713    establishment of integrated proviral latency    A process by which the virus integrates into the host genome and establishes as a stable provirus or prophage.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019068    virion assembly    A late phase of the viral life cycle during which all the components necessary for the formation of a mature virion collect at a particular site in the cell and the basic structure of the virus particle is formed.
cellular component
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019013    viral nucleocapsid    The complete protein-nucleic acid complex that is the packaged form of the genome in a virus particle.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        POL_MLVMS | P033551d0e 1d1u 1i6j 1mml 1n4l 1nnd 1qai 1ztt 1ztw 2fjv 2fjw 2fjx 2fvp 2fvq 2fvr 2fvs 2hb5 2m9u 2mqv 2ms0 2ms1 2r2r 2r2s 2r2t 2r2u 3fsi 3nnq 4m94 4m95 4mh8 4nzg 4xo0 4xpc 4xpe 5dmq 5dmr

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1QAJ)