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(-) Description

Title :  STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN CLASS III RIBONUCLEOTIDE REDUCTASES, NATIVE NRDD
 
Authors :  K. -M. Larsson, J. Andersson, B. -M. Sjoeberg, P. Nordlund, D. T. Logan
Date :  04 Jul 01  (Deposition) - 28 Mar 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Oxidoreductase, Reductase, Allosteric Regulation, Substrate Specificity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. -M. Larsson, J. Andersson, B. -M. Sjoeberg, P. Nordlund, D. T. Logan
Structural Basis For Allosteric Substrate Specificty Regulation In Anaerobic Ribonucleotide Reductase
Structure V. 9 739 2001
PubMed-ID: 11587648  |  Reference-DOI: 10.1016/S0969-2126(01)00627-X

(-) Compounds

Molecule 1 - ANAEROBIC RIBONUCLEOTIDE-TRIPHOSPHATE REDUCTASE LARGE CHAIN
    Chains: A
    EC Number: 1.17.4.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29T4NRDD(G580A)
    Expression System Strain: JM109(DE3)
    Expression System Taxid: 562
    Fragment: ACTIVE SITE SUBUNIT, RESIDUES 1-605
    Mutation: YES
    Organism Scientific: BACTERIOPHAGE T4
    Organism Taxid: 10665
    Other Details: SEQUENCE DETERMINATION. YOUNG, P., OHMAN, M., XU, M.Q.
    Synonym: ANAEROBIC NTP REDUCTASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:66 , ALA A:445 , GLU A:446 , ASN A:447 , LEU A:448 , HOH A:2098BINDING SITE FOR RESIDUE PO4 A1588

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1H7B)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ser A:71 -Pro A:72
2Phe A:231 -Pro A:232
3Tyr A:266 -Pro A:267

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H7B)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLY_RADICAL_2PS51149 Glycine radical domain profile.NRDD_BPT4482-605  1A:482-587
2GLY_RADICAL_1PS00850 Glycine radical domain signature.NRDD_BPT4575-583  1A:575-583
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLY_RADICAL_2PS51149 Glycine radical domain profile.NRDD_BPT4482-605  2A:482-587
2GLY_RADICAL_1PS00850 Glycine radical domain signature.NRDD_BPT4575-583  2A:575-583

(-) Exons   (0, 0)

(no "Exon" information available for 1H7B)

(-) 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:534
 aligned with NRDD_BPT4 | P07071 from UniProtKB/Swiss-Prot  Length:605

    Alignment length:562
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585  
            NRDD_BPT4    26 DSRVFPTQRDLMAGIVSKHIAKNMVPSFIMKAHESGIIHVHDIDYSPALPFTNCCLVDLKGMLENGFKLGNAQIETPKSIGVATAIMAQITAQVASHQYGGTTFANVDKVLSPYVKRTYAKHIEDAEKWQIADALNYAQSKTEKDVYDAFQAYEYEVNTLFSSNGQTPFVTITFGTGTDWTERMIQKAILKNRIKGLGRDGITPIFPKLVMFVEEGVNLYKDDPNYDIKQLALECASKRMYPDIISAKNNKAITGSSVPVSPMGCRSFLSVWKDSTGNEILDGRNNLGVVTLNLPRIALDSYIGTQFNEQKFVELFNERMDLCFEALMCRISSLKGVKATVAPILYQEGAFGVRLKPDDDIIELFKNGRSSVSLGYIGIHELNILVGRDIGREILTKMNAHLKQWTERTGFAFSLYSTPAENLCYRFCKLDTEKYGSVKDVTDKGWYTNSFHVSVEENITPFEKISREAPYHFIATGGHISYVELPDMKNNLKGLEAVWDYAAQHLDYFGVNMPVDKCFTCGSTHEMTPTENGFVCSICGETDPKKMNTIRRTCGYLGNPNE 587
               SCOP domains d1h7ba_ A: Class III anaerobic ribonucleotide reductase NRDD subunit                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1h7bA00 A:26-587  [code=3.20.70.20, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..eee..............ee.hhhhhhhh.eee..eee....hhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeee....hhhhhhhhhhhhhhhhhh...........eeeeee...........hhhhhhhhhhhhhhhh..eeeehhhhhhhhh..............................eeeeeeeehhhhhhh.ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh.............hhhhhh....eeeeeeehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhh......eeee......hhhhhhhhhhhhhhhh.eeeee..eee.----------------------------.eee............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLY_RADICAL_2  PDB: A:482-587 UniProt: 482-605                                                             PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLY_RADIC---- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h7b A  26 DSRVFPTQRDLMAGIVSKHIAKNMVPSFIMKAHESGIIHVHDIDYSPALPFTNCCLVDLKGMLENGFKLGNAQIETPKSIGVATAIMAQITAQVASHQYGGTTFANVDKVLSPYVKRTYAKHIEDAEKWQIADALNYAQSKTEKDVYDAFQAYEYEVNTLFSSNGQTPFVTITFGTGTDWTERMIQKAILKNRIKGLGRDGITPIFPKLVMFVEEGVNLYKDDPNYDIKQLALECASKRMYPDIISAKNNKAITGSSVPVSPMGCRSFLSVWKDSTGNEILDGRNNLGVVTLNLPRIALDSYIGTQFNEQKFVELFNERMDLCFEALMCRISSLKGVKATVAPILYQEGAFGVRLKPDDDIIELFKNGRSSVSLGYIGIHELNILVGRDIGREILTKMNAHLKQWTERTGFAFSLYSTPAENLCYRFCKLDTEKYGSVKDVTDKGWYTNSFHVSVEENITPFEKISREAPYHFIATGGHISYVELPDMKNNLKGLEAVWDYAAQHLDYFGVNMPVDKC----------------------------MNTIRRTCAYLGNPNE 587
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       | -         -         -      |575       585  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               543                          572
   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, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1H7B)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (NRDD_BPT4 | P07071)
molecular function
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0008998    ribonucleoside-triphosphate reductase activity    Catalysis of the reaction: 2'-deoxyribonucleoside triphosphate + thioredoxin disulfide + H2O = ribonucleoside triphosphate + thioredoxin.
biological process
    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.
    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:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NRDD_BPT4 | P07071: 1h78 1h79 1h7a 1hk8

(-) Related Entries Specified in the PDB File

1h77 STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX WITH DGTP.
1h78 STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX WITH DCTP.
1h79 STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX WITH DTTP
1h7a STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX WITH DATP.