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(-) Description

Title :  STRUCTURAL MECHANISM OF ALLOSTERIC SUBSTRATE SPECIFICITY IN A RIBONUCLEOTIDE REDUCTASE: DGTP-ADP COMPLEX
 
Authors :  K. -M. Larsson, A. Jordan, R. Eliasson, P. Reichard, D. T. Logan, P. Nord
Date :  23 Sep 04  (Deposition) - 22 Nov 05  (Release) - 06 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.12
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ribonucleotide Reductase, 10 Alpha-Beta Barrel, Allosteric Regulation, Substrate Specificity, Protein-Nucleotide Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. -M. Larsson, A. Jordan, R. Eliasson, P. Reichard, D. T. Logan, P. Nordlund
Structural Mechanism Of Allosteric Substrate Specificity Regulation In A Ribonucleotide Reductase.
Nat. Struct. Mol. Biol. V. 11 1142 2004
PubMed-ID: 15475969  |  Reference-DOI: 10.1038/NSMB838

(-) Compounds

Molecule 1 - RIBONUCLEOTIDE REDUCTASE, B12-DEPENDENT
    Chains: A, B
    EC Number: 1.17.4.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-644
    Gene: NRDJ
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2DGT2Ligand/Ion2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDGT A:1003 , HOH A:1105BINDING SITE FOR RESIDUE MG A 1005
2AC2SOFTWAREDGT B:1004 , HOH B:1057 , HOH B:1083BINDING SITE FOR RESIDUE MG B 1006
3AC3SOFTWAREASN A:90 , SER A:91 , ALA A:133 , GLY A:161 , GLY A:162 , LYS A:202 , ALA A:210 , ASN A:320 , PRO A:321 , CYS A:322 , GLU A:324 , ALA A:489 , PRO A:490 , THR A:491 , GLY A:492 , SER A:493 , ILE A:494 , HOH A:1103 , HOH A:1119 , HOH A:1144BINDING SITE FOR RESIDUE ADP A 1001
4AC4SOFTWAREASN B:90 , SER B:91 , ALA B:133 , GLY B:161 , GLY B:162 , LYS B:202 , ASN B:320 , PRO B:321 , CYS B:322 , GLU B:324 , ALA B:489 , PRO B:490 , THR B:491 , GLY B:492 , SER B:493 , ILE B:494 , HOH B:1061 , HOH B:1114BINDING SITE FOR RESIDUE ADP B 1002
5AC5SOFTWAREASP A:141 , SER A:142 , ILE A:143 , ARG A:171 , VAL A:177 , ALA A:178 , ALA A:184 , SER A:185 , PHE A:190 , MG A:1005 , HOH A:1015 , HOH A:1016 , HOH A:1064 , HOH A:1105 , LYS B:158 , VAL B:200 , VAL B:201BINDING SITE FOR RESIDUE DGT A 1003
6AC6SOFTWAREHIS A:127 , LEU A:128 , LYS A:158 , VAL A:200 , VAL A:201 , ASP B:141 , SER B:142 , ILE B:143 , ARG B:171 , VAL B:177 , ALA B:178 , SER B:185 , PHE B:190 , MG B:1006 , HOH B:1009 , HOH B:1057 , HOH B:1083 , HOH B:1086BINDING SITE FOR RESIDUE DGT B 1004

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Asp A:295 -Pro A:296
2Tyr A:311 -Pro A:312
3Lys B:230 -Glu B:231
4Asp B:295 -Pro B:296
5Tyr B:311 -Pro B:312

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XJK)

(-) Exons   (0, 0)

(no "Exon" information available for 1XJK)

(-) 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:624
 aligned with O33839_THEMT | O33839 from UniProtKB/TrEMBL  Length:827

    Alignment length:633
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630   
         O33839_THEMT     1 MKLSDLISRWIDVEPSKNAQIILRDRYFMKDLDGNYLETKWEDVARRVARVVATAELLNPSYKKNEKLDRIKEWEDIFFRVLKARLFIPNSPTLFNAGLGVKHDLLWKPIDQMTLEDYEEIYRSRNHLHMLSACFVVPVGDSIEEIFEAVKEYALITKVGGGVGSNFSELRPKGSFVAGTHGKASGPVSFMHVFNSAISVVKQGYRRRGALMGILNINHPDIEEFIDAKKENTGEAVLNFFNLSVGFPMDKKEILKLYEEDGELELSHPRSTIRKKVKIRELFRKIATNAWKSGDPGLAFLGEMNKYYPLYPHRKINSTNPCGEIGLSDYEACNLGSIDVAKFYNNGFVDLEALQELVQIAVRFLDNVIDVNVFPIDKITKAVKESRRLGLGIMGFADLLYKLEIPYNSQEARDFAANLMAFIALHAHRTSYELGKEKGNFPLLEISRYRTEDNFVPFAMGMSNYDDEIREVMKMTKEFRRNVALLTIAPTGSISNIADTSSGLEPNFLLAYTRFVTKEDGTKEPLLYVNQVLREKLNPEILKRIEKELIEKGSLKDIPDVPEKIKKVFVVALDIDPMDHLLMQDAFQRYVDNNISKTINMPQSATVDDVLNVYLEALRTNVRGITVYRDGSL 633
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh....hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..eeehhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh........eee.....hhhhhhhhhhhhhhhhhh..eeeee...................hhhhhhhhhhhhhhhhh...----.eeeeee....hhhhhhh....-----....eeeeee...hhhhhhhhhhh..eeee........eeeehhhhhhhhhhhhhhhh..eeehhhhhhh.........eeee......eee...eeeeeeee....ee..eehhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeehhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.................hhhhhhhhhhhh................hhhhhh............eee.............eeehhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh.hhhhhhhhhhhhhhhhhhh........eeee....hhhhhhhhhhhhhhh...eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xjk A   1 MKLSDLISRWIDVEPSKNAQIILRDRYFMKDLDGNYLETKWEDVARRVARVVATAELLNPSYKKNEKLDRIKEWEDIFFRVLKARLFIPNSPTLFNAGLGVKHDLLWKPIDQMTLEDYEEIYRSRNHLHMLSACFVVPVGDSIEEIFEAVKEYALITKVGGGVGSNFSELRPKGSFVAGTHGKASGPVSFMHVFNSAISVVKQGS----ALMGILNINHPDIEEFIDAKKE-----VLNFFNLSVGFPMDKKEILKLYEEDGELELSHPRSTIRKKVKIRELFRKIATNAWKSGDPGLAFLGEMNKYYPLYPHRKINSTNPCGEIGLSDYEACNLGSIDVAKFYNNGFVDLEALQELVQIAVRFLDNVIDVNVFPIDKITKAVKESRRLGLGIMGFADLLYKLEIPYNSQEARDFAANLMAFIALHAHRTSYELGKEKGNFPLLEISRYRTEDNFVPFAMGMSNYDDEIREVMKMTKEFRRNVALLTIAPTGSISNIADTSSGLEPNFLLAYTRFVTKDDGTKEPLLYVNQVLREKLNPEILKRIEKELIEKGSLKDIPDVPEKIKKVFVVALDIDPMDHLLMQDAFQRYVDNNISKTINMPQSATVDDVLNVYLEALRTNVRGITVYRDGSL 633
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    |  210       220       230|     |240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630   
                                                                                                                                                                                                                                      205  210                  231   237                                                                                                                                                                                                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:608
 aligned with O33839_THEMT | O33839 from UniProtKB/TrEMBL  Length:827

    Alignment length:632
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630  
         O33839_THEMT     1 MKLSDLISRWIDVEPSKNAQIILRDRYFMKDLDGNYLETKWEDVARRVARVVATAELLNPSYKKNEKLDRIKEWEDIFFRVLKARLFIPNSPTLFNAGLGVKHDLLWKPIDQMTLEDYEEIYRSRNHLHMLSACFVVPVGDSIEEIFEAVKEYALITKVGGGVGSNFSELRPKGSFVAGTHGKASGPVSFMHVFNSAISVVKQGYRRRGALMGILNINHPDIEEFIDAKKENTGEAVLNFFNLSVGFPMDKKEILKLYEEDGELELSHPRSTIRKKVKIRELFRKIATNAWKSGDPGLAFLGEMNKYYPLYPHRKINSTNPCGEIGLSDYEACNLGSIDVAKFYNNGFVDLEALQELVQIAVRFLDNVIDVNVFPIDKITKAVKESRRLGLGIMGFADLLYKLEIPYNSQEARDFAANLMAFIALHAHRTSYELGKEKGNFPLLEISRYRTEDNFVPFAMGMSNYDDEIREVMKMTKEFRRNVALLTIAPTGSISNIADTSSGLEPNFLLAYTRFVTKEDGTKEPLLYVNQVLREKLNPEILKRIEKELIEKGSLKDIPDVPEKIKKVFVVALDIDPMDHLLMQDAFQRYVDNNISKTINMPQSATVDDVLNVYLEALRTNVRGITVYRDGS 632
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh....hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..eeehhhhhhhh....hhhhhh.hhhhhhhhhhhhhhhh.........eee.....hhhhhhhhhhhhhhhhhhh.eeeee.hhh...............hhhhhhhhhhhhhhhhh.------.eeeeee....hhhhhhh....----.....eeeeee...hhhhhhhhhhh..eeee........eeeehhhhhhhhhhhhhhhh..eeehhhhhhhh..........ee......ee....eeeeeeee....ee..eehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.eeeeeehhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh............hhhhhhhhhhhh................hhhhhh................--------------.hhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhh......hhhhhhhhhhhhhh........eeee....hhhhhhhhhhhhhhh...eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xjk B   1 MKLSDLISRWIDVEPSKNAQIILRDRYFMKDLDGNYLETKWEDVARRVARVVATAELLNPSYKKNEKLDRIKEWEDIFFRVLKARLFIPNSPTLFNAGLGVKHDLLWKPIDQMTLEDYEEIYRSRNHLHMLSACFVVPVGDSIEEIFEAVKEYALITKVGGGVGSNFSELRPKGSFVAGTHGKASGPVSFMHVFNSAISVVKQ------ALMGILNINHPDIEEFIDAKKE----AVLNFFNLSVGFPMDKKEILKLYEEDGELELSHPRSTIRKKVKIRELFRKIATNAWKSGDPGLAFLGEMNKYYPLYPHRKINSTNPCGEIGLSDYEACNLGSIDVAKFYNNGFVDLEALQELVQIAVRFLDNVIDVNVFPIDKITKAVKESRRLGLGIMGFADLLYKLEIPYNSQEARDFAANLMAFIALHAHRTSYELGKEKGNFPLLEISRYRTEDNFVPFAMGMSNYDDEIREVMKMTKEFRRNVALLTIAPTGSISNIADTSSGLEPNFLLAYTR--------------VNQVLREKLNPEILKRIEKELIEKGSLKDIPDVPEKIKKVFVVALDIDPMDHLLMQDAFQRYVDNNISKTINMPQSATVDDVLNVYLEALRTNVRGITVYRDGS 632
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  |    210       220       230|    | 240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510   |     -       530       540       550       560       570       580       590       600       610       620       630  
                                                                                                                                                                                                                                    203    210                  231  236                                                                                                                                                                                                                                                                                   514            529
   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 1XJK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1XJK)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O33839_THEMT | O33839)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0031419    cobalamin binding    Interacting selectively and non-covalently with cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004748    ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor    Catalysis of the reaction: 2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin. Thioredoxin disulfide is the oxidized form of 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: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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  O33839_THEMT | O33839
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 Related Entries

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

UniProtKB/TrEMBL
        O33839_THEMT | O33839: 1xje 1xjf 1xjg 1xjj 1xjm 1xjn 3o0n 3o0o 3o0q

(-) Related Entries Specified in the PDB File

1xje THERMOTOGA MARITIMA NRDJ IN COMPLEX WITH DTTP AND GDP
1xjf THERMOTOGA MARITIMA NRDJ IN COMPLEX WITH DATP
1xjg THERMOTOGA MARITIMA NRDJ IN COMPLEX WITH DATP AND UDP
1xjj THERMOTOGA MARITIMA NRDJ IN COMPLEX WITH DGTP
1xjm THERMOTOGA MARITIMA NRDJ IN COMPLEX WITH DTTP
1xjn THERMOTOGA MARITIMA NRDJ IN COMPLEX WITH CDP AND DATP