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(-) Description

Title :  THERMOTOGA MARITIMA RIBONUCLEOTIDE REDUCTASE, NRDJ, IN COMPLEX WITH DTTP, GDP AND ADENOSINE
 
Authors :  K. -M. Larsson, D. T. Logan, P. Nordlund
Date :  19 Jul 10  (Deposition) - 28 Jul 10  (Release) - 27 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  10 Alpha/Beta Barrel, Adenosylcobalamin Dependent, Ribonucleotide Reductase, Reduction Ribonucleotide 2'-Oh Position, Effector, Dttp, Substrate, Gdp, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. M. Larsson, D. T. Logan, P. Nordlund
Structural Basis For Adenosylcobalamin Activation In Adocbl-Dependent Ribonucleotide Reductases.
Acs Chem. Biol. V. 5 933 2010
PubMed-ID: 20672854  |  Reference-DOI: 10.1021/CB1000845

(-) Compounds

Molecule 1 - RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE
    Chains: A, B
    EC Number: 1.17.4.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Gene: NRDJ, TM_0118
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Strain: MSB8

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
1ADN2Ligand/IonADENOSINE
2CL1Ligand/IonCHLORIDE ION
3GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
4MG2Ligand/IonMAGNESIUM ION
5TTP2Ligand/IonTHYMIDINE-5'-TRIPHOSPHATE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:141 , SER A:142 , ILE A:143 , ARG A:171 , VAL A:177 , ALA A:178 , GLY A:179 , ALA A:184 , SER A:185 , PHE A:190 , HOH A:646 , HOH A:706 , HOH A:707 , HOH A:718 , HOH A:779 , HOH A:786 , MG A:1002 , LYS B:158 , VAL B:200 , VAL B:201 , LYS B:202BINDING SITE FOR RESIDUE TTP A 1001
2AC2SOFTWAREHOH A:705 , HOH A:706 , HOH A:707 , TTP A:1001BINDING SITE FOR RESIDUE MG A 1002
3AC3SOFTWAREASN A:90 , SER A:91 , ALA A:133 , GLY A:161 , ARG A:207 , ARG A:208 , 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:730 , HOH A:766 , HOH A:793 , HOH A:802 , HOH A:891 , HOH A:970BINDING SITE FOR RESIDUE GDP A 1003
4AC4SOFTWAREMET A:212 , ASN A:242 , LEU A:243 , SER A:244 , ASP A:295 , GLY A:297 , CYS A:322 , THR A:598 , THR A:626 , HOH A:762 , HOH A:763BINDING SITE FOR RESIDUE ADN A 1004
5AC5SOFTWAREVAL A:607BINDING SITE FOR RESIDUE CL A 1005
6AC6SOFTWARELYS A:158 , VAL A:200 , VAL A:201 , LYS A:202 , ASP B:141 , SER B:142 , ILE B:143 , ARG B:171 , VAL B:177 , ALA B:178 , GLY B:179 , ALA B:184 , SER B:185 , PHE B:190 , HOH B:751 , HOH B:763 , HOH B:937 , HOH B:979 , MG B:1002BINDING SITE FOR RESIDUE TTP B 1001
7AC7SOFTWAREHOH B:703 , HOH B:704 , TTP B:1001BINDING SITE FOR RESIDUE MG B 1002
8AC8SOFTWAREASN B:90 , SER B:91 , ALA B:133 , GLY B:161 , ARG B:207 , ARG B:208 , ALA B:210 , 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:646 , HOH B:664 , HOH B:790 , HOH B:819 , HOH B:900 , HOH B:961 , HOH B:1038BINDING SITE FOR RESIDUE GDP B 1003
9AC9SOFTWAREASN B:242 , LEU B:243 , SER B:244 , ASP B:295 , CYS B:322 , PRO B:490 , SER B:596 , LYS B:597 , THR B:598 , THR B:626 , HOH B:671 , HOH B:739 , HOH B:760 , HOH B:773 , HOH B:789BINDING SITE FOR RESIDUE ADN B 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O0Q)

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O0Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3O0Q)

(-) Exons   (0, 0)

(no "Exon" information available for 3O0Q)

(-) 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:617
 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...hhhhhhhhhhhhhhhhhhhhhh..eeehhhhhhhh....hhhhhh.hhhhhhhhhhhhhhhhh........eee.....hhhhhhhhhhhhhhhhhh..eeeee.........ee....ee..hhhhhhhhhhhhhh..ee...ee..eeeeee....hhhhhhh..-------....eeeeee...hhhhhhhhhhh..eeee........eeeehhhhhhhhhhhhhhhh..eeehhhhhhhh........eeee......eee...eeeeeeee....ee..eehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.eeeeeehhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh............hhhhhhhhhhhh................hhhhhh............eeee.---------.eeeehhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh.hhhhhhhhhhhhhhhhhhh........eeee....hhhhhhhhhhhhhhh...eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o0q A   1 MKLSDLISRWIDVEPSKNAQIILRDRYFMKDLDGNYLETKWEDVARRVARVVATAELLNPSYKKNEKLDRIKEWEDIFFRVLKARLFIPNSPTLFNAGLGVKHDLLWKPIDQMTLEDYEEIYRSRNHLHMLSACFVVPVGDSIEEIFEAVKEYALITKVGGGVGSNFSELRPKGSFVAGTHGKASGPVSFMHVFNSAISVVKQGSRRRGALMGILNINHPDIEEFIDAK-------VLNFFNLSVGFPMDKKEILKLYEEDGELELSHPRSTIRKKVKIRELFRKIATNAWKSGDPGLAFLGEMNKYYPLYPHRKINSTNPCGEIGLSDYEACNLGSIDVAKFYNNGFVDLEALQELVQIAVRFLDNVIDVNVFPIDKITKAVKESRRLGLGIMGFADLLYKLEIPYNSQEARDFAANLMAFIALHAHRTSYELGKEKGNFPLLEISRYRTEDNFVPFAMGMSNYDDEIREVMKMTKEFRRNVALLTIAPTGSISNIADTSSGLEPNFLLAYTRF---------PLLYVNQVLREKLNPEILKRIEKELIEKGSLKDIPDVPEKIKKVFVVALDIDPMDHLLMQDAFQRYVDNNISKTINMPQSATVDDVLNVYLEALRTNVRGITVYRDGSL 633
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220        |-      |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   
                                                                                                                                                                                                                                                              229     237                                                                                                                                                                                                                                                                                   515       525                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:617
 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...........hhhhhhhhhhhhhhhhh........eee.....hhhhhhhhhhhhhhhhhhh.eeeee.........ee....ee..hhhhhhhhhhhhhh...........eeeeee....hhhhhhh...------....eeeeee...hhhhhhhhhhh..eeee........eeeehhhhhhhhhhhhhhhh..eeehhhhhhhh..........ee......ee....eeeeeeee....ee..eehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.eeeeeehhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh............hhhhhhhhhhhh................hhhhhh............eee..----------.eeehhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh.hhhhhhhhhhhhhhhhhhh........eeee....hhhhhhhhhhhhhhh...eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o0q B   1 MKLSDLISRWIDVEPSKNAQIILRDRYFMKDLDGNYLETKWEDVARRVARVVATAELLNPSYKKNEKLDRIKEWEDIFFRVLKARLFIPNSPTLFNAGLGVKHDLLWKPIDQMTLEDYEEIYRSRNHLHMLSACFVVPVGDSIEEIFEAVKEYALITKVGGGVGSNFSELRPKGSFVAGTHGKASGPVSFMHVFNSAISVVKQGSRRRGALMGILNINHPDIEEFIDAKK------VLNFFNLSVGFPMDKKEILKLYEEDGELELSHPRSTIRKKVKIRELFRKIATNAWKSGDPGLAFLGEMNKYYPLYPHRKINSTNPCGEIGLSDYEACNLGSIDVAKFYNNGFVDLEALQELVQIAVRFLDNVIDVNVFPIDKITKAVKESRRLGLGIMGFADLLYKLEIPYNSQEARDFAANLMAFIALHAHRTSYELGKEKGNFPLLEISRYRTEDNFVPFAMGMSNYDDEIREVMKMTKEFRRNVALLTIAPTGSISNIADTSSGLEPNFLLAYTRF----------LLYVNQVLREKLNPEILKRIEKELIEKGSLKDIPDVPEKIKKVFVVALDIDPMDHLLMQDAFQRYVDNNISKTINMPQSATVDDVLNVYLEALRTNVRGITVYRDGSL 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    |    -     | 530       540       550       560       570       580       590       600       610       620       630   
                                                                                                                                                                                                                                                               230    237                                                                                                                                                                                                                                                                                   515        526
   Legend:   → Mismatch (orange background)
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  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 3O0Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O0Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3O0Q)

(-) 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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  3o0q
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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 1xjk 1xjm 1xjn 3o0n 3o0o

(-) Related Entries Specified in the PDB File

1xje 1xjf 1xjg 1xjj 1xjm 1xjn 3o0n 3o0o