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(-) Description

Title :  CRYSTAL STRUCTURE OF BACILLUS CEREUS RIBONUCLEOTIDE REDUCTASE DI-IRON NRDF IN COMPLEX WITH NRDI (1.8 A RESOLUTION)
 
Authors :  M. Hammerstad, H. -P. Hersleth, A. K. Rohr, K. K. Andersson
Date :  10 May 13  (Deposition) - 19 Mar 14  (Release) - 19 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Hammerstad, H. Hersleth, A. B. Tomter, A. K. Rohr, K. K. Andersson
Crystal Structure Of Bacillus Cereus Class Ib Ribonucleotide Reductase Di-Iron Nrdf In Complex With Nrdi.
Acs Chem. Biol. V. 9 526 2014
PubMed-ID: 24295378  |  Reference-DOI: 10.1021/CB400757H

(-) Compounds

Molecule 1 - RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SUBUNIT BETA
    Atcc: 14579
    Chains: A
    EC Number: 1.17.4.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BACILLUS CEREUS
    Organism Taxid: 1396
    Synonym: RIBONUCLEOTIDE REDUCTASE NRDF
 
Molecule 2 - NRDI
    Atcc: 14579
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BACILLUS CEREUS
    Organism Taxid: 1396

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
2FE22Ligand/IonFE (II) ION
3FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FE24Ligand/IonFE (II) ION
3FMN2Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:17 , CL A:1293 , SER B:7 , MET B:8 , THR B:9 , GLY B:10 , ASN B:11 , VAL B:12 , TYR B:41 , THR B:42 , THR B:43 , GLY B:44 , PHE B:45 , GLY B:46 , SER B:69 , GLY B:70 , ASN B:71 , TRP B:74 , MET B:77 , PHE B:78 , GLY B:79 , LEU B:99 , HOH B:2003 , HOH B:2025 , HOH B:2042BINDING SITE FOR RESIDUE FMN B1120
2AC2SOFTWAREASP A:62 , GLU A:93 , HIS A:96 , GLU A:195BINDING SITE FOR RESIDUE FE2 A1323
3AC3SOFTWAREGLU A:93 , GLU A:161 , GLU A:195 , HIS A:198BINDING SITE FOR RESIDUE FE2 A1324
4AC4SOFTWARESER A:196 , TRP B:74 , FMN B:1120BINDING SITE FOR RESIDUE CL A1293
5AC5SOFTWARETHR A:63 , LYS A:64 , LYS A:83BINDING SITE FOR RESIDUE CL A1294
6AC6SOFTWAREGLU A:271BINDING SITE FOR RESIDUE CL A1295
7AC7SOFTWAREGLY A:248 , LEU A:249 , VAL A:250 , HOH A:2120 , HOH A:2123BINDING SITE FOR RESIDUE CL A1296
8AC8SOFTWAREGLU A:275BINDING SITE FOR RESIDUE CL A1297

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BMO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4BMO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BMO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4BMO)

(-) Exons   (0, 0)

(no "Exon" information available for 4BMO)

(-) 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:290
 aligned with Q81G55_BACCR | Q81G55 from UniProtKB/TrEMBL  Length:322

    Alignment length:290
                                    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
         Q81G55_BACCR     1 MRAVNWNKKEDDFSLMFWKQNIAQFWTEEEIAVSSDKNTWVQLSKEEQIAYKRVLGGLTLLDTKQGGEGMPLVLVHLENLQAKSVLAFMGAMEEVHAKSYSHIFTTLATEEEIDDIFDWVDNHPLLEKKAGIITSYYRRLLKPEVTKKELYMAMVASVFLESYLFYSGFFYPLYLAGQGKLTASGEIINLIIRDESIHGVFVGILAQQIFAELSAEEQQEVQKETQELLMELYEIEMAYTEEIYTSIGLVEDVNRFVRYNANKGLMNLGLEPKFEEEEINPIVLNGLRTD 290
               SCOP domains d4bmoa_ A: automated matches                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhh.hhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bmo A   1 MRAVNWNKKEDDFSLMFWKQNIAQFWTEEEIAVSSDKNTWVQLSKEEQIAYKRVLGGLTLLDTKQGGEGMPLVLVHLENLQAKSVLAFMGAMEEVHAKSYSHIFTTLATEEEIDDIFDWVDNHPLLEKKAGIITSYYRRLLKPEVTKKELYMAMVASVFLESYLFYSGFFYPLYLAGQGKLTASGEIINLIIRDESIHGVFVGILAQQIFAELSAEEQQEVQKETQELLMELYEIEMAYTEEIYTSIGLVEDVNRFVRYNANKGLMNLGLEPKFEEEEINPIVLNGLRTD 290
                                    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


Chain B from PDB  Type:PROTEIN  Length:119
 aligned with B0YPL1_BACCE | B0YPL1 from UniProtKB/TrEMBL  Length:119

    Alignment length:119
                                    10        20        30        40        50        60        70        80        90       100       110         
         B0YPL1_BACCE     1 MLVAYDSMTGNVKRFIHKLNMPAVQIDEDLVIDEDFILITYTTGFGNVPERVLDFLERNNEKLKGVSASGNRNWGDMFGASADKISTKYEVPIVSKFELSGTNNDVEYFKERVREIATH 119
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhh.....eee..........eeeee........hhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 4bmo B   1 MLVAYDSMTGNVKRFIHKLNMPAVQIDEDLVIDEDFILITYTTGFGNVPERVLDFLERNNEKLKGVSASGNRNWGDMFGASADKISTKYEVPIVSKFELSGTNNDVEYFKERVREIATH 119
                                    10        20        30        40        50        60        70        80        90       100       110
   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: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BMO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BMO)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q81G55_BACCR | Q81G55)
molecular function
    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: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:0009186    deoxyribonucleoside diphosphate metabolic process    The chemical reactions and pathways involving a deoxyribonucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with diphosphate on the sugar.
    GO:0009263    deoxyribonucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    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.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005971    ribonucleoside-diphosphate reductase complex    An enzyme complex composed of 2-4 or more subunits, which usually contains nonheme iron and requires ATP for catalysis. Catalyzes the formation of 2'-deoxyribonucleoside diphosphate from ribonucleoside diphosphate, using either thioredoxin disulfide or glutaredoxin disulfide as an acceptor.

Chain B   (B0YPL1_BACCE | B0YPL1)
molecular function
    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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q81G55_BACCR | Q81G55: 4bmp 4bmq 4bmr 4bmt 4bmu

(-) Related Entries Specified in the PDB File

4bmp CRYSTAL STRUCTURE OF BACILLUS CEREUS RIBONUCLEOTIDE REDUCTASE DI-IRON NRDF IN COMPLEX WITH NRDI (2.1 A RESOLUTION)