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(-) Description

Title :  NADR PROTEIN FROM HAEMOPHILUS INFLUENZAE
 
Authors :  S. K. Singh, O. V. Kurnasov, B. Chen, H. Robinson, N. V. Grishin, A. L. Ost H. Zhang
Date :  30 May 02  (Deposition) - 07 Aug 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Nad, Nmn, Nmn Adenylyl Transferase, Ribosylnicotinamide Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. K. Singh, O. V. Kurnasov, B. Chen, H. Robinson, N. V. Grishin, A. L. Osterman, H. Zhang
Crystal Structure Of Haemophilus Influenzae Nadr Protein. A Bifunctional Enzyme Endowed With Nmn Adenyltransferase And Ribosylnicotinimide Kinase Activities.
J. Biol. Chem. V. 277 33291 2002
PubMed-ID: 12068016  |  Reference-DOI: 10.1074/JBC.M204368200

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR NADR
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentNADR
    GeneNADR
    Organism ScientificHAEMOPHILUS INFLUENZAE
    Organism Taxid727

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (4x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3SO45Ligand/IonSULFATE ION
Biological Unit 1 (3, 52)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE
2NAD8Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3SO420Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:202 , ALA A:203 , THR A:204 , ARG A:207 , NAD A:601BINDING SITE FOR RESIDUE SO4 A 501
2AC2SOFTWAREARG A:222 , HIS A:296BINDING SITE FOR RESIDUE SO4 A 603
3AC3SOFTWARELYS A:219 , ARG A:295 , HIS A:296BINDING SITE FOR RESIDUE SO4 A 604
4AC4SOFTWARENAD A:605BINDING SITE FOR RESIDUE SO4 A 606
5AC5SOFTWAREASN A:244 , TRP A:256 , NAD A:605BINDING SITE FOR RESIDUE SO4 A 607
6AC6SOFTWAREPHE A:64 , GLY A:65 , LYS A:66 , PHE A:67 , HIS A:71 , HIS A:74 , CYS A:93 , ARG A:98 , GLU A:139 , PRO A:143 , TYR A:145 , ASN A:147 , GLY A:148 , TRP A:149 , TRP A:152 , SER A:172 , SER A:173 , GLU A:174 , ASP A:193 , ARG A:196 , PHE A:199 , VAL A:201 , SO4 A:501BINDING SITE FOR RESIDUE NAD A 601
7AC7SOFTWARELYS A:126 , TYR A:127 , SER A:254 , ALA A:255 , TRP A:256 , TYR A:289 , TYR A:292 , SO4 A:606 , SO4 A:607BINDING SITE FOR RESIDUE NAD A 605

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LW7)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:68 -Pro A:69

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LW7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1LW7)

(-) Exons   (0, 0)

(no "Exon" information available for 1LW7)

(-) 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:344
 aligned with NADR_HAEIN | P44308 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:355
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406     
           NADR_HAEIN    57 EKKVGVIFGKFYPVHTGHINMIYEAFSKVDELHVIVCSDTVRDLKLFYDSKMKRMPTVQDRLRWMQQIFKYQKNQIFIHHLVEDGIPSYPNGWQSWSEAVKTLFHEKHFEPSIVFSSEPQDKAPYEKYLGLEVSLVDPDRTFFNVSATKIRTTPFQYWKFIPKEARPFFAKTVAILGGESSGKSVLVNKLAAVFNTTSAWEYGREFVFEKLGGDEQAMQYSDYPQMALGHQRYIDYAVRHSHKIAFIDTDFITTQAFCIQYEGKAHPFLDSMIKEYPFDVTILLKNNTEWVDDGLRSLGSQKQRQQFQQLLKKLLDKYKVPYIEIESPSYLDRYNQVKAVIEKVLNEEEISELQN 411
               SCOP domains d1lw7a1 A:57-219 Transcriptional regulator NadR, NMN-adenylyltransferase domain                                                                                    d1lw7a2 A:220-411 Transcriptional regulator NadR, ribosylnicotinamide kinase domain                                                                                                              SCOP domains
               CATH domains 1lw7A01 A:57-225 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                   1lw7A02 A:226-394 P-loop containing nucleotide triphosphate hydrolases                                                                                                   ----------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAA_28-1lw7A01 A:228-389                                                                                                                                          ---------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhh...eeeeeeeehhhhhhhhhhhh......hhhhhhhhhhhhh......eeeeeee.........hhhhhhhhhhhhhhhh.....eee..hhhhhhhhhhhh..eee...........hhhhhhhhhhhhhhhh...hhhhh.eeeeee....hhhhhhhhhhhhhh..eee...hhhhhhhh...........hhhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhh..hhhhhhhhhhh...eeeeee....-----------..hhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lw7 A  57 EKKVGVIFGKFYPVHTGHINmIYEAFSKVDELHVIVCSDTVRDLKLFYDSKmKRmPTVQDRLRWmQQIFKYQKNQIFIHHLVEDGIPSYPNGWQSWSEAVKTLFHEKHFEPSIVFSSEPQDKAPYEKYLGLEVSLVDPDRTFFNVSATKIRTTPFQYWKFIPKEARPFFAKTVAILGGESSGKSVLVNKLAAVFNTTSAWEYGREFVFEKLGGDEQAMQYSDYPQmALGHQRYIDYAVRHSHKIAFIDTDFITTQAFCIQYEGKAHPFLDSmIKEYPFDVTILLKNNTE-----------QKQRQQFQQLLKKLLDKYKVPYIEIESPSYLDRYNQVKAVIEKVLNEEEISELQN 411
                                    66        76|       86        96       106 |  |  116    |  126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276     | 286       296       306       316       326 |     336        |-         -|      366       376       386       396       406     
                                               77-MSE                        108-MSE      121-MSE                                                                                                                                                          282-MSE                                       328-MSE          345         357                                                      
                                                                                111-MSE                                                                                                                                                                                                                                                                                                        

   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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)
Chain A   (NADR_HAEIN | P44308)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000309    nicotinamide-nucleotide adenylyltransferase activity    Catalysis of the reaction: ATP + nicotinamide nucleotide = diphosphate + NAD+.
    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:0050262    ribosylnicotinamide kinase activity    Catalysis of the reaction: N-ribosylnicotinamide + ATP = ADP + 2 H(+) + nicotinamide mononucleotide.
    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.
biological process
    GO:0009435    NAD biosynthetic process    The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide, a coenzyme present in most living cells and derived from the B vitamin nicotinic acid; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    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:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0019363    pyridine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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