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(-) Description

Title :  CRYSTAL STRUCTURE OF GIDA FROM E. COLI
 
Authors :  A. Scrima, S. Meyer, W. Versees, A. Wittinghofer
Date :  30 Mar 08  (Deposition) - 24 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Fad, Nad, Oxidoreductase, Trna, Cytoplasm, Flavoprotein, Trna Processing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Meyer, A. Scrima, W. Versees, A. Wittinghofer
Crystal Structures Of The Conserved Trna-Modifying Enzyme Gida: Implications For Its Interaction With Mnme And Substrate
J. Mol. Biol. V. 380 532 2008
PubMed-ID: 18565343  |  Reference-DOI: 10.1016/J.JMB.2008.04.072
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRNA URIDINE 5-CARBOXYMETHYLAMINOMETHYL MODIFICATION ENZYME GIDA
    Chains: A
    EC Number: 1.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 14B
    Expression System Strain: BL21 DE3
    Expression System Vector Type: PLASMID
    Gene: GIDA
    Organism Scientific: ESCHERICHIA COLI
    Strain: K12
    Synonym: GLUCOSE-INHIBITED DIVISION PROTEIN A

 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
1SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:16 , ALA A:17 , GLN A:370BINDING SITE FOR RESIDUE SO4 A 630

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CP2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn A:222 -Pro A:223

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CP2)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GIDA_2PS01281 Glucose inhibited division protein A family signature 2.MNMG_ECOLI368-391  1A:368-391
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GIDA_2PS01281 Glucose inhibited division protein A family signature 2.MNMG_ECOLI368-391  2A:368-391

(-) Exons   (0, 0)

(no "Exon" information available for 3CP2)

(-) 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:491
 aligned with MNMG_ECOLI | P0A6U3 from UniProtKB/Swiss-Prot  Length:629

    Alignment length:553
                                    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   
           MNMG_ECOLI     1 MFYPDPFDVIIIGGGHAGTEAAMAAARMGQQTLLLTHNIDTLGQMSCNPAIGGIGKGHLVKEVDALGGLMAKAIDQAGIQFRILNASKGPAVRATRAQADRVLYRQAVRTALENQPNLMIFQQAVEDLIVENDRVVGAVTQMGLKFRAKAVVLTVGTFLDGKIHIGLDNYSGGRAGDPPSIPLSRRLRELPLRVGRLKTGTPPRIDARTIDFSVLAQQHGDNPMPVFSFMGNASQHPQQVPCYITHTNEKTHDVIRSNLDRSPMYAGVIEGVGPRYCPSIEDKVMRFADRNQHQIFLEPEGLTSNEIYPNGISTSLPFDVQMQIVRSMQGMENAKIVRPGYAIEYDFFDPRDLKPTLESKFIQGLFFAGQINGTTGYEEAAAQGLLAGLNAARLSADKEGWAPARSQAYLGVLVDDLCTLGTKEPYRMFTSRAEYRLMLREDNADLRLTEIGRELGLVDDERWARFNEKLENIERERQRLKSTWVTPSAEAAAEVNAHLTAPLSREASGEDLLRRPEMTYEKLTTLTPFAPALTDEQAAEQVEIQVKYEGYIA 553
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee...hhhhhhhhhhhhh...eeee..............eee..hhhhhhhhhhhh..hhhhhhhhheeeeeee.........eeeeeehhhhhhhhhhhhhhh...eeee.....eeeee..eeeeee.....eee..eeee.....----------------------hhhhhhhhh.......eeeee...ee.hhh.....eee.............hhhhh.....eeee...----------------------------------------......eeeee......eeee.......hhhhhhhhhhh.............eeeee...hhhhh...........eee.hhhhh..hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh....hhhhh...hhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhee.....hhhhhh..........eehhhhhh....hhhhhhhhhhhh....hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GIDA_2  PDB: A:368-391  ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cp2 A   1 MFYPDPFDVIIIGGGHAGTEAAMAAARMGQQTLLLTHNIDTLGQMSCNPAIGGIGKGHLVKEVDALGGLMAKAIDQAGIQFRILNASKGPAVRATRAQADRVLYRQAVRTALENQPNLMIFQQAVEDLIVENDRVVGAVTQMGLKFRAKAVVLTVGTF----------------------IPLSRRLRELPLRVGRLKTGTPPRIDARTIDFSVLAQQHGDNPMPVFSFMGNASQHPQQVPCYITHTN----------------------------------------DRNQHQIFLEPEGLTSNEIYPNGISTSLPFDVQMQIVRSMQGMENAKIVRPGYAIEYDFFDPRDLKPTLESKFIQGLFFAGQINGTTGYEEAAAQGLLAGLNAARLSADKEGWAPARSQAYLGVLVDDLCTLGTKEPYRMFTSRAEYRLMLREDNADLRLTEIGRELGLVDDERWARFNEKLENIERERQRLKSTWVTPSAEAAAEVNAHLTAPLSREASGEDLLRRPEMTYEKLTTLTPFAPALTDEQAAEQVEIQVKYEGYIA 553
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       | -         -         -|      190       200       210       220       230       240       | -         -         -         -       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   
                                                                                                                                                                                       158                    181                                                                248                                      289
   Legend:   → Mismatch (orange background)
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  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 3CP2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3CP2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CP2)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (MNMG_ECOLI | P0A6U3)
molecular function
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    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.
    GO:0030488    tRNA methylation    The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
    GO:0002098    tRNA wobble uridine modification    The process in which a uridine in position 34 of a tRNA is post-transcriptionally modified.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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        MNMG_ECOLI | P0A6U3: 3ces

(-) Related Entries Specified in the PDB File

3cp8 CRYSTAL STRUCTURE OF GIDA FROM CHLOROBIUM TEPIDUM