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(-) Description

Title :  STRUCTURE OF N-TERMINAL FAD BINDING MOTIF OF MOUSE MICAL
 
Authors :  M. Nadella, M. A. Bianchet, S. B. Gabelli, L. M. Amzel
Date :  04 May 05  (Deposition) - 01 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transport, Axon Guidance, Vesicle Transport, Flavoprotein, Redox, Plexin, Coiled Coil, Cytoskeleton, Fad, Lim Domain, Metal-Binding, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Nadella, M. A. Bianchet, S. B. Gabelli, J. Barrila, L. M. Amzel
Structure And Activity Of The Axon Guidance Protein Mical.
Proc. Natl. Acad. Sci. Usa V. 102 16830 2005
PubMed-ID: 16275926  |  Reference-DOI: 10.1073/PNAS.0504838102

(-) Compounds

Molecule 1 - NEDD9 INTERACTING PROTEIN WITH CALPONIN HOMOLOGY AND LIM DOMAINS
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: DE3
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Expression System Variant: PLYS
    Fragment: N-TERMINAL DOMAIN, RESIDUES 1-484
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: MICAL, MOLECULE INTERACTING WITH CASL PROTEIN 1
    Tissue: MAMMARY TUMOR

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS B:23 , PHE B:119 , ARG B:158BINDING SITE FOR RESIDUE CL B1486
2AC2SOFTWAREVAL A:90 , GLY A:91 , GLY A:93 , PRO A:94 , CYS A:95 , VAL A:113 , GLU A:114 , LYS A:115 , ARG A:116 , ARG A:121 , ASN A:123 , LEU A:125 , ILE A:157 , LYS A:180 , PHE A:181 , ALA A:217 , ALA A:218 , GLY A:219 , TYR A:293 , GLY A:392 , ASP A:393 , TRP A:400 , HOH A:2167 , HOH A:2199 , HOH A:2255 , HOH A:2318 , HOH A:2319 , HOH A:2320 , HOH A:2321 , HOH A:2322 , HOH A:2323 , HOH A:2324BINDING SITE FOR RESIDUE FAD A1485
3AC3SOFTWAREVAL B:90 , GLY B:91 , GLY B:93 , PRO B:94 , CYS B:95 , VAL B:113 , GLU B:114 , LYS B:115 , ARG B:116 , ARG B:121 , ASN B:123 , LEU B:125 , ILE B:157 , LYS B:180 , PHE B:181 , ALA B:217 , ALA B:218 , GLY B:219 , TYR B:293 , GLY B:392 , ASP B:393 , TRP B:400 , HOH B:2098 , HOH B:2109 , HOH B:2166 , HOH B:2287 , HOH B:2288 , HOH B:2289 , HOH B:2290 , HOH B:2291 , HOH B:2292 , HOH B:2293BINDING SITE FOR RESIDUE FAD B1485

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BRA)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gln A:199 -Pro A:200
2Gln B:199 -Pro B:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BRA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BRA)

(-) Exons   (0, 0)

(no "Exon" information available for 2BRA)

(-) 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:473
 aligned with MICA1_MOUSE | Q8VDP3 from UniProtKB/Swiss-Prot  Length:1048

    Alignment length:477
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       
          MICA1_MOUSE     8 NPAHDHFETFVQAQLCQDVLSSFQGLCRALGVESGGGLSQYHKIKAQLNYWSAKSLWAKLDKRASQPVYQQGQACTNTKCLVVGAGPCGLRAAVELALLGARVVLVEKRIKFSRHNVLHLWPFTIHDLRALGAKKFYGRFCTGTLDHISIRQLQLLLLKVALLLGVEIHWGVKFTGLQPPPRKGSGWRAQLQPNPPAQLASYEFDVLISAAGGKFVPEGFTIREMRGKLAIGITANFVNGRTVEETQVPEISGVARIYNQKFFQSLLKATGIDLENIVYYKDETHYFVMTAKKQCLLRLGVLRQDLSETDQLLGKANVVPEALQRFARAAADFATHGKLGKLEFAQDARGRPDVAAFDFTSMMRAESSARVQEKHGARLLLGLVGDCLVEPFWPLGTGVARGFLAAFDAAWMVKRWAEGAGPLEVLAERESLYQLLSQTSPENMHRNVAQYGLDPATRYPNLNLRAVTPNQVQDLYD 484
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhh.eeeeee.........eee.hhhhhhhhhhhhhhhhh..----...eeehhhhhhhhhhhhhhh..eeee..eeeeee.........eeeee...hhhhhh....eeee...........eeeeee....eeeeeeee...hhhhhh.............hhhhhhhhhhh..eeeeeeee..eeeeeeeehhhhhhhh........hhhhhh.....hhhhhhhhhhhhhhhhh..................eeeee..eeeee...eeeeee..eeeeeee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.......hhhhh..hhhhh..........hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bra A   8 NPAHDHFETFVQAQLCQDVLSSFQGLCRALGVESGGGLSQYHKIKAQLNYWSAKSLWAKLDKRASQPVYQQGQACTNTKCLVVGAGPCGLRAAVELALLGARVVLVEKRIKFSRHNVLHLWPFTIHDLRALGAAAFYGR----TLDHISIRQLQLLLLKVALLLGVEIHWGVKFTGLQPPPRKGSGWRAQLQPNPPAQLASYEFDVLISAAGGKFVPEGFTIREMRGKLAIGITANFVNGRTVEETQVPEISGVARIYNQKFFQSLLKATGIDLENIVYYKDETHYFVMTAKKQCLLRLGVLRQDLSETDQLLGKANVVPEALQRFARAAADFATHGKLGKLEFAQDARGRPDVAAFDFTSMMRAESSARVQEKHGARLLLGLVGDCLVEPFWPLGTGVARGFLAAFDAAWMVKRWAEGAGPLEVLAERESLYQLLSQTSPENMHRNVAQYGLDPATRYPNLNLRAVTPNQVQDLYD 484
                                    17        27        37        47        57        67        77        87        97       107       117       127       137        |-   |   157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       
                                                                                                                                                                    146  151                                                                                                                                                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:478
 aligned with MICA1_MOUSE | Q8VDP3 from UniProtKB/Swiss-Prot  Length:1048

    Alignment length:484
                                    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    
          MICA1_MOUSE     1 MASPASTNPAHDHFETFVQAQLCQDVLSSFQGLCRALGVESGGGLSQYHKIKAQLNYWSAKSLWAKLDKRASQPVYQQGQACTNTKCLVVGAGPCGLRAAVELALLGARVVLVEKRIKFSRHNVLHLWPFTIHDLRALGAKKFYGRFCTGTLDHISIRQLQLLLLKVALLLGVEIHWGVKFTGLQPPPRKGSGWRAQLQPNPPAQLASYEFDVLISAAGGKFVPEGFTIREMRGKLAIGITANFVNGRTVEETQVPEISGVARIYNQKFFQSLLKATGIDLENIVYYKDETHYFVMTAKKQCLLRLGVLRQDLSETDQLLGKANVVPEALQRFARAAADFATHGKLGKLEFAQDARGRPDVAAFDFTSMMRAESSARVQEKHGARLLLGLVGDCLVEPFWPLGTGVARGFLAAFDAAWMVKRWAEGAGPLEVLAERESLYQLLSQTSPENMHRNVAQYGLDPATRYPNLNLRAVTPNQVQDLYD 484
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhh..eeeee..........eee.hhhhhhhhhhhhhhhhh..-----..eeehhhhhhhhhhhhhhh..eee...eeeeee.........eeeee...hhhhhh....eeee...........eeeee.....eeeeeeee...hhhhhhh..eeeee..-..hhhhhhhhhhh..eeeeeeee..eeeeeeeehhhhhhhh........hhhhhh.....hhhhhhhhhhhhhhhhhh.................eeeee.....ee...eeeeee..eeeeeee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.......hhhhh..hhhhh..........hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bra B   1 MASPASTNPAHDHFETFVQAQLCQDVLSSFQGLCRALGVESGGGLSQYHKIKAQLNYWSAKSLWAKLDKRASQPVYQQGQACTNTKCLVVGAGPCGLRAAVELALLGARVVLVEKRIKFSRHNVLHLWPFTIHDLRALGAAAFYGR-----LDHISIRQLQLLLLKVALLLGVEIHWGVKFTGLQPPPRKGSGWRAQLQPNPPAQLASYEFDVLISAAGGKFVPEGFTIREMRGKLAIGITANFVNGRTVEETQVPEISGVARI-NQKFFQSLLKATGIDLENIVYYKDETHYFVMTAKKQCLLRLGVLRQDLSETDQLLGKANVVPEALQRFARAAADFATHGKLGKLEFAQDARGRPDVAAFDFTSMMRAESSARVQEKHGARLLLGLVGDCLVEPFWPLGTGVARGFLAAFDAAWMVKRWAEGAGPLEVLAERESLYQLLSQTSPENMHRNVAQYGLDPATRYPNLNLRAVTPNQVQDLYD 484
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     |   - |     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    
                                                                                                                                                                           146   152                                                                                                             264 |                                                                                                                                                                                                                          
                                                                                                                                                                                                                                                                                                   266
   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 2BRA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2BRA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BRA)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MICA1_MOUSE | Q8VDP3)
molecular function
    GO:0071949    FAD binding    Interacting selectively and non-covalently with the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0017137    Rab GTPase binding    Interacting selectively and non-covalently with Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases.
    GO:0017124    SH3 domain binding    Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    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:0016709    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from NADH or NADPH and one other donor, and one atom of oxygen is incorporated into one donor.
    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).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0030042    actin filament depolymerization    Disassembly of actin filaments by the removal of actin monomers from a filament.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0043154    negative regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.
    GO:0001933    negative regulation of protein phosphorylation    Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.
    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:0019417    sulfur oxidation    The chemical reactions and pathways resulting the addition of oxygen to elemental sulfur.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MICA1_MOUSE | Q8VDP3: 2bry 2c4c 4txi 4txk

(-) Related Entries Specified in the PDB File

2bry CRYSTAL STRUCTURE OF THE NATIVE MONOOXYGENASE DOMAIN OF MICAL AT 1.45 A RESOLUTION
2c4c CRYSTAL STRUCTURE OF THE NADPH-TREATED MONOOXYGENASE DOMAIN OF MICAL