2C4C - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE NADPH-TREATED MONOOXYGENASE DOMAIN OF MICAL

Authors :   C. Siebold, N. Berrow, T. S. Walter, K. Harlos, R. J. Owens, J. R. Terman, D. I. Stuart, A. L. Kolodkin, R. J. Pasterkamp, E. Y. Jones

Date :   18 Oct 05 (Deposition) - 26 Oct 05 (Release) - 28 Jun 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Cytoskeleton, Fad, Flavoprotein, Lim Domain, Metal-Binding, Signaling Protein, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Siebold, N. Berrow, T. S. Walter, K. Harlos, R. J. Owens, D. I. Stuart J. R. Terman, A. L. Kolodkin, R. J. Pasterkamp, E. Y. Jones
High-Resolution Structure Of The Catalytic Region Of Mical (Molecule Interacting With Casl), A Multidomain Flavoenzyme-Signaling Molecule.
Proc. Natl. Acad. Sci. Usa V. 102 16836 2005
PubMed-ID: 16275925 | Reference-DOI: 10.1073/PNAS.0504997102

Molecule 1 - NEDD9-INTERACTING PROTEIN WITH CALPONIN HOMOLOGY AND LIM DOMAINS
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	MICAL, MOLECULE INTERACTING WITH CASL PROTEIN 1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:23 , LYS A:118 , PHE A:119	BINDING SITE FOR RESIDUE CL A 601
2	AC2	SOFTWARE	CYS B:23 , PHE B:119 , ARG B:158	BINDING SITE FOR RESIDUE CL B 601
3	AC3	SOFTWARE	GLY A:91 , GLY A:93 , PRO A:94 , CYS A:95 , GLU A:114 , LYS A:115 , ARG A:116 , ARG A:121 , ASN A:123 , LEU A:125 , HIS A:126 , VAL A:179 , 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 , GLY A:403 , GLY A:405 , VAL A:406	BINDING SITE FOR RESIDUE FAD A 600
4	AC4	SOFTWARE	VAL B:90 , GLY B:91 , GLY B:93 , PRO B:94 , CYS B:95 , GLU B:114 , LYS B:115 , ARG B:116 , ARG B:121 , ASN B:123 , LEU B:125 , HIS B:126 , ILE B:157 , VAL B:179 , LYS B:180 , PHE B:181 , ALA B:217 , ALA B:218 , GLY B:219 , THR B:241 , TYR B:293 , GLY B:392 , ASP B:393 , TRP B:400 , GLY B:403 , GLY B:405 , VAL B:406 , HOH B:2007	BINDING SITE FOR RESIDUE FAD B 600

(no "SS Bond" information available for 2C4C)

Asymmetric Unit

No.	Residues
1	Gln A:199	-	Pro A:200
2	Asp A:354	-	Ala A:355
3	Gln B:199	-	Pro B:200
4	Gly B:220	-	Lys B:221
5	Phe B:222	-	Val B:223

(no "SAP(SNP)/Variant" information available for 2C4C)

(no "PROSITE Motif" information available for 2C4C)

(no "Exon" information available for 2C4C)

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:476
 aligned with MICA1_MOUSE | Q8VDP3 from UniProtKB/Swiss-Prot  Length:1048

    Alignment length:481
                                    16        26        36        46        56        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       416       426       436       446       456       466       476       486 
          MICA1_MOUSE     7 TNPAHDHFETFVQAQLCQDVLSSFQGLCRALGVESGGGLSQYHKIKAQLNYWSAKSLWAKLDKRASQPVYQQGQACTNTKCLVVGAGPCGLRAAVELALLGARVVLVEKRIKFSRHNVLHLWPFTIHDLRALGAKKFYGRFCTGTLDHISIRQLQLLLLKVALLLGVEIHWGVKFTGLQPPPRKGSGWRAQLQPNPPAQLASYEFDVLISAAGGKFVPEGFTIREMRGKLAIGITANFVNGRTVEETQVPEISGVARIYNQKFFQSLLKATGIDLENIVYYKDETHYFVMTAKKQCLLRLGVLRQDLSETDQLLGKANVVPEALQRFARAAADFATHGKLGKLEFAQDARGRPDVAAFDFTSMMRAESSARVQEKHGARLLLGLVGDCLVEPFWPLGTGVARGFLAAFDAAWMVKRWAEGAGPLEVLAERESLYQLLSQTSPENMHRNVAQYGLDPATRYPNLNLRAVTPNQVQDLYDMMD 487
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhhh.eeeee..........eee.hhhhhhhhhhhhhhhhh.........eeehhhhhhhhhhhhhhh..eee...eeeeee.........eeeee...hhhhhhh...eeee...........eeeeee....eeeeeeee..............-----..hhhhhhh.......eeeeeeee..eeeeeeeehhhhhh..........hhhhhh.....hhhhhhhhhhhhhhhhh..................eeeee..eeeee...eeeeee..eeeeeee.............hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh............hhhhh..hhhhh.................eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c4c A   7 TNPAHDHFETFVQAQLCQDVLSSFQGLCRALGVESGGGLSQYHKIKAQLNYWSAKSLWAKLDKRASQPVYQQGQACTNTKCLVVGAGPCGLRAAVELALLGARVVLVEKRIKFSRHNVLHLWPFTIHDLRALGAKKFYGRFCTGTLDHISIRQLQLLLLKVALLLGVEIHWGVKFTGLQPPPRKGSGWRAQLQPNPPAQLASYEFDVLISAAGGKFVPEGFTIREMRGKLAIGITANFVNGRTVEETQVPEIS-----YNQKFFQSLLKATGIDLENIVYYKDETHYFVMTAKKQCLLRLGVLRQDLSETDQLLGKANVVPEALQRFARAAADFATHGKLGKLEFAQDARGRPDVAAFDFTSMMRAESSARVQEKHGARLLLGLVGDCLVEPFWPLGTGVARGFLAAFDAAWMVKRWAEGAGPLEVLAERESLYQLLSQTSPENMHRNVAQYGLDPATRYPNLNLRAVTPNQVQDLYDMMD 487
                                    16        26        36        46        56        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       416       426       436       446       456       466       476       486 
                                                                                                                                                                                                                                                                                      259   265

Chain B from PDB  Type:PROTEIN  Length:477
 aligned with MICA1_MOUSE | Q8VDP3 from UniProtKB/Swiss-Prot  Length:1048

    Alignment length:481
                                    16        26        36        46        56        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       416       426       436       446       456       466       476       486 
          MICA1_MOUSE     7 TNPAHDHFETFVQAQLCQDVLSSFQGLCRALGVESGGGLSQYHKIKAQLNYWSAKSLWAKLDKRASQPVYQQGQACTNTKCLVVGAGPCGLRAAVELALLGARVVLVEKRIKFSRHNVLHLWPFTIHDLRALGAKKFYGRFCTGTLDHISIRQLQLLLLKVALLLGVEIHWGVKFTGLQPPPRKGSGWRAQLQPNPPAQLASYEFDVLISAAGGKFVPEGFTIREMRGKLAIGITANFVNGRTVEETQVPEISGVARIYNQKFFQSLLKATGIDLENIVYYKDETHYFVMTAKKQCLLRLGVLRQDLSETDQLLGKANVVPEALQRFARAAADFATHGKLGKLEFAQDARGRPDVAAFDFTSMMRAESSARVQEKHGARLLLGLVGDCLVEPFWPLGTGVARGFLAAFDAAWMVKRWAEGAGPLEVLAERESLYQLLSQTSPENMHRNVAQYGLDPATRYPNLNLRAVTPNQVQDLYDMMD 487
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhhh.eeeee..........eee.hhhhhhhhhhhhhhhhh.........eeehhhhhhhhhhhhhhh..eee...eeeeee.........eeeee...hhhhhh....eeee............eeee.....eeeeeeee...............----..hhhhhhh.......eeeeeeee..eeeeeeeehhhhhhhh........hhhhhh.....hhhhhhhhhhhhhhhhh.................eeeeee...eeee...eeeeee..eeeeeee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhh..hhhhh.................eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c4c B   7 TNPAHDHFETFVQAQLCQDVLSSFQGLCRALGVESGGGLSQYHKIKAQLNYWSAKSLWAKLDKRASQPVYQQGQACTNTKCLVVGAGPCGLRAAVELALLGARVVLVEKRIKFSRHNVLHLWPFTIHDLRALGAKKFYGRFCTGTLDHISIRQLQLLLLKVALLLGVEIHWGVKFTGLQPPPRKGSGWRAQLQPNPPAQLASYEFDVLISAAGGKFVPEGFTIREMRGKLAIGITANFVNGRTVEETQVPEISG----YNQKFFQSLLKATGIDLENIVYYKDETHYFVMTAKKQCLLRLGVLRQDLSETDQLLGKANVVPEALQRFARAAADFATHGKLGKLEFAQDARGRPDVAAFDFTSMMRAESSARVQEKHGARLLLGLVGDCLVEPFWPLGTGVARGFLAAFDAAWMVKRWAEGAGPLEVLAERESLYQLLSQTSPENMHRNVAQYGLDPATRYPNLNLRAVTPNQVQDLYDMMD 487
                                    16        26        36        46        56        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       416       426       436       446       456       466       476       486 
                                                                                                                                                                                                                                                                                       260  265

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 '\|'

(no "SCOP Domain" information available for 2C4C)

(no "CATH Domain" information available for 2C4C)

(no "Pfam Domain" information available for 2C4C)

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.

Asymmetric Unit
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		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asp A:354 - Ala A:355	[ RasMol ]
		Gln A:199 - Pro A:200	[ RasMol ]
		Gln B:199 - Pro B:200	[ RasMol ]
		Gly B:220 - Lys B:221	[ RasMol ]
		Phe B:222 - Val B:223	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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

2bra	STRUCTURE OF N-TERMINAL FAD BINDING MOTIF OF MOUSE MICAL
2bry	CRYSTAL STRUCTURE OF THE NATIVE MONOOXYGENASE DOMAIN OF MICAL AT 1.45 A RESOLUTION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Gene Ontology (18, 18)

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