3KUO - JenaLib

Title :   X-RAY STRUCTURE OF THE METCYANO FORM OF DEHALOPEROXIDASE FROM AMPHITRITE ORNATA: EVIDENCE FOR PHOTOREDUCTIVE LYSIS OF IRON-CYANIDE BOND

Authors :   V. S. Serrano, Z. Chen, J. F. Gaff, R. Rose, S. Franzen

Date :   27 Nov 09 (Deposition) - 30 Jun 10 (Release) - 28 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.26

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

Keywords :   Crystal Structure Of Metcyano Form Of Dehaloperoxydase, Heme, Oxygen Transport, Peroxidase, Transport, Transport Protein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. S. De Serrano, M. F. Davis, J. F. Gaff, Q. Zhang, Z. Chen, E. L. D'Antonio, E. F. Bowden, R. Rose, S. Franzen
X-Ray Structure Of The Metcyano Form Of Dehaloperoxidase From Amphitrite Ornata: Evidence For Photoreductive Dissociation Of The Iron-Cyanide Bond.
Acta Crystallogr. , Sect. D V. 66 770 2010
PubMed-ID: 20606257 | Reference-DOI: 10.1107/S0907444910014605

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:24 , GLU A:31 , TYR A:34 , PHE A:35 , HIS A:55 , LYS A:58 , VAL A:59 , MET A:63 , LEU A:83 , MET A:86 , GLN A:88 , HIS A:89 , LEU A:92 , ASN A:96 , PHE A:97 , CYN A:188 , HOH A:282 , HOH A:313	BINDING SITE FOR RESIDUE HEM A 139
2	AC2	SOFTWARE	PHE A:21 , PHE A:35 , HIS A:55 , VAL A:59 , HEM A:139	BINDING SITE FOR RESIDUE CYN A 188
3	AC3	SOFTWARE	GLY A:1 , PHE A:2 , LYS A:3 , ASP A:116 , HOH A:276 , HOH A:603 , ARG B:32 , VAL B:39 , GLY B:40 , HOH B:242	BINDING SITE FOR RESIDUE SO4 A 195
4	AC4	SOFTWARE	ARG A:32 , VAL A:39 , GLY A:40 , HOH A:224 , HOH A:234 , HOH A:235 , GLY B:1 , PHE B:2 , LYS B:3 , ASP B:116 , HOH B:219 , HOH B:289	BINDING SITE FOR RESIDUE SO4 A 196
5	AC5	SOFTWARE	ARG A:109 , SER A:117 , GLN A:118 , HOH A:311 , HOH B:612	BINDING SITE FOR RESIDUE SO4 A 198
6	AC6	SOFTWARE	PHE B:24 , GLU B:31 , TYR B:34 , PHE B:35 , LYS B:36 , ASP B:54 , HIS B:55 , LYS B:58 , VAL B:59 , MET B:63 , MET B:86 , GLN B:88 , HIS B:89 , LEU B:92 , ASN B:96 , PHE B:97 , LEU B:127 , CYN B:189 , HOH B:525	BINDING SITE FOR RESIDUE HEM B 139
7	AC7	SOFTWARE	PHE B:21 , PHE B:35 , HIS B:55 , VAL B:59 , HEM B:139	BINDING SITE FOR RESIDUE CYN B 189
8	AC8	SOFTWARE	ASP A:30 , LYS A:99 , HOH A:259 , GLU B:31 , ARG B:33 , TYR B:34 , ASN B:96 , LYS B:99 , HOH B:499 , HOH B:601	BINDING SITE FOR RESIDUE SO4 B 197

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:137
 aligned with Q9NAV8_9ANNE | Q9NAV8 from UniProtKB/TrEMBL  Length:138

    Alignment length:137
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       
         Q9NAV8_9ANNE     2 GFKQDIATIRGDLRTYAQDIFLAFLNKYPDERRYFKNYVGKSDQELKSMAKFGDHTEKVFNLMMEVADRATDCVPLASDANTLVQMKQHSSLTTGNFEKLFVALVEYMRASGQSFDSQSWDRFGKNLVSALSSAGMK 138
               SCOP domains d3kuoa_ A: Dehaloperoxidase                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kuo A   1 GFKQDIATIRGDLRTYAQDIFLAFLNKYPDERRYFKNYVGKSDQELKSMAKFGDHTEKVFNLMMEVADRATDSVPLASDANTLVQMKQHSSLTTGNFEKLFVALVEYMRASGQSFDSQSWDRFGKNLVSALSSAGMK 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain B from PDB  Type:PROTEIN  Length:137
 aligned with Q9NAV8_9ANNE | Q9NAV8 from UniProtKB/TrEMBL  Length:138

    Alignment length:137
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       
         Q9NAV8_9ANNE     2 GFKQDIATIRGDLRTYAQDIFLAFLNKYPDERRYFKNYVGKSDQELKSMAKFGDHTEKVFNLMMEVADRATDCVPLASDANTLVQMKQHSSLTTGNFEKLFVALVEYMRASGQSFDSQSWDRFGKNLVSALSSAGMK 138
               SCOP domains d3kuob_ B: Dehaloperoxidase                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Globin-3kuoB01 B:2-128                                                                                                         --------- Pfam domains (1)
           Pfam domains (2) -Globin-3kuoB02 B:2-128                                                                                                         --------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kuo B   1 GFKQDIATIRGDLRTYAQDIFLAFLNKYPDERRYFKNYVGKSDQELKSMAKFGDHTEKVFNLMMEVADRATDSVPLASDANTLVQMKQHSSLTTGNFEKLFVALVEYMRASGQSFDSQSWDRFGKNLVSALSSAGMK 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

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	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, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (8, 8)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q9NAV8_9ANNE | Q9NAV8)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0019825	oxygen binding	Interacting selectively and non-covalently with oxygen (O2).
	GO:0005344	oxygen transporter activity	Enables the directed movement of oxygen into, out of or within a cell, or between cells.
	GO:0004601	peroxidase activity	Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
biological process
	GO:0098869	cellular oxidant detoxification	Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
	GO:0015671	oxygen transport	The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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.

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