1E5D - JenaLib

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Title :   RUBREDOXIN OXYGEN:OXIDOREDUCTASE (ROO) FROM ANAEROBE DESULFOVIBRIO GIGAS

Authors :   C. Frazao, G. Silva, C. M. Gomes, P. Matias, R. Coelho, L. Sieker, S. Macedo, M. Y. Liu, S. Oliveira, M. Teixeira, A. V. Xavier, C. Rodrigues-Pousada, M. A. Carrondo, J. Le Gall

Date :   24 Jul 00 (Deposition) - 17 Nov 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B

Keywords :   Oxidoreductase, Oxygenreductase, Diiron-Centre, Flavoproteins, Lactamase-Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Frazao, G. Silva, C. M. Gomes, P. Matias, R. Coelho, L. Sieker, S. Macedo, M. Y. Liu, S. Oliveira, M. Teixeira, A. V. Xavier, C. Rodrigues-Pousada, M. A. Carrondo, J. Le Gall
Structure Of A Dioxygen Reduction Enzyme From Desulfovibrio Gigas
Nat. Struct. Biol. V. 7 1041 2000
PubMed-ID: 11062560 | Reference-DOI: 10.1038/80961
(for further references see the PDB file header)

Molecule 1 - RUBREDOXIN:OXYGEN OXIDOREDUCTASE
	Chains	:	A, B
	Organism Scientific	:	DESULFOVIBRIO GIGAS
	Organism Taxid	:	879

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	FEO	2	Ligand/Ion	MU-OXO-DIIRON
2	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
3	OXY	2	Ligand/Ion	OXYGEN MOLECULE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:261 , MET A:262 , TRP A:263 , HIS A:264 , SER A:265 , THR A:266 , PRO A:312 , THR A:313 , HIS A:314 , ASN A:315 , ASN A:316 , SER A:344 , PHE A:345 , GLY A:346 , TRP A:347 , SER A:348 , GLY A:349 , ASN A:375 , HOH A:2061 , HOH A:2084 , GLU B:81 , TRP B:147	BINDING SITE FOR RESIDUE FMN A 403
2	AC2	SOFTWARE	HIS A:79 , GLU A:81 , ASP A:83 , HIS A:146 , ASP A:165 , HIS A:226 , OXY A:405 , HOH A:2044	BINDING SITE FOR RESIDUE FEO A 404
3	AC3	SOFTWARE	TYR A:26 , GLU A:81 , ASP A:165 , TYR A:193 , ILE A:197 , HIS A:226 , FEO A:404	BINDING SITE FOR RESIDUE OXY A 405
4	AC4	SOFTWARE	GLU A:81 , TRP A:147 , ILE A:197 , SER B:261 , MET B:262 , TRP B:263 , HIS B:264 , SER B:265 , THR B:266 , PRO B:312 , THR B:313 , HIS B:314 , ASN B:315 , ASN B:316 , SER B:344 , PHE B:345 , GLY B:346 , TRP B:347 , SER B:348 , GLY B:349 , ASN B:375 , HOH B:2056 , HOH B:2086	BINDING SITE FOR RESIDUE FMN B 403
5	AC5	SOFTWARE	HIS B:79 , GLU B:81 , ASP B:83 , HIS B:146 , ASP B:165 , HIS B:226 , OXY B:405 , HOH B:2018	BINDING SITE FOR RESIDUE FEO B 404
6	AC6	SOFTWARE	PHE B:23 , TYR B:26 , GLU B:81 , ASP B:165 , TYR B:193 , ILE B:197 , HIS B:226 , FEO B:404	BINDING SITE FOR RESIDUE OXY B 405

(no "SS Bond" information available for 1E5D)

Asymmetric/Biological Unit

No.	Residues
1	Leu A:145	-	His A:146
2	Leu B:145	-	His B:146

(no "SAP(SNP)/Variant" information available for 1E5D)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FLAVODOXIN_LIKE	PS50902	Flavodoxin-like domain profile.	ROO_DESGI	255-393	2	A:255-393 B:255-393

(no "Exon" information available for 1E5D)

Asymmetric/Biological 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:401
 aligned with ROO_DESGI | Q9F0J6 from UniProtKB/Swiss-Prot  Length:402

    Alignment length:401
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401 
            ROO_DESGI     2 QATKIIDGFHLVGAIDWNSRDFHGYTLSPMGTTYNAYLVEDEKTTLFDTVKAEYKGELLCGIASVIDPKKIDYLVIQHLELDHAGALPALIEACQPEKIFTSSLGQKAMESHFHYKDWPVQVVKHGETLSLGKRTVTFYETRMLHWPDSMVSWFADEKVLISNDIFGQNIAASERFSDQIPVHTLERAMREYYANIVNPYAPQTLKAIETLVGAGVAPEFICPDHGVIFRGADQCTFAVQKYVEYAEQKPTNKVVIFYDSMWHSTEKMARVLAESFRDEGCTVKLMWCKACHHSQIMSEISDAGAVIVGSPTHNNGILPYVAGTLQYIKGLRPQNKIGGAFGSFGWSGESTKVLAEWLTGMGFDMPATPVKVKNVPTHADYEQLKTMAQTIARALKAKLAA 402
               SCOP domains d1e5da2 A:2-250 Rubredoxin oxygen:oxidoreductase (ROO), N-terminal domain                                                                                                                                                                                d1e5da1 A:251-402 Rubredoxin oxygen:oxidoreductase (ROO), C-terminal domain                                                                              SCOP domains
               CATH domains 1e5dA02 A:2-248 Metallo-beta-lactamase, chain A                                                                                                                                                                                                        -----1e5dA01 A:254-396  [code=3.40.50.360, no name defined]                                                                                         ------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeeeeee....ee...ee....eeeeeeee.....eee...hhhhhhhhhhhhhh..hhhhh.eeee...hhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhh.....eeee....eee....eeeeee.........eeeee....eeeee.............hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhhh.....eeeeeeee...hhhhhhhhhhhhhh........eeee...hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FLAVODOXIN_LIKE  PDB: A:255-393 UniProt: 255-393                                                                                           --------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e5d A   2 QATKIIDGFHLVGAIDWNSRDFHGYTLSPMGTTYNAYLVEDEKTTLFDTVKAEYKGELLCGIASVIDPKKIDYLVIQHLELDHAGALPALIEACQPEKIFTSSLGQKAMESHFHYKDWPVQVVKHGETLSLGKRTVTFYETRMLHWPDSMVSWFADEKVLISNDIFGQNIAASERFSDQIPVHTLERAMREYYANIVNPYAPQTLKAIETLVGAGVAPEFICPDHGVIFRGADQCTFAVQKYVEYAEQKPTNKVVIFYDSMWHSTEKMARVLAESFRDEGCTVKLMWCKACHHSQIMSEISDAGAVIVGSPTHNNGILPYVAGTLQYIKGLRPQNKIGGAFGSFGWSGESTKVLAEWLTGMGFDMPATPVKVKNVPTHADYEQLKTMAQTIARALKAKLAA 402
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401

Chain B from PDB  Type:PROTEIN  Length:401
 aligned with ROO_DESGI | Q9F0J6 from UniProtKB/Swiss-Prot  Length:402

    Alignment length:401
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401 
            ROO_DESGI     2 QATKIIDGFHLVGAIDWNSRDFHGYTLSPMGTTYNAYLVEDEKTTLFDTVKAEYKGELLCGIASVIDPKKIDYLVIQHLELDHAGALPALIEACQPEKIFTSSLGQKAMESHFHYKDWPVQVVKHGETLSLGKRTVTFYETRMLHWPDSMVSWFADEKVLISNDIFGQNIAASERFSDQIPVHTLERAMREYYANIVNPYAPQTLKAIETLVGAGVAPEFICPDHGVIFRGADQCTFAVQKYVEYAEQKPTNKVVIFYDSMWHSTEKMARVLAESFRDEGCTVKLMWCKACHHSQIMSEISDAGAVIVGSPTHNNGILPYVAGTLQYIKGLRPQNKIGGAFGSFGWSGESTKVLAEWLTGMGFDMPATPVKVKNVPTHADYEQLKTMAQTIARALKAKLAA 402
               SCOP domains d1e5db2 B:2-250 Rubredoxin oxygen:oxidoreductase (ROO), N-terminal domain                                                                                                                                                                                d1e5db1 B:251-402 Rubredoxin oxygen:oxidoreductase (ROO), C-terminal domain                                                                              SCOP domains
               CATH domains 1e5dB02 B:2-248 Metallo-beta-lactamase, chain A                                                                                                                                                                                                        -----1e5dB01 B:254-396  [code=3.40.50.360, no name defined]                                                                                         ------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeeeeee....ee...ee....eeeeeeee.....eee...hhhhhhhhhhhhhh..hhhhh.eeee...hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhh.....eee.....eee....eeeeee.........eeeee....eeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhhhh....eeeeeeee...hhhhhhhhhhhhh.........eeee...hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FLAVODOXIN_LIKE  PDB: B:255-393 UniProt: 255-393                                                                                           --------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e5d B   2 QATKIIDGFHLVGAIDWNSRDFHGYTLSPMGTTYNAYLVEDEKTTLFDTVKAEYKGELLCGIASVIDPKKIDYLVIQHLELDHAGALPALIEACQPEKIFTSSLGQKAMESHFHYKDWPVQVVKHGETLSLGKRTVTFYETRMLHWPDSMVSWFADEKVLISNDIFGQNIAASERFSDQIPVHTLERAMREYYANIVNPYAPQTLKAIETLVGAGVAPEFICPDHGVIFRGADQCTFAVQKYVEYAEQKPTNKVVIFYDSMWHSTEKMARVLAESFRDEGCTVKLMWCKACHHSQIMSEISDAGAVIVGSPTHNNGILPYVAGTLQYIKGLRPQNKIGGAFGSFGWSGESTKVLAEWLTGMGFDMPATPVKVKNVPTHADYEQLKTMAQTIARALKAKLAA 402
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.360, no name defined] (150)

Desulfovibrio gigas. Organism_taxid: 879 (1)

1a	1e5dA01	A:254-396
1b	1e5dB01	B:254-396

Architecture: 4-Layer Sandwich (459)

Topology: Metallo-beta-lactamase; Chain A (92)

Homologous Superfamily: Metallo-beta-lactamase, chain A (92)

Desulfovibrio gigas. Organism_taxid: 879 (1)

2a	1e5dA02	A:2-248
2b	1e5dB02	B:2-248

(no "Pfam Domain" information available for 1E5D)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ROO_DESGI | Q9F0J6)

molecular function
	GO:0010181	FMN binding	Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
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:0022904	respiratory electron transport chain	A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.

Asymmetric/Biological Unit
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Description

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Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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