3VCP - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   THE 2.2 ANGSTROM STRUCTURE OF STC2 WITH PROLINE BOUND IN THE ACTIVE SITE

Authors :   K. D. Daughtry, Y. Xiao, D. Stoner-Ma, E. Cho, A. M. Orville, P. Liu, K. N.

Date :   04 Jan 12 (Deposition) - 08 Feb 12 (Release) - 22 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A
Biol. Unit 1: A  (3x)

Keywords :   Rieske-Type, Mononuclear Non-Heme Iron, N-Demethylase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. D. Daughtry, Y. Xiao, D. Stoner-Ma, E. Cho, A. M. Orville, P. Liu, K. N. Allen
Quaternary Ammonium Oxidative Demethylation: X-Ray Crystallographic, Resonance Raman, And Uv-Visible Spectroscopic Analysis Of A Rieske-Type Demethylase.
J. Am. Chem. Soc. V. 134 2823 2012
PubMed-ID: 22224443 | Reference-DOI: 10.1021/JA2111898

Molecule 1 - RING-HYDROXYLATING DIOXYGENASE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PASK-IBA5+
	Gene	:	NP_435646, RA0400, SMA0751
	Organism Common	:	ENSIFER MELILOTI
	Organism Scientific	:	SINORHIZOBIUM MELILOTI
	Organism Taxid	:	266834
	Strain	:	1021

		1
Asymmetric Unit	:	A
Biological Unit 1 (3x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	FE	1	Ligand/Ion	FE (III) ION
2	FES	1	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
3	PRO	1	Mod. Amino Acid	PROLINE

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION
2	FES	3	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
3	PRO	3	Mod. Amino Acid	PROLINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:86 , HIS A:88 , ARG A:89 , SER A:91 , CYS A:106 , HIS A:109 , TRP A:111	BINDING SITE FOR RESIDUE FES A 500
2	AC2	SOFTWARE	HIS A:204 , HIS A:209 , ASP A:360 , PRO A:502 , HOH A:753	BINDING SITE FOR RESIDUE FE A 501
3	AC3	SOFTWARE	ASN A:199 , GLU A:201 , HIS A:204 , CYS A:205 , HIS A:209 , LEU A:212 , ALA A:223 , TRP A:353 , THR A:356 , ASP A:360 , FE A:501 , HOH A:702 , HOH A:753	BINDING SITE FOR RESIDUE PRO A 502

Asymmetric Unit

No.	Residues
1	A:202	-	A:205

Asymmetric Unit

No.	Residues
1	Ala A:289	-	Pro A:290
2	Tyr A:301	-	Pro A:302

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

(no "PROSITE Motif" information available for 3VCP)

(no "Exon" information available for 3VCP)

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:398
 aligned with Q92ZP9_RHIME | Q92ZP9 from UniProtKB/TrEMBL  Length:412

    Alignment length:403
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405   
         Q92ZP9_RHIME     6 TSIHQRLDRRLSGFSLEQPFYTSPEVYALDLQHIFYKQWLYAVPVCQLAKAGSYTTLRVGAYEVVIVRSRDGEVRAFHNSCRHRGSLICKARQGQVAKLVCPYHQWTYELDGKLIWANDMGPDFDASKYGLKPVNLRNLDGLIYICLSDTPPDFQTFAQLARPYLEVHDLKDAKVAFTSTIIEKGNWKLVWENNRECYHCSSNHPALCRSFPLDPEVAGVQADGGVSKKLQAHFDRCEAAGTPAQFVLAGDGQYRLARMPLQEKALSYTMDGKAAVSRHLGRVAPPDAGTLLMFHYPSTWNHFLPDHSLTFRVMPISPTETEVTTTWLVHKDAVEGVDYDLKRLTEVWIATNDEDREIVETNQQGILSPAYVPGPYSPGQESGVMQFVDWYAASLERALAPRQ 408
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh......hhhhhhhhhhhhhhhhhh....eeeeee.hhhh...eeeeeee..eeeeeee.....eeeee..............eee...ee......ee.....eee........hhhhh...eeeeeee..eeeee.......hhhhhhhhhhhhhhhhhh.eeeeeeeeeee..hhhhhhhhhh...hhhhhh.hhhhh...hhhhhh.----..hhhhhhhhhhhhhh......ee.....eeeeee..............................eeeeee...eeeee....eeeeeeeeee..eeeeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh..-. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vcp A   6 TSIHQRLDRRLSGFSLEQPFYTSPEVYALDLQHIFYKQWLYAVPVCQLAKAGSYTTLRVGAYEVVIVRSRDGEVRAFHNSCRHRGSLICKARQGQVAKLVCPYHQWTYELDGKLIWANDMGPDFDASKYGLKPVNLRNLDGLIYICLSDTPPDFQTFAQLARPYLEVHDLKDAKVAFTSTIIEKGNWKLVWENNRECYHCSSNHPALCRSFPLDPEVAGV----GVSKKLQAHFDRCEAAGTPAQFVLAGDGQYRLARMPLQEKALSYTMDGKAAVSRHLGRVAPPDAGTLLMFHYPSTWNHFLPDHSLTFRVMPISPTETEVTTTWLVHKDAVEGVDYDLKRLTEVWIATNDEDREIVETNQQGILSPAYVPGPYSPGQESGVMQFVDWYAASLERALAP-P 502
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225    |  235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405| |
                                                                                                                                                                                                                                                     225  230                                                                                                                                                                             406 |
                                                                                                                                                                                                                                                                                                                                                                                                                                            502

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 3VCP)

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

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

Asymmetric Unit(hide GO term definitions)

Chain A (Q92ZP9_RHIME | Q92ZP9)

molecular function
	GO:0051537	2 iron, 2 sulfur cluster binding	Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
	GO:0051213	dioxygenase activity	Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	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.
	GO:0016705	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
	GO:0016708	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of two atoms of oxygen into one donor	Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from NADH or NADPH and one other donor, and two atoms of oxygen are incorporated into one donor.
biological process
	GO:0019439	aromatic compound catabolic process	The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
	GO:0006725	cellular aromatic compound metabolic process	The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
	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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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		FES	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PRO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:289 - Pro A:290	[ RasMol ]
		Tyr A:301 - Pro A:302	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	3vcp
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	Q92ZP9_RHIME \| Q92ZP9	:	3vca 4qup 4quq 4qur 5hl4

Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (1, 1)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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