1VZ5 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   SUCCINATE COMPLEX OF ATSK

Authors :   I. Mueller, A. C. Stueckl, I. Uson, M. Kertesz

Date :   14 May 04 (Deposition) - 15 Nov 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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

Keywords :   Non-Heme Fe(Ii) Alphaketoglutarate Dependent Dioxygenase, Alkylsulfatase, Jelly Roll, Oxidoreductase, Sulfatase, Self Hydroxylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. Mueller, A. C. Stueckl, J. Wakeley, M. Kertesz, I. Uson
Succinate Complex Crystal Structures Of The Alpha-Ketoglutarate-Dependent Dioxygenase Atsk: Steric Aspects Of Enzyme Self-Hydroxylation
J. Biol. Chem. V. 280 5716 2005
PubMed-ID: 15542595 | Reference-DOI: 10.1074/JBC.M410840200

Molecule 1 - PUTATIVE ALKYLSULFATASE ATSK
	Chains	:	A, B, C, D
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	303
	Other Details	:	ATSK-SUCCINATE COMPLEX
	Strain	:	S-313

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	SIN	4	Ligand/Ion	SUCCINIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:135 , HIS A:264 , ALA A:266 , ARG A:275 , ARG A:279 , HOH A:2061	BINDING SITE FOR RESIDUE SIN A1301
2	AC2	SOFTWARE	THR B:135 , TRP B:257 , HIS B:264 , ARG B:275 , ARG B:279 , HOH B:2138	BINDING SITE FOR RESIDUE SIN B1301
3	AC3	SOFTWARE	LEU C:96 , THR C:135 , HIS C:264 , ALA C:266 , ARG C:275 , VAL C:277 , ARG C:279 , HOH C:2047	BINDING SITE FOR RESIDUE SIN C1300
4	AC4	SOFTWARE	THR D:135 , HIS D:264 , ARG D:275 , ARG D:279 , HOH D:2108	BINDING SITE FOR RESIDUE SIN D1300

(no "SS Bond" information available for 1VZ5)

(no "Cis Peptide Bond" information available for 1VZ5)

(no "SAP(SNP)/Variant" information available for 1VZ5)

(no "PROSITE Motif" information available for 1VZ5)

(no "Exon" information available for 1VZ5)

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:254
 aligned with ATSK_PSEPU | Q9WWU5 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:288
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292        
           ATSK_PSEPU    13 LELDVHPVAGRIGAEIRGVKLSPDLDAATVEAIQAALVRHKVIFFRGQTHLDDQSQEGFAKLLGEPVAHPTVPVVDGTRYLLQLDGAQGQRANSWHTDVTFVEAYPKASILRSVVAPASGGDTVWANTAAAYQELPEPLRELADKLWAVHSNEYDYASLKPDIDPAKLERHRKVFTSTVYETEHPVVRVHPISGERALQLGHFVKRIKGYSLADSQHLFAVLQGHVTRLENTVRWRWEAGDVAIWDNRATQHYAVDDYGTQPRIVRRVTLAGEVPVGVDGQLSRTTRK 300
               SCOP domains d1vz5a_ A: Putative alkylsulfatase AtsK                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1vz5A00 A:13-300 Clavaminate synthase-like                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee......eeee........hhhhhhhhhhhhhhhheeee......hhhhhhhhhhh......----.........eee.-----.................eeeeeeee.......eeeeehhhhhhh.hhhhhhhhhhheeeee..-------------------------..eeeee.eee......eee.....eeee...hhhhhhhhhhhhhhhhhh...eeee......eeeee...eeeee.........eeeeeee.............eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vz5 A  13 LELDVHPVAGRIGAEIRGVKLSPDLDAATVEAIQAALVRHKVIFFRGQTHLDDQSQEGFAKLLGEPVA----PVVDGTRYLLQLD-----RANSWHTDVTFVEAYPKASILRSVVAPASGGDTVWANTAAAYQELPEPLRELADKLWAVHSNE-------------------------VYETEHPVVRVHPISGERALQLGHFVKRIKGYSLADSQHLFAVLQGHVTRLENTVRWRWEAGDVAIWDNRATQHYAVDDYGTQPRIVRRVTLAGEVPVGVDGQLSRTTRK 300
                                    22        32        42        52        62        72       | -  |     92    |    -|      112       122       132       142       152       162  |      -         -       192       202       212       222       232       242       252       262       272       282       292        
                                                                                              80   85          97   103                                                           165                       191

Chain B from PDB  Type:PROTEIN  Length:254
 aligned with ATSK_PSEPU | Q9WWU5 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:288
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292        
           ATSK_PSEPU    13 LELDVHPVAGRIGAEIRGVKLSPDLDAATVEAIQAALVRHKVIFFRGQTHLDDQSQEGFAKLLGEPVAHPTVPVVDGTRYLLQLDGAQGQRANSWHTDVTFVEAYPKASILRSVVAPASGGDTVWANTAAAYQELPEPLRELADKLWAVHSNEYDYASLKPDIDPAKLERHRKVFTSTVYETEHPVVRVHPISGERALQLGHFVKRIKGYSLADSQHLFAVLQGHVTRLENTVRWRWEAGDVAIWDNRATQHYAVDDYGTQPRIVRRVTLAGEVPVGVDGQLSRTTRK 300
               SCOP domains d1vz5b_ B: Putative alkylsulfatase AtsK                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1vz5B00 B:13-300 Clavaminate synthase-like                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee......eeee........hhhhhhhhhhhhhhhheeee......hhhhhhhhhh.......----.........eee.-----.................eeeeeeee.......eeeeehhhhhhh.hhhhhhhhh..eeeee..-------------------------..eeeee.eee......eee.....eeee...hhhhhhhhhhhhhhhhhh...eeee......eeeee...eeeee.........eeeeeee.............eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vz5 B  13 LELDVHPVAGRIGAEIRGVKLSPDLDAATVEAIQAALVRHKVIFFRGQTHLDDQSQEGFAKLLGEPVA----PVVDGTRYLLQLD-----RANSWHTDVTFVEAYPKASILRSVVAPASGGDTVWANTAAAYQELPEPLRELADKLWAVHSNE-------------------------VYETEHPVVRVHPISGERALQLGHFVKRIKGYSLADSQHLFAVLQGHVTRLENTVRWRWEAGDVAIWDNRATQHYAVDDYGTQPRIVRRVTLAGEVPVGVDGQLSRTTRK 300
                                    22        32        42        52        62        72       | -  |     92    |    -|      112       122       132       142       152       162  |      -         -       192       202       212       222       232       242       252       262       272       282       292        
                                                                                              80   85          97   103                                                           165                       191

Chain C from PDB  Type:PROTEIN  Length:244
 aligned with ATSK_PSEPU | Q9WWU5 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:287
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       
           ATSK_PSEPU    13 LELDVHPVAGRIGAEIRGVKLSPDLDAATVEAIQAALVRHKVIFFRGQTHLDDQSQEGFAKLLGEPVAHPTVPVVDGTRYLLQLDGAQGQRANSWHTDVTFVEAYPKASILRSVVAPASGGDTVWANTAAAYQELPEPLRELADKLWAVHSNEYDYASLKPDIDPAKLERHRKVFTSTVYETEHPVVRVHPISGERALQLGHFVKRIKGYSLADSQHLFAVLQGHVTRLENTVRWRWEAGDVAIWDNRATQHYAVDDYGTQPRIVRRVTLAGEVPVGVDGQLSRTTR 299
               SCOP domains d1vz5c_ C: Putative alkylsulfatase AtsK                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1vz5C00 C:13-299 Clavaminate synthase-like                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee......eeee........hhhhhhhhhhhhhhhheeee......hhhhhhhhhhh.....-----------...eee------.................eeeeeeee.......eeeeehhhhhhh.hhhhhhhhh..eeeee..--------------------------.eeeee.eee......eee.....eeee...hhhhhhhhhhhhhhhhhhhh.eeee......eeeee...eeeee.........eeeeeee.............eeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vz5 C  13 LELDVHPVAGRIGAEIRGVKLSPDLDAATVEAIQAALVRHKVIFFRGQTHLDDQSQEGFAKLLGEPV-----------RYLLQL------RANSWHTDVTFVEAYPKASILRSVVAPASGGDTVWANTAAAYQELPEPLRELADKLWAVHSNE--------------------------YETEHPVVRVHPISGERALQLGHFVKRIKGYSLADSQHLFAVLQGHVTRLENTVRWRWEAGDVAIWDNRATQHYAVDDYGTQPRIVRRVTLAGEVPVGVDGQLSRTTR 299
                                    22        32        42        52        62        72      |  -        92   |     -|      112       122       132       142       152       162  |      -         -       192       202       212       222       232       242       252       262       272       282       292       
                                                                                             79          91   96    103                                                           165                        192

Chain D from PDB  Type:PROTEIN  Length:244
 aligned with ATSK_PSEPU | Q9WWU5 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:287
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       
           ATSK_PSEPU    13 LELDVHPVAGRIGAEIRGVKLSPDLDAATVEAIQAALVRHKVIFFRGQTHLDDQSQEGFAKLLGEPVAHPTVPVVDGTRYLLQLDGAQGQRANSWHTDVTFVEAYPKASILRSVVAPASGGDTVWANTAAAYQELPEPLRELADKLWAVHSNEYDYASLKPDIDPAKLERHRKVFTSTVYETEHPVVRVHPISGERALQLGHFVKRIKGYSLADSQHLFAVLQGHVTRLENTVRWRWEAGDVAIWDNRATQHYAVDDYGTQPRIVRRVTLAGEVPVGVDGQLSRTTR 299
               SCOP domains d1vz5d_ D: Putative alkylsulfatase AtsK                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1vz5D00 D:13-299 Clavaminate synthase-like                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee......eeee........hhhhhhhhhhhhhhhheeee......hhhhhhhhhhh.....----------....eee.------................eeeeeeee.......eeeeehhhhhhh.hhhhhhhhh..eeeee.---------------------------.eeeee.eee......eee.....eeee...hhhhhhhhhhhhhhhhhhhh.eeee......eeeee...eeeee.........eeeeeee.............eeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vz5 D  13 LELDVHPVAGRIGAEIRGVKLSPDLDAATVEAIQAALVRHKVIFFRGQTHLDDQSQEGFAKLLGEPV----------TRYLLQLD------ANSWHTDVTFVEAYPKASILRSVVAPASGGDTVWANTAAAYQELPEPLRELADKLWAVHSN---------------------------YETEHPVVRVHPISGERALQLGHFVKRIKGYSLADSQHLFAVLQGHVTRLENTVRWRWEAGDVAIWDNRATQHYAVDDYGTQPRIVRRVTLAGEVPVGVDGQLSRTTR 299
                                    22        32        42        52        62        72      |  -       |92    |    - |     112       122       132       142       152       162 |       -         -       192       202       212       222       232       242       252       262       272       282       292       
                                                                                             79         90     97    104                                                         164                         192

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Double-stranded beta-helix (580)

Superfamily: Clavaminate synthase-like (197)

Family: TauD/TfdA-like (13)

Protein domain: Putative alkylsulfatase AtsK (6)

Pseudomonas putida [TaxId: 303] (6)

1a	d1vz5a_	A:
1b	d1vz5b_	B:
1c	d1vz5c_	C:
1d	d1vz5d_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 4-Layer Sandwich (459)

Topology: Double-stranded beta-helix (19)

Homologous Superfamily: Clavaminate synthase-like (19)

Pseudomonas putida. Organism_taxid: 303. Strain: s-313 (2)

1a	1vz5A00	A:13-300
1b	1vz5B00	B:13-300
1c	1vz5C00	C:13-299
1d	1vz5D00	D:13-299

(no "Pfam Domain" information available for 1VZ5)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (ATSK_PSEPU | Q9WWU5)

molecular function
	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: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.

Asymmetric/Biological Unit
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	ATSK_PSEPU \| Q9WWU5	:	1oih 1oii 1oij 1oik 1vz4

1oih	CRYSTAL STRUCTURE OF THE ALKYLSULFATASE ATSK, A NON-HEME FE(II) ALPHAKETOGLUTARATE DEPENDENT DIOXYGENASE
1oii	CRYSTAL STRUCTURE OF THE ALKYLSULFATASE ATSK, A NON-HEME FE(II) ALPHAKETOGLUTARATE DEPENDENT DIOXYGENASE
1oij	CRYSTAL STRUCTURE OF THE ALKYLSULFATASE ATSK, A NON-HEME FE(II) ALPHAKETOGLUTARATE DEPENDENT DIOXYGENASE
1oik	CRYSTAL STRUCTURE OF THE ALKYLSULFATASE ATSK, A NON-HEME FE(II) ALPHAKETOGLUTARATE DEPENDENT DIOXYGENASE
1vz4	FE-SUCCINATE COMPLEX OF ATSK

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 4)

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Gene Ontology (4, 4)

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