1FMJ - JenaLib

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Title :   CRYSTAL STRUCTURE OF MERCURY DERIVATIVE OF RETINOL DEHYDRATASE IN A COMPLEX WITH RETINOL AND PAP

Authors :   S. Pakhomova, M. Kobayashi, J. Buck, M. E. Newcomer

Date :   17 Aug 00 (Deposition) - 02 May 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Sulfotransferase, Dehydratase, Retinol, Adenosine 3', 5'- Diphosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Pakhomova, M. Kobayashi, J. Buck, M. E. Newcomer
A Helical Lid Converts A Sulfotransferase To A Dehydratase.
Nat. Struct. Biol. V. 8 447 2001
PubMed-ID: 11323722 | Reference-DOI: 10.1038/87617
(for further references see the PDB file header)

Molecule 1 - RETINOL DEHYDRATASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-15B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	FALL ARMYWORM
	Organism Scientific	:	SPODOPTERA FRUGIPERDA
	Organism Taxid	:	7108

		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 (4, 12)

No.	Name	Count	Type	Full Name
1	A3P	2	Ligand/Ion	ADENOSINE-3'-5'-DIPHOSPHATE
2	CA	2	Ligand/Ion	CALCIUM ION
3	HG	6	Ligand/Ion	MERCURY (II) ION
4	RTL	2	Ligand/Ion	RETINOL

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	A3P	1	Ligand/Ion	ADENOSINE-3'-5'-DIPHOSPHATE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	HG	-1	Ligand/Ion	MERCURY (II) ION
4	RTL	1	Ligand/Ion	RETINOL

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	A3P	1	Ligand/Ion	ADENOSINE-3'-5'-DIPHOSPHATE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	HG	-1	Ligand/Ion	MERCURY (II) ION
4	RTL	1	Ligand/Ion	RETINOL

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:250 , ASP A:254 , GLY A:257 , CYS A:258 , ARG A:261	BINDING SITE FOR RESIDUE HG A 451
02	AC2	SOFTWARE	CYS A:279 , GLU A:280	BINDING SITE FOR RESIDUE HG A 452
03	AC3	SOFTWARE	CYS A:318 , ASP A:321	BINDING SITE FOR RESIDUE HG A 453
04	AC4	SOFTWARE	GLU A:118 , ASN A:121 , ASP A:122	BINDING SITE FOR RESIDUE CA A 402
05	AC5	SOFTWARE	ASP B:250 , ASP B:254 , CYS B:258	BINDING SITE FOR RESIDUE HG B 551
06	AC6	SOFTWARE	CYS B:279	BINDING SITE FOR RESIDUE HG B 552
07	AC7	SOFTWARE	CYS B:318 , ASP B:321	BINDING SITE FOR RESIDUE HG B 553
08	AC8	SOFTWARE	GLU B:118 , ASN B:121 , ASP B:122	BINDING SITE FOR RESIDUE CA B 502
09	AC9	SOFTWARE	ARG A:73 , SER A:74 , GLY A:75 , THR A:76 , THR A:77 , MET A:78 , ARG A:185 , SER A:193 , TYR A:248 , LEU A:282 , PHE A:284 , PHE A:287 , ARG A:312 , LYS A:313 , GLY A:314 , HOH A:454 , HOH A:477 , HOH A:483 , HOH A:511 , HOH A:588	BINDING SITE FOR RESIDUE A3P A 400
10	BC1	SOFTWARE	TYR A:105 , TYR A:112 , TYR A:120 , LEU A:139 , SER A:142 , LYS A:162 , HIS A:164 , HIS A:197 , MET A:295 , PHE A:310 , HOH A:588	BINDING SITE FOR RESIDUE RTL A 401
11	BC2	SOFTWARE	ARG B:73 , SER B:74 , GLY B:75 , THR B:76 , THR B:77 , MET B:78 , ARG B:185 , SER B:193 , TYR B:248 , LEU B:282 , PHE B:284 , PHE B:287 , ARG B:312 , LYS B:313 , GLY B:314 , HOH B:556 , HOH B:573 , HOH B:600 , HOH B:683 , HOH B:691	BINDING SITE FOR RESIDUE A3P B 500
12	BC3	SOFTWARE	TYR B:105 , TYR B:112 , TYR B:120 , SER B:142 , LYS B:162 , HIS B:164 , HIS B:197 , MET B:295 , ILE B:303 , PHE B:310 , HOH B:691	BINDING SITE FOR RESIDUE RTL B 501

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

Asymmetric Unit

No.	Residues
1	Thr A:225	-	Pro A:226
2	Thr B:225	-	Pro B:226

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

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

(no "Exon" information available for 1FMJ)

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:342
 aligned with Q26490_SPOFR | Q26490 from UniProtKB/TrEMBL  Length:351

    Alignment length:342
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347  
         Q26490_SPOFR     8 PFPYEFRELNPEEDKLVKANLGAFPTTYVKLGPKGYMVYRPYLKDAANIYNMPLRPTDVFVASYQRSGTTMTQELVWLIENDLNFEAAKTYMSLRYIYLDGFMIYDPEKQEEYNDILPNPENLDMERYLGLLEYFSRPGSSLLAAVPPTEKRFVKTHLPLSLMPPNMLDTVKMVYLARDPRDVAVSSFHHARLLYLLNKQSNFKDFWEMFHRGLYTLTPYFEHVKEAWAKRHDPNMLFLFYEDYLKDLPGCIARIADFLGKKLSEEQIQRLCEHLNFEKFKNNGAVNMEDYREIGILADGEHFIRKGKAGCWRDYFDEEMTKQAEKWIKDNLKDTDLRYPNM 349
               SCOP domains d1fmja_ A: Retinol dehydratase                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1fmjA00 A:8-349 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....ee..hhhhhhhhhh........eeee....eeee..hhhhhhhhhhh......eeeee....hhhhhhhhhhhhhh....hhhhhhhhhhhee.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhh......eeee..hhhhh..hhhhh.eeeeee.hhhhhhhhhhhhhhhh.......hhhhhhhhhhh......hhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.....hhhhh.................hhhhhh.hhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1fmj A   8 PFPYEFRELNPEEDKLVKANLGAFPTTYVKLGPKGYMVYRPYLKDAANIYNMPLRPTDVFVASYQRSGTTMTQELVWLIENDLNFEAAKTYMSLRYIYLDGFMIYDPEKQEEYNDILPNPENLDMERYLGLLEYSSRPGSSLLAAVPPTEKRFVKTHLPLSLMPPNMLDTVKMVYLARDPRDVAVSSFHHARLLYLLNKQSNFKDFWEMFHRGLYTLTPYFEHVKEAWAKRHDPNMLFLFYEDYLKDLPGCIARIADFLGKKLSEEQIQRLCEHLNFEKFKNNGAVNMEDYREIGILADGEHFIRKGKAGCWRDYFDEEMTKQAEKWIKDNLKDTDLRYPNM 349
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347

Chain B from PDB  Type:PROTEIN  Length:342
 aligned with Q26490_SPOFR | Q26490 from UniProtKB/TrEMBL  Length:351

    Alignment length:342
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347  
         Q26490_SPOFR     8 PFPYEFRELNPEEDKLVKANLGAFPTTYVKLGPKGYMVYRPYLKDAANIYNMPLRPTDVFVASYQRSGTTMTQELVWLIENDLNFEAAKTYMSLRYIYLDGFMIYDPEKQEEYNDILPNPENLDMERYLGLLEYFSRPGSSLLAAVPPTEKRFVKTHLPLSLMPPNMLDTVKMVYLARDPRDVAVSSFHHARLLYLLNKQSNFKDFWEMFHRGLYTLTPYFEHVKEAWAKRHDPNMLFLFYEDYLKDLPGCIARIADFLGKKLSEEQIQRLCEHLNFEKFKNNGAVNMEDYREIGILADGEHFIRKGKAGCWRDYFDEEMTKQAEKWIKDNLKDTDLRYPNM 349
               SCOP domains d1fmjb_ B: Retinol dehydratase                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1fmjB00 B:8-349 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....ee..hhhhhhhhhh........eeee....eeee..hhhhhhhhhhh......eeeee....hhhhhhhhhhhhhh....hhhhhhhhhhhee.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhh......eeee..hhhhh..hhhhh.eeeeee.hhhhhhhhhhhhhhhh.......hhhhhhhhhhh......hhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.....hhhhh.................hhhhhh.hhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1fmj B   8 PFPYEFRELNPEEDKLVKANLGAFPTTYVKLGPKGYMVYRPYLKDAANIYNMPLRPTDVFVASYQRSGTTMTQELVWLIENDLNFEAAKTYMSLRYIYLDGFMIYDPEKQEEYNDILPNPENLDMERYLGLLEYSSRPGSSLLAAVPPTEKRFVKTHLPLSLMPPNMLDTVKMVYLARDPRDVAVSSFHHARLLYLLNKQSNFKDFWEMFHRGLYTLTPYFEHVKEAWAKRHDPNMLFLFYEDYLKDLPGCIARIADFLGKKLSEEQIQRLCEHLNFEKFKNNGAVNMEDYREIGILADGEHFIRKGKAGCWRDYFDEEMTKQAEKWIKDNLKDTDLRYPNM 349
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347

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 Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Fall armyworm (Spodoptera frugiperda) (5)

1a	1fmjA00	A:8-349
1b	1fmjB00	B:8-349

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q26490_SPOFR | Q26490)

molecular function
	GO:0046872		metal ion binding		Interacting selectively and non-covalently with any metal ion.
	GO:0008146		sulfotransferase activity		Catalysis of the transfer of a sulfate group from 3'-phosphoadenosine 5'-phosphosulfate to the hydroxyl group of an acceptor, producing the sulfated derivative and 3'-phosphoadenosine 5'-phosphate.

Asymmetric Unit
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	Cis Peptide Bonds
		Thr A:225 - Pro A:226	[ RasMol ]
		Thr B:225 - Pro B:226	[ RasMol ]

Biological Units
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	1fmj
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	Q26490_SPOFR \| Q26490	:	1fml 1x8j 1x8k 1x8l

1fml	1FML CONTAINS THE NATIVE FORM OF THE SAME PROTEIN.

Description

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Chains, Units

Ligands, Modified Residues, Ions (4, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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