3RC9 - JenaLib

Title :   CRYSTAL STRUCTURE OF THE K102A MUTANT OF KIJD10, A 3-KETOREDUCTASE FROM ACTINOMADURA KIJANIATA IN COMPLEX WITH TDP-BENZENE AND NADP

Authors :   H. M. Holden, R. L. Kubiak

Date :   30 Mar 11 (Deposition) - 08 Jun 11 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.91

Chains :   Asym./Biol. Unit : A

Keywords :   Sugar Biosynthesis, Ketoreductase, Tdp Binding, Nadp Binding, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. L. Kubiak, H. M. Holden
Combined Structural And Functional Investigation Of A C-3''-Ketoreductase Involved In The Biosynthesis Of Dtdp-L-Digitoxose.
Biochemistry V. 50 5905 2011
PubMed-ID: 21598943 | Reference-DOI: 10.1021/BI200514B

Compounds

Molecule 1 - SUGAR 3-KETOREDUCTASE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	ROSETTA 2
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	KIJD10
	Mutation	:	YES
	Organism Scientific	:	ACTINOMADURA KIJANIATA
	Organism Taxid	:	46161

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 6)

Asymmetric/Biological Unit (5, 6)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	NA	1	Ligand/Ion	SODIUM ION
3	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4	PO4	1	Ligand/Ion	PHOSPHATE ION
5	TLO	2	Ligand/Ion	5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHENOXY)PHOSPHORYL]OXY}PHOSPHORYL]THYMIDINE

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:16 , CYS A:17 , ALA A:18 , SER A:42 , ARG A:43 , ARG A:47 , TYR A:63 , PRO A:78 , LEU A:79 , PRO A:80 , LEU A:83 , HIS A:84 , ALA A:102 , PRO A:103 , VAL A:175 , ASP A:182 , TLO A:337 , HOH A:462 , HOH A:464	BINDING SITE FOR RESIDUE NAP A 333
2	AC2	SOFTWARE	ASN A:256 , HIS A:270	BINDING SITE FOR RESIDUE CL A 334
3	AC3	SOFTWARE	ARG A:323 , THR A:324 , ALA A:326 , ASP A:328	BINDING SITE FOR RESIDUE NA A 335
4	AC4	SOFTWARE	HIS A:285 , LYS A:290 , HOH A:423	BINDING SITE FOR RESIDUE PO4 A 336
5	AC5	SOFTWARE	ILE A:20 , ARG A:23 , ARG A:24 , PHE A:159 , ILE A:161 , PRO A:162 , TYR A:186 , TYR A:240 , THR A:260 , GLN A:274 , NAP A:333 , HOH A:503 , HOH A:519 , HOH A:524 , HOH A:535	BINDING SITE FOR RESIDUE TLO A 337
6	AC6	SOFTWARE	MET A:126 , LEU A:132 , HIS A:133 , HIS A:137 , ARG A:138 , ALA A:141 , ARG A:189 , LEU A:193 , GLU A:307 , TRP A:308 , ASP A:311 , HOH A:360 , HOH A:361 , HOH A:370 , HOH A:420 , HOH A:483	BINDING SITE FOR RESIDUE TLO A 338

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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)
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Chain A from PDB  Type:PROTEIN  Length:314
 aligned with B3TMR8_9ACTN | B3TMR8 from UniProtKB/TrEMBL  Length:332

    Alignment length:325
                                    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     
         B3TMR8_9ACTN     8 NPIRVGVIGCADIAWRRALPALEAEPLTEVTAIASRRWDRAKRFTERFGGEPVEGYPALLERDDVDAVYVPLPAVLHAEWIDRALRAGKHVLAEKPLTTDRPQAERLFAVARERGLLLMENFMFLHHPQHRQVADMLDEGVIGEIRSFAASFTIPPKPQGDIRYQADVGGGALLDIGVYPIRAAGLFLGADLEFVGAVLRHERDRDVVVGGNALLTTRQGVTAQLTFGMEHAYTNNYEFRGSTGRLWMNRVFTPPATYQPVVHIERQDHAEQFVLPAHDQFAKSIRAFAQAVLSGEHPREWSEDSLRQASLVDAVRTGARDIYFP 332
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhh.eeeehhhhhhh.....eeee..hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhh.....eeeeeeeee...-----------..hhhhhhhhhhhhhhhhhhhh...eeeeeeeeee....eeeeeeeeee.....eeeeeee.....eeeeeeee...eeeee...........eeeeee..eeeeee....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhheeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rc9 A   8 NPIRVGVIGCADIAWRRALPALEAEPLTEVTAIASRRWDRAKRFTERFGGEPVEGYPALLERDDVDAVYVPLPAVLHAEWIDRALRAGKHVLAEAPLTTDRPQAERLFAVARERGLLLMENFMFLHHPQHRQVADMLDEGVIGEIRSFAASFTIPP-----------VGGGALLDIGVYPIRAAGLFLGADLEFVGAVLRHERDRDVVVGGNALLTTRQGVTAQLTFGMEHAYTNNYEFRGSTGRLWMNRVFTPPATYQPVVHIERQDHAEQFVLPAHDQFAKSIRAFAQAVLSGEHPREWSEDSLRQASLVDAVRTGARDIYFP 332
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157     |   -       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327     
                                                                                                                                                                                     163         175

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (3, 3)

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		Phe A:331 - Pro A:332	[ RasMol ]

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

3rbv	SAME PROTEIN, BINARY COMPLEX WITH NADP
3rc1	SAME PROTEIN, TERNARY COMPLEX WITH TDP-BENZENE AND NADP; CLOSED CONFORMATION
3rc2	SAME PROTEIN, TERNARY COMPLEX WITH TDP-BENZENE AND NADP; OPEN CONFORMATION
3rc7	SAME PROTEIN, TERNARY COMPLEX WITH TDP-BENZENE AND NADP; Y186F MUTANT
3rcb

Description