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Title :   CRYSTAL STRUCTURE OF RV2002 GENE PRODUCT FROM MYCOBACTERIUM TUBERCULOSIS

Authors :   J. K. Yang, M. S. Park, G. S. Waldo, S. W. Suh, Tb Structural Genomics C (Tbsgc)

Date :   14 Dec 02 (Deposition) - 30 Dec 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Directed Evolution, Gfp, Sdr, Hydroxysteroid Dehydrogenase, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. K. Yang, M. S. Park, G. S. Waldo, S. W. Suh
Directed Evolution Approach To A Structural Genomics Project: Rv2002 From Mycobacterium Tuberculosis
Proc. Natl. Acad. Sci. Usa V. 100 455 2003
PubMed-ID: 12524453 | Reference-DOI: 10.1073/PNAS.0137017100

Molecule 1 - PUTATIVE OXIDOREDUCTASE RV2002
	Chains	:	A, B
	EC Number	:	1.1.1.53
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Synonym	:	RV2002 GENE PRODUCT

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	NAD	4	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:14 , ARG A:17 , GLY A:18 , MET A:19 , ASP A:38 , ILE A:39 , LEU A:40 , LEU A:60 , ASP A:61 , VAL A:62 , ASN A:88 , ALA A:89 , GLY A:90 , ILE A:91 , ILE A:138 , SER A:139 , SER A:140 , TYR A:153 , LYS A:157 , PRO A:183 , GLY A:184 , VAL A:186 , THR A:188 , PRO A:189 , MET A:190 , THR A:191 , HOH A:1302 , HOH A:1315 , HOH A:1318 , HOH A:1326 , HOH A:1376 , HOH A:1449	BINDING SITE FOR RESIDUE NAD A 1300
2	AC2	SOFTWARE	GLY B:14 , ARG B:17 , GLY B:18 , MET B:19 , ASP B:38 , LEU B:40 , LEU B:60 , ASP B:61 , VAL B:62 , ASN B:88 , GLY B:90 , ILE B:91 , ILE B:138 , SER B:139 , SER B:140 , TYR B:153 , LYS B:157 , PRO B:183 , GLY B:184 , VAL B:186 , THR B:188 , PRO B:189 , MET B:190 , THR B:191 , HOH B:2302 , HOH B:2312 , HOH B:2351 , HOH B:2353 , HOH B:2402 , HOH B:2463 , HOH B:2477	BINDING SITE FOR RESIDUE NAD B 2300

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	HSD_MYCTO	140-168	2	A:140-168 B:140-168
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	HSD_MYCTU	140-168	2	A:140-168 B:140-168

Biological Unit 1 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	HSD_MYCTO	140-168	4	A:140-168 B:140-168
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	HSD_MYCTU	140-168	4	A:140-168 B:140-168

(no "Exon" information available for 1NFF)

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:244
 aligned with HSD_MYCTO | P9WGT0 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:244
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    
            HSD_MYCTO     2 SGRLIGKVALVSGGARGMGASHVRAMVAEGAKVVFGDILDEEGKAVAAELADAARYVHLDVTQPAQWTAAVDTAVTAFGGLHVLVNNAGILNIGTIEDYALTEWQRILDVNLTGVFLGIRAVVKPMKEAGRGSIINISSIEGLAGTVACHGYTATKFAVRGLTKSTALELGPGGIRVNSIHPGLVKTPMTDWVPEDIFQTALGRAAEPVEVSNLVVYLASDESSYSTGAEFVVDGGTVAGLAHN 245
               SCOP domains d1nffa_ A: Putative oxidoreductase Rv2002                                                                                                                                                                                                            SCOP domains
               CATH domains 1nffA00 A:2-245 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhh...............hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:140-168    ----------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nff A   2 SGRLTGKVALVSGGARGMGASHVRAMVAEGAKVVFGDILDEEGKAMAAELADAARYVHLDVTQPAQWKAAVDTAVTAFGGLHVLVNNAGILNIGTIEDYALTEWQRILDVNLTGVFLGIRAVVKPMKEAGRGSIINISSIEGLAGTVACHGYTATKFAVRGLTKSTALELGPSGIRVNSIHPGLVKTPMTDWVPEDIFQTALGRAAEPVEVSNLVVYLASDESSYSTGAEFVVDGGTVAGLAHN 245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

Chain A from PDB  Type:PROTEIN  Length:244
 aligned with HSD_MYCTU | P9WGT1 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:244
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    
            HSD_MYCTU     2 SGRLIGKVALVSGGARGMGASHVRAMVAEGAKVVFGDILDEEGKAVAAELADAARYVHLDVTQPAQWTAAVDTAVTAFGGLHVLVNNAGILNIGTIEDYALTEWQRILDVNLTGVFLGIRAVVKPMKEAGRGSIINISSIEGLAGTVACHGYTATKFAVRGLTKSTALELGPSGIRVNSIHPGLVKTPMTDWVPEDIFQTALGRAAEPVEVSNLVVYLASDESSYSTGAEFVVDGGTVAGLAHN 245
               SCOP domains d1nffa_ A: Putative oxidoreductase Rv2002                                                                                                                                                                                                            SCOP domains
               CATH domains 1nffA00 A:2-245 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhh...............hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:140-168    ----------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nff A   2 SGRLTGKVALVSGGARGMGASHVRAMVAEGAKVVFGDILDEEGKAMAAELADAARYVHLDVTQPAQWKAAVDTAVTAFGGLHVLVNNAGILNIGTIEDYALTEWQRILDVNLTGVFLGIRAVVKPMKEAGRGSIINISSIEGLAGTVACHGYTATKFAVRGLTKSTALELGPSGIRVNSIHPGLVKTPMTDWVPEDIFQTALGRAAEPVEVSNLVVYLASDESSYSTGAEFVVDGGTVAGLAHN 245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

Chain B from PDB  Type:PROTEIN  Length:244
 aligned with HSD_MYCTO | P9WGT0 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:244
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    
            HSD_MYCTO     2 SGRLIGKVALVSGGARGMGASHVRAMVAEGAKVVFGDILDEEGKAVAAELADAARYVHLDVTQPAQWTAAVDTAVTAFGGLHVLVNNAGILNIGTIEDYALTEWQRILDVNLTGVFLGIRAVVKPMKEAGRGSIINISSIEGLAGTVACHGYTATKFAVRGLTKSTALELGPGGIRVNSIHPGLVKTPMTDWVPEDIFQTALGRAAEPVEVSNLVVYLASDESSYSTGAEFVVDGGTVAGLAHN 245
               SCOP domains d1nffb_ B: Putative oxidoreductase Rv2002                                                                                                                                                                                                            SCOP domains
               CATH domains 1nffB00 B:2-245 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                  CATH domains
           Pfam domains (1) ------adh_short-1nffB01 B:8-172                                                                                                                                            ------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------adh_short-1nffB02 B:8-172                                                                                                                                            ------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhh...............hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:140-168    ----------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nff B   2 SGRLTGKVALVSGGARGMGASHVRAMVAEGAKVVFGDILDEEGKAMAAELADAARYVHLDVTQPAQWKAAVDTAVTAFGGLHVLVNNAGILNIGTIEDYALTEWQRILDVNLTGVFLGIRAVVKPMKEAGRGSIINISSIEGLAGTVACHGYTATKFAVRGLTKSTALELGPSGIRVNSIHPGLVKTPMTDWVPEDIFQTALGRAAEPVEVSNLVVYLASDESSYSTGAEFVVDGGTVAGLAHN 245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

Chain B from PDB  Type:PROTEIN  Length:244
 aligned with HSD_MYCTU | P9WGT1 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:244
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    
            HSD_MYCTU     2 SGRLIGKVALVSGGARGMGASHVRAMVAEGAKVVFGDILDEEGKAVAAELADAARYVHLDVTQPAQWTAAVDTAVTAFGGLHVLVNNAGILNIGTIEDYALTEWQRILDVNLTGVFLGIRAVVKPMKEAGRGSIINISSIEGLAGTVACHGYTATKFAVRGLTKSTALELGPSGIRVNSIHPGLVKTPMTDWVPEDIFQTALGRAAEPVEVSNLVVYLASDESSYSTGAEFVVDGGTVAGLAHN 245
               SCOP domains d1nffb_ B: Putative oxidoreductase Rv2002                                                                                                                                                                                                            SCOP domains
               CATH domains 1nffB00 B:2-245 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                  CATH domains
           Pfam domains (1) ------adh_short-1nffB01 B:8-172                                                                                                                                            ------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------adh_short-1nffB02 B:8-172                                                                                                                                            ------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhh...............hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:140-168    ----------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nff B   2 SGRLTGKVALVSGGARGMGASHVRAMVAEGAKVVFGDILDEEGKAMAAELADAARYVHLDVTQPAQWKAAVDTAVTAFGGLHVLVNNAGILNIGTIEDYALTEWQRILDVNLTGVFLGIRAVVKPMKEAGRGSIINISSIEGLAGTVACHGYTATKFAVRGLTKSTALELGPSGIRVNSIHPGLVKTPMTDWVPEDIFQTALGRAAEPVEVSNLVVYLASDESSYSTGAEFVVDGGTVAGLAHN 245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: Tyrosine-dependent oxidoreductases (503)

Protein domain: Putative oxidoreductase Rv2002 (3)

Mycobacterium tuberculosis [TaxId: 1773] (3)

1a	d1nffa_	A:
1b	d1nffb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Mycobacterium tuberculosis. Organism_taxid: 1773. (15)

1a	1nffA00	A:2-245
1b	1nffB00	B:2-245

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: adh_short (92)

Mycobacterium tuberculosis (6)

1a	adh_short-1nffB01	B:8-172
1b	adh_short-1nffB02	B:8-172

Asymmetric Unit(hide GO term definitions)

Chain A,B (HSD_MYCTO | P9WGT0)

molecular function
	GO:0047044	androstan-3-alpha,17-beta-diol dehydrogenase activity	Catalysis of the reaction: NAD+ + androstan-3-alpha,17-beta-diol = 17-beta-hydroxyandrostan-3-one + NADH + H+.
	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:0008207	C21-steroid hormone metabolic process	The chemical reactions and pathways involving C21-steroid hormones, steroid compounds containing 21 carbons which function as hormones.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	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:0008202	steroid metabolic process	The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.

Chain A,B (HSD_MYCTU | P9WGT1)

molecular function
	GO:0047044	androstan-3-alpha,17-beta-diol dehydrogenase activity	Catalysis of the reaction: NAD+ + androstan-3-alpha,17-beta-diol = 17-beta-hydroxyandrostan-3-one + NADH + H+.
	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:0008207	C21-steroid hormone metabolic process	The chemical reactions and pathways involving C21-steroid hormones, steroid compounds containing 21 carbons which function as hormones.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	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:0008202	steroid metabolic process	The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
cellular component
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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	HSD_MYCTO \| P9WGT0	:	1nfq 1nfr
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1nfq	COMPLEXED WITH NADH AND ANDROSTERONE
1nfr	SELENOMETHIONINE SUBSTITUTED STRUCTURE RELATED ID: RV2002 RELATED DB: TARGETDB

Description

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Ligands, Modified Residues, Ions (1, 2)

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Related Entries Specified in the PDB File