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Title :   CRYSTAL STRUCTURE OF A PUTATIVE CARVEOL DEHYDROGENASE FROM MYCOBACTERIUM PARATUBERCULOSIS BOUND TO NICOTINAMIDE ADENINE DINUCLEOTIDE

Authors :   Seattle Structural Genomics Center For Infectious Disease (S

Date :   02 Nov 10 (Deposition) - 24 Nov 10 (Release) - 08 Feb 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Carveol Dehydrogenase, Short Chain Dehydrogenase/Reductase Superfamily, Oxidoreductase, Nicotinamide Adenine Dinucleotide, Nad, Putative Uncharacterized Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. H. Haft, P. G. Pierce, S. J. Mayclin, A. Sullivan, A. S. Gardberg, J. Abendroth, D. W. Begley, I. Q. Phan, B. L. Staker, P. J. Myler, V. M. Marathias, D. D. Lorimer, T. E. Edwards
Mycofactocin-Associated Mycobacterial Dehydrogenases With Non-Exchangeable Nad Cofactors.
Sci Rep V. 7 41074 2017
PubMed-ID: 28120876 | Reference-DOI: 10.1038/SREP41074
(for further references see the PDB file header)

Molecule 1 - CARVEOL DEHYDROGENASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	AVA0421
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MAP_4146
	Organism Scientific	:	MYCOBACTERIUM AVIUM
	Organism Taxid	:	1770
	Strain	:	PARATUBERCULOSIS

		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	NAD	4	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:18 , ARG A:21 , GLY A:22 , GLN A:23 , ASP A:42 , ILE A:43 , VAL A:47 , ALA A:56 , LEU A:80 , ASP A:81 , VAL A:82 , ASN A:108 , ALA A:109 , GLY A:110 , VAL A:111 , VAL A:131 , VAL A:159 , SER A:160 , TYR A:174 , LYS A:178 , PRO A:204 , SER A:206 , VAL A:207 , THR A:209 , PRO A:210 , MET A:211 , ILE A:212 , HOH A:298 , HOH A:303 , HOH A:311 , HOH A:397	BINDING SITE FOR RESIDUE NAD A 277
2	AC2	SOFTWARE	GLY B:18 , ARG B:21 , GLN B:23 , ASP B:42 , ILE B:43 , VAL B:47 , ALA B:56 , LEU B:80 , ASP B:81 , VAL B:82 , ASN B:108 , ALA B:109 , GLY B:110 , VAL B:111 , VAL B:131 , VAL B:159 , SER B:160 , SER B:161 , TYR B:174 , LYS B:178 , PRO B:204 , SER B:206 , VAL B:207 , THR B:209 , PRO B:210 , MET B:211 , ILE B:212 , HOH B:284 , HOH B:292 , HOH B:302 , HOH B:323 , HOH B:503	BINDING SITE FOR RESIDUE NAD B 277
3	AC3	SOFTWARE	GLY C:18 , ARG C:21 , GLY C:22 , GLN C:23 , ASP C:42 , ILE C:43 , VAL C:47 , ALA C:56 , LEU C:80 , ASP C:81 , VAL C:82 , ASN C:108 , ALA C:109 , GLY C:110 , VAL C:111 , VAL C:131 , VAL C:159 , SER C:160 , SER C:161 , TYR C:174 , LYS C:178 , PRO C:204 , SER C:206 , VAL C:207 , THR C:209 , PRO C:210 , MET C:211 , ILE C:212 , HOH C:313 , HOH C:326 , HOH C:377 , HOH C:748 , HOH C:753	BINDING SITE FOR RESIDUE NAD C 277
4	AC4	SOFTWARE	GLY D:18 , ARG D:21 , GLY D:22 , GLN D:23 , ASP D:42 , ILE D:43 , VAL D:47 , ALA D:56 , LEU D:80 , ASP D:81 , VAL D:82 , ASN D:108 , ALA D:109 , GLY D:110 , VAL D:111 , VAL D:131 , VAL D:159 , SER D:160 , SER D:161 , TYR D:174 , LYS D:178 , PRO D:204 , SER D:206 , VAL D:207 , THR D:209 , PRO D:210 , MET D:211 , ILE D:212 , HOH D:278 , HOH D:301 , HOH D:369 , HOH D:752 , HOH D:782	BINDING SITE FOR RESIDUE NAD D 277

(no "SS Bond" information available for 3PGX)

(no "Cis Peptide Bond" information available for 3PGX)

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

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	Y4146_MYCPA	160-188	4	A:161-189 B:161-189 C:161-189 D:161-189

(no "Exon" information available for 3PGX)

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:270
 aligned with Y4146_MYCPA | Q73SC8 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:270
                                    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
          Y4146_MYCPA     6 GSLQGRVAFITGAARGQGRSHAVRLAAEGADIIACDICAPVSASVTYAPASPEDLDETARLVEDQGRKALTRVLDVRDDAALRELVADGMEQFGRLDVVVANAGVLSWGRVWELTDEQWDTVIGVNLTGTWRTLRATVPAMIEAGNGGSIVVVSSSAGLKATPGNGHYSASKHGLTALTNTLAIELGEYGIRVNSIHPYSVETPMIEPEAMMEIFARHPSFVHSFPPMPVQPNGFMTADEVADVVAWLAGDGSGTLTGTQIPVDKGALKY 275
               SCOP domains d3pgxa_ A: automated matches                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee..............hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee........hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:161-189    --------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3pgx A   7 GSLQGRVAFITGAARGQGRSHAVRLAAEGADIIACDICAPVSASVTYAPASPEDLDETARLVEDQGRKALTRVLDVRDDAALRELVADGMEQFGRLDVVVANAGVLSWGRVWELTDEQWDTVIGVNLTGTWRTLRATVPAMIEAGNGGSIVVVSSSAGLKATPGNGHYSASKHGLTALTNTLAIELGEYGIRVNSIHPYSVETPMIEPEAMMEIFARHPSFVHSFPPMPVQPNGFMTADEVADVVAWLAGDGSGTLTGTQIPVDKGALKY 276
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276

Chain B from PDB  Type:PROTEIN  Length:270
 aligned with Y4146_MYCPA | Q73SC8 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:270
                                    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
          Y4146_MYCPA     6 GSLQGRVAFITGAARGQGRSHAVRLAAEGADIIACDICAPVSASVTYAPASPEDLDETARLVEDQGRKALTRVLDVRDDAALRELVADGMEQFGRLDVVVANAGVLSWGRVWELTDEQWDTVIGVNLTGTWRTLRATVPAMIEAGNGGSIVVVSSSAGLKATPGNGHYSASKHGLTALTNTLAIELGEYGIRVNSIHPYSVETPMIEPEAMMEIFARHPSFVHSFPPMPVQPNGFMTADEVADVVAWLAGDGSGTLTGTQIPVDKGALKY 275
               SCOP domains d3pgxb_ B: automated matches                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee..............hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:161-189    --------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3pgx B   7 GSLQGRVAFITGAARGQGRSHAVRLAAEGADIIACDICAPVSASVTYAPASPEDLDETARLVEDQGRKALTRVLDVRDDAALRELVADGMEQFGRLDVVVANAGVLSWGRVWELTDEQWDTVIGVNLTGTWRTLRATVPAMIEAGNGGSIVVVSSSAGLKATPGNGHYSASKHGLTALTNTLAIELGEYGIRVNSIHPYSVETPMIEPEAMMEIFARHPSFVHSFPPMPVQPNGFMTADEVADVVAWLAGDGSGTLTGTQIPVDKGALKY 276
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276

Chain C from PDB  Type:PROTEIN  Length:270
 aligned with Y4146_MYCPA | Q73SC8 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:270
                                    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
          Y4146_MYCPA     6 GSLQGRVAFITGAARGQGRSHAVRLAAEGADIIACDICAPVSASVTYAPASPEDLDETARLVEDQGRKALTRVLDVRDDAALRELVADGMEQFGRLDVVVANAGVLSWGRVWELTDEQWDTVIGVNLTGTWRTLRATVPAMIEAGNGGSIVVVSSSAGLKATPGNGHYSASKHGLTALTNTLAIELGEYGIRVNSIHPYSVETPMIEPEAMMEIFARHPSFVHSFPPMPVQPNGFMTADEVADVVAWLAGDGSGTLTGTQIPVDKGALKY 275
               SCOP domains d3pgxc_ C: automated matches                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee..............hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: C:161-189    --------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3pgx C   7 GSLQGRVAFITGAARGQGRSHAVRLAAEGADIIACDICAPVSASVTYAPASPEDLDETARLVEDQGRKALTRVLDVRDDAALRELVADGMEQFGRLDVVVANAGVLSWGRVWELTDEQWDTVIGVNLTGTWRTLRATVPAMIEAGNGGSIVVVSSSAGLKATPGNGHYSASKHGLTALTNTLAIELGEYGIRVNSIHPYSVETPMIEPEAMMEIFARHPSFVHSFPPMPVQPNGFMTADEVADVVAWLAGDGSGTLTGTQIPVDKGALKY 276
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276

Chain D from PDB  Type:PROTEIN  Length:270
 aligned with Y4146_MYCPA | Q73SC8 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:270
                                    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
          Y4146_MYCPA     6 GSLQGRVAFITGAARGQGRSHAVRLAAEGADIIACDICAPVSASVTYAPASPEDLDETARLVEDQGRKALTRVLDVRDDAALRELVADGMEQFGRLDVVVANAGVLSWGRVWELTDEQWDTVIGVNLTGTWRTLRATVPAMIEAGNGGSIVVVSSSAGLKATPGNGHYSASKHGLTALTNTLAIELGEYGIRVNSIHPYSVETPMIEPEAMMEIFARHPSFVHSFPPMPVQPNGFMTADEVADVVAWLAGDGSGTLTGTQIPVDKGALKY 275
               SCOP domains d3pgxd_ D: automated matches                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee..............hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee........hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: D:161-189    --------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3pgx D   7 GSLQGRVAFITGAARGQGRSHAVRLAAEGADIIACDICAPVSASVTYAPASPEDLDETARLVEDQGRKALTRVLDVRDDAALRELVADGMEQFGRLDVVVANAGVLSWGRVWELTDEQWDTVIGVNLTGTWRTLRATVPAMIEAGNGGSIVVVSSSAGLKATPGNGHYSASKHGLTALTNTLAIELGEYGIRVNSIHPYSVETPMIEPEAMMEIFARHPSFVHSFPPMPVQPNGFMTADEVADVVAWLAGDGSGTLTGTQIPVDKGALKY 276
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276

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(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

)

Organisms( (-)

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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: automated matches (447)

Protein domain: automated matches (447)

Mycobacterium avium [TaxId: 1770] (2)

1a	d3pgxa_	A:
1b	d3pgxb_	B:
1c	d3pgxc_	C:
1d	d3pgxd_	D:

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (Y4146_MYCPA | Q73SC8)

molecular function
	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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3oec	SIMILAR STRUCTURE FROM MYCOBACTERIUM THERMORESISTIBILE WITHOUT COENZYME RELATED ID: MYPAA.01326.B RELATED DB: TARGETDB

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Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

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