2PW9 - JenaLib

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Title :   CRYSTAL STRUCTURE OF A PUTATIVE FORMATE DEHYDROGENASE ACCESSORY PROTEIN FROM DESULFOTALEA PSYCHROPHILA

Authors :   J. B. Bonanno, M. Dickey, K. T. Bain, C. Logan, R. Romero, D. Smith, S. Was J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center Structural Genomics (Nysgxrc)

Date :   10 May 07 (Deposition) - 22 May 07 (Release) - 24 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Structural Genomics, Unknown Function, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. B. Bonanno, M. Dickey, K. T. Bain, C. Logan, R. Romero, D. Smith, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of A Putative Formate Dehydrogenase Accessory Protein From Desulfotalea Psychrophila.
To Be Published
PubMed: search

Molecule 1 - PUTATIVE FORMATE DEHYDROGENASE ACCESSORY PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	MODIFIED PET26
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET
	Expression System Vector Type	:	PLASMID
	Gene	:	DP1777
	Organism Scientific	:	DESULFOTALEA PSYCHROPHILA LSV54
	Organism Taxid	:	177439
	Strain	:	LSV54, DSM 12343

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:154 , ARG A:173 , ARG A:200 , HOH A:603 , HOH A:618 , HOH A:657 , HIS B:154 , ARG B:173 , ARG B:200 , HOH B:270	BINDING SITE FOR RESIDUE SO4 A 601
2	AC2	SOFTWARE	HIS C:154 , ARG C:173 , ARG C:200 , HOH C:605 , HOH C:620 , HOH C:645 , HOH C:646 , HIS D:154 , ARG D:173 , ARG D:200	BINDING SITE FOR RESIDUE SO4 C 602

(no "SS Bond" information available for 2PW9)

Asymmetric Unit

No.	Residues
1	Pro C:19	-	Gly C:20

(no "SAP(SNP)/Variant" information available for 2PW9)

(no "PROSITE Motif" information available for 2PW9)

(no "Exon" information available for 2PW9)

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:231
 aligned with Q6AMB9_DESPS | Q6AMB9 from UniProtKB/TrEMBL  Length:258

    Alignment length:251
                                    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 
         Q6AMB9_DESPS     7 PLSIMQKSVVIRPGGRQEMDEHVAIETPYAIALNDRVIGSSMVLPVDLEEFGAGFLFGQGYIKKAEEIREILVCPQGRISVYADVENEEPREVIITSGCGGTGKIPKEMLEGEFAPLADYCLPFAEIKSFIREALHSSPLGPQTHCVHGCGLWNNGRLQVYHEDVGRHNAVDKVLGSILLGRASNNSAVYTTGRLTSDMVLKCARIGIPIIMSRTSPSSLGLALAKRSGATLVAYSRPERINVFNAPERIL 257
               SCOP domains d2pw9a1 A:7-257 Uncharacterized protein DP1777                                                                                                                                                                                                              SCOP domains
               CATH domains 2pw9A01 A:7-31           2pw9A02 A:32-110  [code=3.10.20.10, no name defined]                           2pw9A03   -------2pw9A03 A:111-120,A:128-257 Cytidine Deaminase, domain 2                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee....eeeeeeeee..eeeeeee..eeeeeeee...hhhhhhhhhhhhhh...hhh.eeeeeee...eeeeee.-------------------..hhhhhh-.........ee..hhhhhhhhhhh..hhhhhhh..eeeeeee..eeeeeeee.hhhhhhhhhhhhhhh.......eeee....hhhhhhhhhhhh..eeee....hhhhhhhhhhhh.eeeeeee..eeeeeehhh.ee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pw9 A   7 PLSIMQKSVVIRPGGRQEMDEHVAIETPYAIALNDRVIGSSMVLPVDLEEFGAGFLFGQGYIKKAEEIREILVCPQGRISVYAD-------------------KIPKEMLE-EFAPLADYCLPFAEIKSFIREALHSSPLGPQTHCVHGCGLWNNGRLQVYHEDVGRHNAVDKVLGSILLGRASNNSAVYTTGRLTSDMVLKCARIGIPIIMSRTSPSSLGLALAKRSGATLVAYSRPERINVFNAPERIL 257
                                    16        26        36        46        56        66        76        86   |     -         -   |   116| |    126       136       146       156       166       176       186       196       206       216       226       236       246       256 
                                                                                                              90                 110    117 |                                                                                                                                          
                                                                                                                                          119

Chain B from PDB  Type:PROTEIN  Length:230
 aligned with Q6AMB9_DESPS | Q6AMB9 from UniProtKB/TrEMBL  Length:258

    Alignment length:251
                                    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 
         Q6AMB9_DESPS     7 PLSIMQKSVVIRPGGRQEMDEHVAIETPYAIALNDRVIGSSMVLPVDLEEFGAGFLFGQGYIKKAEEIREILVCPQGRISVYADVENEEPREVIITSGCGGTGKIPKEMLEGEFAPLADYCLPFAEIKSFIREALHSSPLGPQTHCVHGCGLWNNGRLQVYHEDVGRHNAVDKVLGSILLGRASNNSAVYTTGRLTSDMVLKCARIGIPIIMSRTSPSSLGLALAKRSGATLVAYSRPERINVFNAPERIL 257
               SCOP domains d2pw9b_ B: Uncharacterized protein DP1777                                                                                                                                                                                                                   SCOP domains
               CATH domains 2pw9B01 B:7-31           2pw9B02 B:32-110  [code=3.10.20.10, no name defined]                           2pw9B03   B:111-257 Cytidine Deaminase, domain 2                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee..eeeeeeeeee..eeeeeee..eeeeeeee...hhhhhhhhhhhhh....hhh.eeeeeee...eeeeee.-------------------..hhhhhh--........ee.hhhhhhhhhhhhh.hhhhhhh..eeeeeee..eeeeeeee.hhhhhhhhhhhhhhh.......eeee....hhhhhhhhhhhh..eeee....hhhhhhhhhhhh.eeeeeee..eeeeeehhh.ee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pw9 B   7 PLSIMQKSVVIRPGGRQEMDEHVAIETPYAIALNDRVIGSSMVLPVDLEEFGAGFLFGQGYIKKAEEIREILVCPQGRISVYAD-------------------KIPKEMLE--FAPLADYCLPFAEIKSFIREALHSSPLGPQTHCVHGCGLWNNGRLQVYHEDVGRHNAVDKVLGSILLGRASNNSAVYTTGRLTSDMVLKCARIGIPIIMSRTSPSSLGLALAKRSGATLVAYSRPERINVFNAPERIL 257
                                    16        26        36        46        56        66        76        86   |     -         -   |   116|  |   126       136       146       156       166       176       186       196       206       216       226       236       246       256 
                                                                                                              90                 110    117  |                                                                                                                                         
                                                                                                                                           120

Chain C from PDB  Type:PROTEIN  Length:221
 aligned with Q6AMB9_DESPS | Q6AMB9 from UniProtKB/TrEMBL  Length:258

    Alignment length:251
                                    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 
         Q6AMB9_DESPS     7 PLSIMQKSVVIRPGGRQEMDEHVAIETPYAIALNDRVIGSSMVLPVDLEEFGAGFLFGQGYIKKAEEIREILVCPQGRISVYADVENEEPREVIITSGCGGTGKIPKEMLEGEFAPLADYCLPFAEIKSFIREALHSSPLGPQTHCVHGCGLWNNGRLQVYHEDVGRHNAVDKVLGSILLGRASNNSAVYTTGRLTSDMVLKCARIGIPIIMSRTSPSSLGLALAKRSGATLVAYSRPERINVFNAPERIL 257
               SCOP domains d2pw9c_ C: Uncharacterized protein DP1777                                                                                                                                                                                                                   SCOP domains
               CATH domains 2pw9C01 C:7-31           2pw9C02 C:32-89  [code=3.10.20.10, no name defined]       ------------------------------2pw9C03 C:120-257 Cytidine Deaminase, domain 2                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee..eeeeeeeeee..eeeeeee..eeeeeeee...hhhhhhhhhhhhhh..........eeee...eeee..------------------------------........ee..hhhhhhhhhhh..hhhhhhh..eeeeeee..eeeeeeee.hhhhhhhhhhhhhhh.......eeee....hhhhhhhhhhhh..eeee....hhhhhhhhhhhh.eeeeeee..eeeeeehhh.ee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pw9 C   7 PLSIMQKSVVIRPGGRQEMDEHVAIETPYAIALNDRVIGSSMVLPVDLEEFGAGFLFGQGYIKKAEEIREILVCPQGRISVYA------------------------------FAPLADYCLPFAEIKSFIREALHSSPLGPQTHCVHGCGLWNNGRLQVYHEDVGRHNAVDKVLGSILLGRASNNSAVYTTGRLTSDMVLKCARIGIPIIMSRTSPSSLGLALAKRSGATLVAYSRPERINVFNAPERIL 257
                                    16        26        36        46        56        66        76        86  |      -         -         -   |   126       136       146       156       166       176       186       196       206       216       226       236       246       256 
                                                                                                             89                            120

Chain D from PDB  Type:PROTEIN  Length:237
 aligned with Q6AMB9_DESPS | Q6AMB9 from UniProtKB/TrEMBL  Length:258

    Alignment length:251
                                    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 
         Q6AMB9_DESPS     7 PLSIMQKSVVIRPGGRQEMDEHVAIETPYAIALNDRVIGSSMVLPVDLEEFGAGFLFGQGYIKKAEEIREILVCPQGRISVYADVENEEPREVIITSGCGGTGKIPKEMLEGEFAPLADYCLPFAEIKSFIREALHSSPLGPQTHCVHGCGLWNNGRLQVYHEDVGRHNAVDKVLGSILLGRASNNSAVYTTGRLTSDMVLKCARIGIPIIMSRTSPSSLGLALAKRSGATLVAYSRPERINVFNAPERIL 257
               SCOP domains d2pw9d_ D: Uncharacterized protein DP1777                                                                                                                                                                                                                   SCOP domains
               CATH domains 2pw9D01 D:7-31           2pw9D02 D:32-110  [code=3.10.20.10, no name defined]                           2pw9D03  D:111-257 Cytidine Deaminase, domain 2                                                                                                     CATH domains
           Pfam domains (1) -----------------------FdhD-NarQ-2pw9D01 D:30-257                                                                                                                                                                                                           Pfam domains (1)
           Pfam domains (2) -----------------------FdhD-NarQ-2pw9D02 D:30-257                                                                                                                                                                                                           Pfam domains (2)
           Pfam domains (3) -----------------------FdhD-NarQ-2pw9D03 D:30-257                                                                                                                                                                                                           Pfam domains (3)
           Pfam domains (4) -----------------------FdhD-NarQ-2pw9D04 D:30-257                                                                                                                                                                                                           Pfam domains (4)
         Sec.struct. author ..eeeeeeeee....eeeeeeeee..eeeeeee..eeeeeeee...hhhhhhhhhhhhh....hhh.eeeeeee...eeeeee.......-------------..hhhhhh-.........ee..hhhhhhhhhhh..hhhhhhh..eeeeeee..eeeeeeee.hhhhhhhhhhhhhhh.......eeee....hhhhhhhhhhh...eeee....hhhhhhhhhhhh.eeeeeee..eeeeeehhh.ee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pw9 D   7 PLSIMQKSVVIRPGGRQEMDEHVAIETPYAIALNDRVIGSSMVLPVDLEEFGAGFLFGQGYIKKAEEIREILVCPQGRISVYADVENEEP-------------KIPKEMLE-EFAPLADYCLPFAEIKSFIREALHSSPLGPQTHCVHGCGLWNNGRLQVYHEDVGRHNAVDKVLGSILLGRASNNSAVYTTGRLTSDMVLKCARIGIPIIMSRTSPSSLGLALAKRSGATLVAYSRPERINVFNAPERIL 257
                                    16        26        36        46        56        66        76        86        96         -   |   116| |    126       136       146       156       166       176       186       196       206       216       226       236       246       256 
                                                                                                                    96           110    117 |                                                                                                                                          
                                                                                                                                          119

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: Cytidine deaminase-like (78)

Superfamily: Cytidine deaminase-like (76)

Family: FdhD/NarQ (1)

Protein domain: Uncharacterized protein DP1777 (1)

Desulfotalea psychrophila [TaxId: 84980] (1)

1a	d2pw9a1	A:7-257
1b	d2pw9b_	B:
1c	d2pw9c_	C:
1d	d2pw9d_	D:

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: FdhD-NarQ] (1)

Family: FdhD-NarQ (1)

Desulfotalea psychrophila (1)

1a	FdhD-NarQ-2pw9D01	D:30-257
1b	FdhD-NarQ-2pw9D02	D:30-257
1c	FdhD-NarQ-2pw9D03	D:30-257
1d	FdhD-NarQ-2pw9D04	D:30-257

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q6AMB9_DESPS | Q6AMB9)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0097163	sulfur carrier activity	Enables the directed movement of sulfur into, out of or within a cell, or between cells.
	GO:0016783	sulfurtransferase activity	Catalysis of the transfer of sulfur atoms from one compound (donor) to another (acceptor).
biological process
	GO:0006777	Mo-molybdopterin cofactor biosynthetic process	The chemical reactions and pathways resulting in the formation of the Mo-molybdopterin cofactor, essential for the catalytic activity of some enzymes. The cofactor consists of a mononuclear molybdenum (Mo) ion coordinated by one or two molybdopterin ligands.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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