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Title :   CRYSTAL STRUCTURE OF PUTATIVE DINUCLEOTIDE-BINDING OXIDOREDUCTASE (NP_786167.1) FROM LACTOBACILLUS PLANTARUM AT 1.60 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   14 Sep 07 (Deposition) - 02 Oct 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Np_786167. 1, Putative Dinucleotide-Binding Oxidoreductase, Nadp Oxidoreductase Coenzyme F420-Dependent, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Dinucleotide-Binding Oxidoreductase (Np_786167. 1) From Lactobacillus Plantarum At 1. 60 A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PUTATIVE DINUCLEOTIDE-BINDING OXIDOREDUCTASE
	Atcc	:	BAA-793
	Chains	:	A, B, C
	EC Number	:	1.-.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	SPEEDET
	Expression System Strain	:	HK100
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NP_786167.1, LP_2792
	Organism Scientific	:	LACTOBACILLUS PLANTARUM WCFS1
	Organism Taxid	:	220668
	Strain	:	WCFS1, NCIMB 8826

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 20)

No.	Name	Count	Type	Full Name
1	MSE	18	Mod. Amino Acid	SELENOMETHIONINE
2	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (2, 13)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
2	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 2 (2, 14)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
2	NAP	-1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER

(no "Site" information available for 2RAF)

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

(no "Cis Peptide Bond" information available for 2RAF)

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

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

(no "Exon" information available for 2RAF)

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:190
 aligned with F9URQ8_LACPL | F9URQ8 from UniProtKB/TrEMBL  Length:190

    Alignment length:190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
         F9URQ8_LACPL     1 MEITIFGKGNMGQAIGHNFEIAGHEVTYYGSKDQATTLGEIVIMAVPYPALAALAKQYATQLKGKIVVDITNPLNFDTWDDLVVPADSSAAQELQQQLPDSQVLKAFNTTFAATLQSGQVNGKEPTTVLVAGNDDSAKQRFTRALADSPLEVKDAGKLKRARELEAMGFMQMTLAASEQIGWTGGFAVVK 190
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -2rafA01 A:2-169 NAD(P)-binding Rossmann-like Domain                                                                                                                     --------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh..eeeee...........eeee..hhhhhhhhhhhhhhhhh..eeee...................hhhhhhhhhh...eeee.....hhhhhhhhee...ee.eeeeee.hhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhhhhh.......eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2raf A   1 mEITIFGKGNmGQAIGHNFEIAGHEVTYYGSKDQATTLGEIVImAVPYPALAALAKQYATQLKGKIVVDITNPLNFDTWDDLVVPADSSAAQELQQQLPDSQVLKAFNTTFAATLQSGQVNGKEPTTVLVAGNDDSAKQRFTRALADSPLEVKDAGKLKRARELEAmGFmQmTLAASEQIGWTGGFAVVK 190
                            |       10|       20        30        40   |    50        60        70        80        90       100       110       120       130       140       150       160      |170 |     180       190
                            |        11-MSE                           44-MSE                                                                                                                    167-MSE|                  
                            1-MSE                                                                                                                                                                  170-MSE                
                                                                                                                                                                                                     172-MSE

Chain B from PDB  Type:PROTEIN  Length:207
 aligned with F9URQ8_LACPL | F9URQ8 from UniProtKB/TrEMBL  Length:190

    Alignment length:207
                                             1                                                                                                                                                                                             
                                     -       | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       
         F9URQ8_LACPL     - -----------------MEITIFGKGNMGQAIGHNFEIAGHEVTYYGSKDQATTLGEIVIMAVPYPALAALAKQYATQLKGKIVVDITNPLNFDTWDDLVVPADSSAAQELQQQLPDSQVLKAFNTTFAATLQSGQVNGKEPTTVLVAGNDDSAKQRFTRALADSPLEVKDAGKLKRARELEAMGFMQMTLAASEQIGWTGGFAVVK 190
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2rafB01 B:-16-169 NAD(P)-binding Rossmann-like Domain                                                                                                                                     --------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.......eee..eeeee..hhhhhhhhhhhhhh..eeeee...........eeee....hhhhhhhhhhhhhhh..eeee...................hhhhhhhhhh...eeee.....hhhhhhhhee...ee.eeeeee.hhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhhhhh.......eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2raf B -16 SDKIHHHHHHENLYFQGmEITIFGKGNmGQAIGHNFEIAGHEVTYYGSKDQATTLGEIVImAVPYPALAALAKQYATQLKGKIVVDITNPLNFDTWDDLVVPADSSAAQELQQQLPDSQVLKAFNTTFAATLQSGQVNGKEPTTVLVAGNDDSAKQRFTRALADSPLEVKDAGKLKRARELEAmGFmQmTLAASEQIGWTGGFAVVK 190
                                    -7       | 3       |13        23        33        43|       53        63        73        83        93       103       113       123       133       143       153       163   |  |173       183       
                                             1-MSE    11-MSE                           44-MSE                                                                                                                    167-MSE|                  
                                                                                                                                                                                                                    170-MSE                
                                                                                                                                                                                                                      172-MSE

Chain C from PDB  Type:PROTEIN  Length:190
 aligned with F9URQ8_LACPL | F9URQ8 from UniProtKB/TrEMBL  Length:190

    Alignment length:190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
         F9URQ8_LACPL     1 MEITIFGKGNMGQAIGHNFEIAGHEVTYYGSKDQATTLGEIVIMAVPYPALAALAKQYATQLKGKIVVDITNPLNFDTWDDLVVPADSSAAQELQQQLPDSQVLKAFNTTFAATLQSGQVNGKEPTTVLVAGNDDSAKQRFTRALADSPLEVKDAGKLKRARELEAMGFMQMTLAASEQIGWTGGFAVVK 190
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -2rafC01 C:2-169 NAD(P)-binding Rossmann-like Domain                                                                                                                     --------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhh...eeeee...........eeee..hhhhhhhhhhhhhhhhh..eeee...................hhhhhhhhhh...eeee.....hhhhhhhhee...ee.eeeeee.hhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2raf C   1 mEITIFGKGNmGQAIGHNFEIAGHEVTYYGSKDQATTLGEIVImAVPYPALAALAKQYATQLKGKIVVDITNPLNFDTWDDLVVPADSSAAQELQQQLPDSQVLKAFNTTFAATLQSGQVNGKEPTTVLVAGNDDSAKQRFTRALADSPLEVKDAGKLKRARELEAmGFmQmTLAASEQIGWTGGFAVVK 190
                            |       10|       20        30        40   |    50        60        70        80        90       100       110       120       130       140       150       160      |170 |     180       190
                            1-MSE    11-MSE                           44-MSE                                                                                                                    167-MSE|                  
                                                                                                                                                                                                   170-MSE                
                                                                                                                                                                                                     172-MSE

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 '\|'

(no "SCOP Domain" information available for 2RAF)

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)

Lactobacillus plantarum wcfs1. Organism_taxid: 220668. Strain: wcfs1,ncimb 8826. (1)

1a	2rafB01	B:-16-169
1b	2rafA01	A:2-169
1c	2rafC01	C:2-169

(no "Pfam Domain" information available for 2RAF)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (F9URQ8_LACPL | F9URQ8)

molecular function
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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.

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(no "Sites" information available for 2raf)

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(no "Cis Peptide Bonds" information available for 2raf)

Biological Units
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