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Title :   CRYSTAL STRUCTURE OF E. COLI HYPOTHETICAL OXIDOREDUCTASE YIAK NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER82.

Authors :   F. Forouhar, I. Lee, J. Benach, K. Kulkarni, R. Xiao, T. B. Acton, R. Shastry, B. Rost, G. T. Montelione, L. Tong, Northeast Structural Genomics Consortium (Nesg)

Date :   11 Feb 03 (Deposition) - 11 Mar 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Hypothetical Protein, Oxidoreductase, Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Forouhar, I. Lee, J. Benach, K. Kulkarni, R. Xiao, T. B. Acton, G. T. Montelione, L. Tong
A Novel Nad-Binding Protein Revealed By The Crystal Structure Of 2, 3-Diketo-L-Gulonate Reductase (Yiak).
J. Biol. Chem. V. 279 13148 2004
PubMed-ID: 14718529 | Reference-DOI: 10.1074/JBC.M313580200
(for further references see the PDB file header)

Molecule 1 - HYPOTHETICAL OXIDOREDUCTASE YIAK
	Chains	:	A, B
	EC Number	:	1.1.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	YIAK OR B3575
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 34)

No.	Name	Count	Type	Full Name
1	MSE	30	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:44 , ARG A:48 , TYR A:180 , GLY A:181 , HOH A:1021 , HOH A:1148 , HOH A:1164	BINDING SITE FOR RESIDUE SO4 A 1001
2	AC2	SOFTWARE	MSE A:173 , SER A:174 , PHE A:178 , SER A:179 , MSE A:182 , HOH A:1007 , HOH A:1066 , HOH A:1067 , HOH A:1217 , LYS B:225	BINDING SITE FOR RESIDUE SO4 A 1002
3	AC3	SOFTWARE	LYS A:225 , MSE B:173 , SER B:174 , PHE B:178 , SER B:179 , HOH B:1092 , HOH B:1127 , HOH B:1166	BINDING SITE FOR RESIDUE SO4 B 1003
4	AC4	SOFTWARE	HIS B:44 , ARG B:48 , TYR B:180 , GLY B:181 , HOH B:1078 , HOH B:1081 , HOH B:1083 , HOH B:1131 , HOH B:1143	BINDING SITE FOR RESIDUE SO4 B 1004

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

Asymmetric/Biological Unit

No.	Residues
1	Thr A:166	-	Pro A:167
2	Thr B:166	-	Pro B:167

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

(no "PROSITE Motif" information available for 1NXU)

(no "Exon" information available for 1NXU)

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:332
 aligned with DLGD_ECOLI | P37672 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:332
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330  
           DLGD_ECOLI     1 MKVTFEQLKAAFNRVLISRGVDSETADACAEMFARTTESGVYSHGVNRFPRFIQQLENGDIIPDAQPKRITSLGAIEQWDAQRSIGNLTAKKMMDRAIELAADHGIGLVALRNANHWMRGGSYGWQAAEKGYIGICWTNSIAVMPPWGAKECRIGTNPLIVAIPSTPITMVDMSMSMFSYGMLEVNRLAGRQLPVDGGFDDEGNLTKEPGVIEKNRRILPMGYWKGSGMSIVLDMIATLLSDGASVAEVTQDNSDEYGISQIFIAIEVDKLIDGPTRDAKLQRIMDYVTSAERADENQAIRLPGHEFTTLLAENRRNGITVDDSVWAKIQAL 332
               SCOP domains d1nxua_ A: 2,3-diketogulonate oxidoreductase (YiaK)                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains -1nxuA01 A:2-64,A:317-332  [code=1.10.1530.10, no name defined] 1nxuA02 A:65-164,A:222-270 Hypothetical oxidoreductase yiak; domain 2                               ----------------1nxuA03 A:181-220                       -1nxuA02 A:65-164,A:222-270                       ----------------------------------------------1nxuA01          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.........eeeeee..eeeee....hhhhhhhhhhhhhhhhhhhhheeeeeeeee.....hhhhhhhhhhh..eeeeee....................eeeee.....eeeee.....hhhhhhhhhhh........ee.....ee.hhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.....eeeeeeee......hhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nxu A   1 mKVTFEQLKAAFNRVLISRGVDSETADACAEmFARTTESGVYSHGVNRFPRFIQQLENGDIIPDAQPKRITSLGAIEQWDAQRSIGNLTAKKmmDRAIELAADHGIGLVALRNANHWmRGGSYGWQAAEKGYIGICWTNSIAVmPPWGAKECRIGTNPLIVAIPSTPITmVDmSmSmFSYGmLEVNRLAGRQLPVDGGFDDEGNLTKEPGVIEKNRRILPmGYWKGSGmSIVLDmIATLLSDGASVAEVTQDNSDEYGISQIFIAIEVDKLIDGPTRDAKLQRImDYVTSAERADENQAIRLPGHEFTTLLAENRRNGITVDDSVWAKIQAL 332
                            |       10        20        30 |      40        50        60        70        80        90  ||   100       110       120       130       140   |   150       160       170  | | |180 |     190       200       210       220|      230    |  240       250       260       270       280    |  290       300       310       320       330  
                            |                             32-MSE                                                       93-MSE                  118-MSE                   144-MSE                   170-MSE| |    |                                    221-MSE 229-MSE |                                               285-MSE                                           
                            1-MSE                                                                                       94-MSE                                                                        173-MSE    |                                                  235-MSE                                                                                             
                                                                                                                                                                                                        175-MSE  |                                                                                                                                                      
                                                                                                                                                                                                          177-MSE|                                                                                                                                                      
                                                                                                                                                                                                               182-MSE

Chain B from PDB  Type:PROTEIN  Length:333
 aligned with DLGD_ECOLI | P37672 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:333
                                                                                                                                                                                                                                                                                                                                                                     332 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330 | 
           DLGD_ECOLI     1 MKVTFEQLKAAFNRVLISRGVDSETADACAEMFARTTESGVYSHGVNRFPRFIQQLENGDIIPDAQPKRITSLGAIEQWDAQRSIGNLTAKKMMDRAIELAADHGIGLVALRNANHWMRGGSYGWQAAEKGYIGICWTNSIAVMPPWGAKECRIGTNPLIVAIPSTPITMVDMSMSMFSYGMLEVNRLAGRQLPVDGGFDDEGNLTKEPGVIEKNRRILPMGYWKGSGMSIVLDMIATLLSDGASVAEVTQDNSDEYGISQIFIAIEVDKLIDGPTRDAKLQRIMDYVTSAERADENQAIRLPGHEFTTLLAENRRNGITVDDSVWAKIQAL-   -
               SCOP domains d1nxub_ B: 2,3-diketogulonate oxidoreductase (YiaK)                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -1nxuB01 B:2-64,B:318-333  [code=1.10.1530.10, no name defined] 1nxuB02 B:65-176,B:222-270 Hypothetical oxidoreductase yiak; domain 2                                           -1nxuB03 B:178-220                          -1nxuB02 B:65-176,B:222-270                       -----------------------------------------------1nxuB01          CATH domains
           Pfam domains (1) Ldh_2-1nxuB01 B:1-332                                                                                                                                                                                                                                                                                                                       - Pfam domains (1)
           Pfam domains (2) Ldh_2-1nxuB02 B:1-332                                                                                                                                                                                                                                                                                                                       - Pfam domains (2)
         Sec.struct. author .eehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.........eeeeee..eeeee....hhhhhhhhhhhhhhhhhhhhheeeeeeeee....hhhhhhhhhhhh.eeeeeee....................eeeee.....eeeee.....hhhhhhhhhhh........ee.....ee.hhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhh......eeeeeeeee.....hhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhee.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nxu B   1 mKVTFEQLKAAFNRVLISRGVDSETADACAEmFARTTESGVYSHGVNRFPRFIQQLENGDIIPDAQPKRITSLGAIEQWDAQRSIGNLTAKKmmDRAIELAADHGIGLVALRNANHWmRGGSYGWQAAEKGYIGICWTNSIAVmPPWGAKECRIGTNPLIVAIPSTPITmVDmSmSmFSYGmLEVNRLAGRQLPVDGGFDDEGNLTKEPGVIEKNRRILPmGYWKGSGmSIVLDmIATLLSDGASVAEVTQDNSDEYGISQIFIAIEVDKLIDGPTRDAKLQRImDYVTSAERADENQAIRLPGHEFTTLLAENRRNGITVDDSVWAKIQALA 333
                            |       10        20        30 |      40        50        60        70        80        90  ||   100       110       120       130       140   |   150       160       170  | | |180 |     190       200       210       220|      230    |  240       250       260       270       280    |  290       300       310       320       330   
                            1-MSE                         32-MSE                                                       93-MSE                  118-MSE                   144-MSE                   170-MSE| |    |                                    221-MSE 229-MSE |                                               285-MSE                                            
                                                                                                                        94-MSE                                                                        173-MSE    |                                                  235-MSE                                                                                              
                                                                                                                                                                                                        175-MSE  |                                                                                                                                                       
                                                                                                                                                                                                          177-MSE|                                                                                                                                                       
                                                                                                                                                                                                               182-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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: L-sulfolactate dehydrogenase-like (12)

Superfamily: L-sulfolactate dehydrogenase-like (12)

Family: L-sulfolactate dehydrogenase-like (7)

Protein domain: 2,3-diketogulonate oxidoreductase (YiaK) (2)

Escherichia coli [TaxId: 562] (2)

1a	d1nxua_	A:
1b	d1nxub_	B:

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Ldh_2] (7)

Family: Ldh_2 (7)

Escherichia coli (strain K12) (3)

1a	Ldh_2-1nxuB01	B:1-332
1b	Ldh_2-1nxuB02	B:1-332

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (DLGD_ECOLI | P37672)

molecular function
	GO:0047559	3-dehydro-L-gulonate 2-dehydrogenase activity	Catalysis of the reaction: 3-dehydro-L-gulonate + NAD(P)+ = (4R,5S)-4,5,6-trihydroxy-2,3-dioxohexanoate + NAD(P)H + H+.
	GO:0070403	NAD+ binding	Interacting selectively and non-covalently with the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
	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.
	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Thr A:166 - Pro A:167	[ RasMol ]
		Thr B:166 - Pro B:167	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 34)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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