1M2W - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   PSEUDOMONAS FLUORESCENS MANNITOL 2-DEHYDROGENASE TERNARY COMPLEX WITH NAD AND D-MANNITOL

Authors :   K. L. Kavanagh, M. Klimacek, B. Nidetzky, D. K. Wilson

Date :   25 Jun 02 (Deposition) - 15 Nov 02 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Rossmann Fold, Di-Nucleotide Binding Motif, Long-Chain Dehydrogenase, Polyol Dehydrogenase, Secondary Alcohol Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. L. Kavanagh, M. Klimacek, B. Nidetzky, D. K. Wilson
Crystal Structure Of Pseudomonas Fluorescens Mannitol 2-Dehydrogenase Binary And Ternary Complexes. Specificity And Catalytic Mechanism
J. Biol. Chem. V. 277 43433 2002
PubMed-ID: 12196534 | Reference-DOI: 10.1074/JBC.M206914200

Molecule 1 - MANNITOL DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.1.1.67
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	MTLD
	Organism Scientific	:	PSEUDOMONAS FLUORESCENS
	Organism Taxid	:	294
	Strain	:	DSM50106

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 26)

No.	Name	Count	Type	Full Name
1	MSE	22	Mod. Amino Acid	SELENOMETHIONINE
2	MTL	2	Ligand/Ion	D-MANNITOL
3	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 1 (3, 13)

No.	Name	Count	Type	Full Name
1	MSE	11	Mod. Amino Acid	SELENOMETHIONINE
2	MTL	1	Ligand/Ion	D-MANNITOL
3	NAD	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 2 (3, 13)

No.	Name	Count	Type	Full Name
1	MSE	11	Mod. Amino Acid	SELENOMETHIONINE
2	MTL	1	Ligand/Ion	D-MANNITOL
3	NAD	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:33 , VAL A:34 , GLY A:35 , GLY A:36 , PHE A:37 , ARG A:66 , ASP A:69 , THR A:130 , ILE A:131 , THR A:132 , GLU A:133 , ASP A:190 , ASN A:191 , ARG A:231 , ILE A:232 , THR A:233 , ARG A:373 , MTL A:5600 , HOH A:5607 , HOH A:5677 , HOH A:5689 , HOH A:5690 , HOH A:5832 , HOH A:5858	BINDING SITE FOR RESIDUE NAD A 5500
2	AC2	SOFTWARE	GLY B:33 , VAL B:34 , GLY B:35 , GLY B:36 , PHE B:37 , ARG B:66 , ASP B:69 , THR B:130 , ILE B:131 , THR B:132 , GLU B:133 , ASP B:190 , ASN B:191 , ARG B:231 , ILE B:232 , THR B:233 , ARG B:373 , MTL B:6600 , HOH B:6604 , HOH B:6614 , HOH B:6682 , HOH B:6853	BINDING SITE FOR RESIDUE NAD B 6500
3	AC3	SOFTWARE	ASN A:191 , ASP A:230 , ARG A:231 , LYS A:295 , ASN A:300 , HIS A:303 , ARG A:373 , VAL A:374 , LYS A:381 , NAD A:5500 , HOH A:5677	BINDING SITE FOR RESIDUE MTL A 5600
4	AC4	SOFTWARE	ASN B:191 , ASP B:230 , ARG B:231 , LYS B:295 , ASN B:300 , HIS B:303 , ARG B:373 , VAL B:374 , LYS B:381 , NAD B:6500 , HOH B:6614	BINDING SITE FOR RESIDUE MTL B 6600

(no "SS Bond" information available for 1M2W)

(no "Cis Peptide Bond" information available for 1M2W)

(no "SAP(SNP)/Variant" information available for 1M2W)

(no "PROSITE Motif" information available for 1M2W)

(no "Exon" information available for 1M2W)

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:492
 aligned with O08355_PSEFL | O08355 from UniProtKB/TrEMBL  Length:493

    Alignment length:492
                                    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       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490  
         O08355_PSEFL     1 MKLNKQNLTQLAPEVKLPAYTLADTRQGIAHIGVGGFHRAHQAYYTDALMNTGEGLDWSICGVGLRSEDRKARDDLAGQDYLFTLYELGDTDDTEVRVIGSISDMLLAEDSAQALIDKLASPEIRIVSLTITEGGYCIDDSNGEFMAHLPQIQHDLAHPSSPKTVFGFICAALTQRRAAGIPAFTVMSCDNLPHNGAVTRKALLAFAALHNAELHDWIKAHVSFPNAMVDRITPMTSTAHRLQLHDEHGIDDAWPVVCEPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEEMKIGLLNGSHLALTYLGFLKGYRFVHETMNDPLFVAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLVDRFSNQAIADQLERVCSDGSSKFPKFTVPTINRLIADGRETERAALVVAAWALYLKGVDENGVSYTIPDPRAEFCQGLVSDDALISQRLLAVEEIFGTAIPNSPEFVAAFERCYGSLRDNGVTTTLKHLLKKP 492
               SCOP domains d1m2wa4 A:1-286 Mannitol 2-dehydrogenase                                                                                                                                                                                                                                                      d1m2wa3 A:287-492 Mannitol 2-dehydrogenase                                                                                                                                                                     SCOP domains
               CATH domains -1m2wA01 A:2-285 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                                         1m2wA02 A:286-492 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhh.........hhhhh.eeeeee..hhhhhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhh....eeeee........eeee..eeeeee...hhhhhhhhhh.....eeee...................hhhhhhhhhh.....hhhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhh....eeee......hhhhhhhhhhhhh......eee....eeeee........hhhhhh.eee..hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...............hhhhhhhhh....hhhhhhh.hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1m2w A   1 mKLNKQNLTQLAPEVKLPAYTLADTRQGIAHIGVGGFHRAHQAYYTDALmNTGEGLDWSICGVGLRSEDRKARDDLAGQDYLFTLYELGDTDDTEVRVIGSISDmLLAEDSAQALIDKLASPEIRIVSLTITEGGYCIDDSNGEFmAHLPQIQHDLAHPSSPKTVFGFICAALTQRRAAGIPAFTVmSCDNLPHNGAVTRKALLAFAALHNAELHDWIKAHVSFPNAmVDRITPmTSTAHRLQLHDEHGIDDAWPVVCEPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEEmKIGLLNGSHLALTYLGFLKGYRFVHETmNDPLFVAYmRAYmDLDVTPNLAPVPGIDLTDYKQTLVDRFSNQAIADQLERVCSDGSSKFPKFTVPTINRLIADGRETERAALVVAAWALYLKGVDENGVSYTIPDPRAEFCQGLVSDDALISQRLLAVEEIFGTAIPNSPEFVAAFERCYGSLRDNGVTTTLKHLLKKP 492
                            |       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|   |  340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490  
                            |                                               50-MSE                                                105-MSE                                  146-MSE                                  187-MSE                                  228-MSE  |                                                        294-MSE                     322-MSE  331-MSE                                                                                                                                                             
                            1-MSE                                                                                                                                                                                                                                   235-MSE                                                                                             335-MSE

Chain B from PDB  Type:PROTEIN  Length:492
 aligned with O08355_PSEFL | O08355 from UniProtKB/TrEMBL  Length:493

    Alignment length:492
                                    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       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490  
         O08355_PSEFL     1 MKLNKQNLTQLAPEVKLPAYTLADTRQGIAHIGVGGFHRAHQAYYTDALMNTGEGLDWSICGVGLRSEDRKARDDLAGQDYLFTLYELGDTDDTEVRVIGSISDMLLAEDSAQALIDKLASPEIRIVSLTITEGGYCIDDSNGEFMAHLPQIQHDLAHPSSPKTVFGFICAALTQRRAAGIPAFTVMSCDNLPHNGAVTRKALLAFAALHNAELHDWIKAHVSFPNAMVDRITPMTSTAHRLQLHDEHGIDDAWPVVCEPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEEMKIGLLNGSHLALTYLGFLKGYRFVHETMNDPLFVAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLVDRFSNQAIADQLERVCSDGSSKFPKFTVPTINRLIADGRETERAALVVAAWALYLKGVDENGVSYTIPDPRAEFCQGLVSDDALISQRLLAVEEIFGTAIPNSPEFVAAFERCYGSLRDNGVTTTLKHLLKKP 492
               SCOP domains d1m2wb4 B:1-286 Mannitol 2-dehydrogenase                                                                                                                                                                                                                                                      d1m2wb3 B:287-492 Mannitol 2-dehydrogenase                                                                                                                                                                     SCOP domains
               CATH domains -1m2wB01 B:2-285 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                                         1m2wB02 B:286-492 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                                                                                                     CATH domains
           Pfam domains (1) --------------------------Mannitol_dh-1m2wB03 B:27-192                                                                                                                                          ---------------------------Mannitol_dh_C-1m2wB01 B:220-465                                                                                                                                                                                                                       --------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------Mannitol_dh-1m2wB04 B:27-192                                                                                                                                          ---------------------------Mannitol_dh_C-1m2wB02 B:220-465                                                                                                                                                                                                                       --------------------------- Pfam domains (2)
         Sec.struct. author ......hhhhh.........hhhhh.eeeeee..hhhhhhhhhhhhhhhhh.......eeeeee...hhhhhhhhhhh....eeeee........eeee..eeeeee...hhhhhhhhhh.....eeee...................hhhhhhhhhh.....hhhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee......hhhhhhhhhhhhh......eee....eeee.........hhhhhh.ee...hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhh.hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1m2w B   1 mKLNKQNLTQLAPEVKLPAYTLADTRQGIAHIGVGGFHRAHQAYYTDALmNTGEGLDWSICGVGLRSEDRKARDDLAGQDYLFTLYELGDTDDTEVRVIGSISDmLLAEDSAQALIDKLASPEIRIVSLTITEGGYCIDDSNGEFmAHLPQIQHDLAHPSSPKTVFGFICAALTQRRAAGIPAFTVmSCDNLPHNGAVTRKALLAFAALHNAELHDWIKAHVSFPNAmVDRITPmTSTAHRLQLHDEHGIDDAWPVVCEPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEEmKIGLLNGSHLALTYLGFLKGYRFVHETmNDPLFVAYmRAYmDLDVTPNLAPVPGIDLTDYKQTLVDRFSNQAIADQLERVCSDGSSKFPKFTVPTINRLIADGRETERAALVVAAWALYLKGVDENGVSYTIPDPRAEFCQGLVSDDALISQRLLAVEEIFGTAIPNSPEFVAAFERCYGSLRDNGVTTTLKHLLKKP 492
                            |       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|   |  340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490  
                            1-MSE                                           50-MSE                                                105-MSE                                  146-MSE                                  187-MSE                                  228-MSE  |                                                        294-MSE                     322-MSE  331-MSE                                                                                                                                                             
                                                                                                                                                                                                                                                                    235-MSE                                                                                             335-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 Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: 6PGD_C (47)

Family: Mannitol_dh_C (2)

Pseudomonas fluorescens (2)

1a	Mannitol_dh_C-1m2wB01	B:220-465
1b	Mannitol_dh_C-1m2wB02	B:220-465

Clan: NADP_Rossmann (1239)

Family: Mannitol_dh (2)

Pseudomonas fluorescens (2)

2a	Mannitol_dh-1m2wB03	B:27-192
2b	Mannitol_dh-1m2wB04	B:27-192

Asymmetric Unit(hide GO term definitions)

Chain A,B (O08355_PSEFL | O08355)

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:0050662	coenzyme binding	Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
	GO:0050086	mannitol 2-dehydrogenase activity	Catalysis of the reaction: D-mannitol + NAD+ = D-fructose + NADH.
	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:0019594	mannitol metabolic process	The chemical reactions and pathways involving mannitol, the alditol derived from D-mannose by reduction of the aldehyde group.
	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.

Asymmetric Unit
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	1m2w
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	O08355_PSEFL \| O08355	:	1lj8

1lj8	PSEUDOMONAS FLUORESCENS MANNITOL 2-DEHYDROGENASE BINARY COMPLEX WITH NAD(H)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 26)

Sites (4, 4)

SS Bonds (0, 0)

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