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(-) Description

Title :  THE CRYSTAL STRUCTURE OF MANNITOL-1-PHOSPHATE DEHYDROGENASE FROM SHIGELLA FLEXNERI
 
Authors :  R. Wu, S. Clancy, A. Joachimiak, Midwest Center For Structural Gen (Mcsg)
Date :  15 Apr 09  (Deposition) - 16 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Mmannitol-1-Phosphate Dehydrogenase, Shigella Flexneri, Psi-2, Protein Structure Initiative, Structural Genomics, Midwest Center For Structural Genomics (Mcsg), Nad, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Wu, S. Clancy, A. Joachimiak
The Crystal Structure Of Mannitol-1-Phosphate Dehydrogenase From Shigella Flexneri
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MANNITOL-1-PHOSPHATE 5-DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDM68
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MTLD, S4134, SF3634
    Organism Scientific: SHIGELLA FLEXNERI 2A STR. 2457T
    Organism Taxid: 198215

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 22)

Asymmetric Unit (5, 22)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3MSE8Mod. Amino AcidSELENOMETHIONINE
4NA5Ligand/IonSODIUM ION
5PO44Ligand/IonPHOSPHATE ION
Biological Unit 1 (4, 34)
No.NameCountTypeFull Name
1ACT8Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
3MSE16Mod. Amino AcidSELENOMETHIONINE
4NA-1Ligand/IonSODIUM ION
5PO48Ligand/IonPHOSPHATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:10 , ILE A:11 , HOH A:529 , HOH A:575 , HOH A:618BINDING SITE FOR RESIDUE ACT A 383
02AC2SOFTWAREPHE A:265 , ASP A:266 , LYS A:269 , HOH A:446BINDING SITE FOR RESIDUE ACT A 384
03AC3SOFTWAREMSE A:123 , VAL A:124 , GLN A:129 , GOL A:386BINDING SITE FOR RESIDUE ACT A 385
04AC4SOFTWAREGLU A:93 , ASN A:136 , SER A:302 , GLY A:304 , ASP A:305 , ACT A:385 , HOH A:522BINDING SITE FOR RESIDUE GOL A 386
05AC5SOFTWAREASP A:266 , HOH A:481 , HOH A:651BINDING SITE FOR RESIDUE NA A 387
06AC6SOFTWARELYS A:186 , THR A:187 , HOH A:651BINDING SITE FOR RESIDUE ACT A 388
07AC7SOFTWAREHOH A:497 , HOH A:498BINDING SITE FOR RESIDUE NA A 389
08AC8SOFTWAREHOH A:477 , HOH A:503 , HOH A:633BINDING SITE FOR RESIDUE NA A 390
09AC9SOFTWARELYS A:18 , ARG A:159BINDING SITE FOR RESIDUE NA A 391
10BC1SOFTWAREGLU A:369 , VAL A:370 , HOH A:508 , HOH A:638BINDING SITE FOR RESIDUE NA A 392
11BC2SOFTWAREASN A:122 , ARG A:299 , LYS A:300 , ARG A:306 , HOH A:510BINDING SITE FOR RESIDUE PO4 A 393
12BC3SOFTWAREARG A:245 , LYS A:249 , GLN A:275 , HOH A:475BINDING SITE FOR RESIDUE PO4 A 394
13BC4SOFTWARETHR A:202 , ASP A:203 , ASN A:204 , LYS A:269BINDING SITE FOR RESIDUE PO4 A 395
14BC5SOFTWAREGLY A:7 , ALA A:30 , ASP A:31 , VAL A:32 , SER A:68 , VAL A:91 , ARG A:94 , ILE A:95 , HOH A:486BINDING SITE FOR RESIDUE PO4 A 396

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H2Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3H2Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H2Z)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MANNITOL_DHGENASEPS00974 Mannitol dehydrogenases signature.MTLD_SHIFL150-162  1A:150-162
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MANNITOL_DHGENASEPS00974 Mannitol dehydrogenases signature.MTLD_SHIFL150-162  2A:150-162

(-) Exons   (0, 0)

(no "Exon" information available for 3H2Z)

(-) Sequences/Alignments

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:377
 aligned with MTLD_SHIFL | Q83PQ0 from UniProtKB/Swiss-Prot  Length:382

    Alignment length:382
                                    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  
           MTLD_SHIFL     1 MKALHFGAGNIGRGFIGKLLADAGIQLTFADVNQVVLDALNARHSYQVHVVGETEQVDTVSGVNAVSSIGDDVVDLIAQVDLVTTAVGPVVLERIAPAIAKGLVKRKEQGNESPLNIIACENMVRGTTQLKGHVMNALPEDAKAWVEEHVGFVDSAVDRIVPPSASATNDPLEVTVETFSEWIVDKTQFKGALPNIPGMELTDNLMAFVERKLFTLNTGHAITAYLGKLAGHQTIRDAILDEKIRAVVKGAMEESGAVLIKRYGFDADKHAAYIQKILGRFENPYLKDDVERVGRQPLRKLSAGDRLIKPLLGTLEYSLPHKNLIQGIAGAMHFRSEDDPQAQELAALIADKGPQAALAQISGLDANSEVVSEAVTAYKAMQ 382
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhheeeeeee...eeeeeee..eeee...hhhhhhhh...eeee..hhhhhhhhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhheeee.eeee.....-----.....eeee...eeeee.hhh.........eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhh.hhhhhh.....hhhhhhhhhhhh..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------MANNITOL_DHGE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h2z A   1 mKALHFGAGNIGRGFIGKLLADAGIQLTFADVNQVVLDALNARHSYQVHVVGETEQVDTVSGVNAVSSIGDDVVDLIAQVDLVTTAVGPVVLERIAPAIAKGLVKRKEQGNESPLNIIACENmVRGTTQLKGHVmNALPEDAKAWVEEHVGFVDSAVDRIVPP-----NDPLEVTVETFSEWIVDKTQFKGALPNIPGmELTDNLmAFVERKLFTLNTGHAITAYLGKLAGHQTIRDAILDEKIRAVVKGAmEESGAVLIKRYGFDADKHAAYIQKILGRFENPYLKDDVERVGRQPLRKLSAGDRLIKPLLGTLEYSLPHKNLIQGIAGAmHFRSEDDPQAQELAALIADKGPQAALAQISGLDANSEVVSEAVTAYKAmQ 382
                            |       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| 
                            |                                                                                                                       123-MSE     135-MSE                     163   169                           199-MSE  |                                           252-MSE                                                                         332-MSE                                          381-MSE
                            1-MSE                                                                                                                                                                                                      206-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3H2Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3H2Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H2Z)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (MTLD_SHIFL | Q83PQ0)
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:0008926    mannitol-1-phosphate 5-dehydrogenase activity    Catalysis of the reaction: D-mannitol 1-phosphate + NAD+ = D-fructose 6-phosphate + NADH + H+.
    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.

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