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(-) Description

Title :  CRYSTAL STRUCTURE OF GDP-MANNOSE 4,6-DEHYDRATASE TERNARY COMPLEX WITH NADPH AND GDP
 
Authors :  A. M. Mulichak, C. P. Bonin, W. -D. Reiter, R. M. Garavito
Date :  14 Nov 02  (Deposition) - 07 Jan 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Rossmann Fold, Sdr, Short-Chain Dehydrogenase/Reductase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Mulichak, C. P. Bonin, W. -D. Reiter, R. M. Garavito
The Structure Of The Mur1 Gdp-Mannose 4, 6-Dehydratase From A. Thaliana: Implications For Ligand Binding And Specificity.
Biochemistry V. 41 15578 2002
PubMed-ID: 12501186  |  Reference-DOI: 10.1021/BI0266683

(-) Compounds

Molecule 1 - GDP-D-MANNOSE-4,6-DEHYDRATASE
    Chains: A, B
    EC Number: 4.2.1.47
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MUR1
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1GDP4Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2NDP4Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:35 , THR A:37 , GLY A:38 , GLN A:39 , ASP A:40 , ARG A:60 , ASP A:91 , LEU A:92 , LEU A:113 , ALA A:114 , ALA A:115 , SER A:117 , TYR A:128 , VAL A:132 , ALA A:160 , GLY A:161 , SER A:162 , TYR A:185 , LYS A:189 , LEU A:212 , ASN A:214 , HIS A:215 , ARG A:220 , HOH A:604 , HOH A:609 , HOH A:611 , HOH A:612 , HOH A:615 , HOH A:617 , HOH A:620 , HOH A:624 , HOH A:637 , HOH A:639 , HOH A:640 , HOH A:643 , ARG B:61 , SER B:62 , SER B:63 , HOH B:840BINDING SITE FOR RESIDUE NDP A 601
2AC2SOFTWAREHIS A:118 , VAL A:119 , GLU A:164 , ASN A:214 , ASN A:223 , PHE A:224 , VAL A:225 , LYS A:228 , LEU A:246 , GLY A:247 , ASN A:248 , ALA A:251 , ARG A:253 , VAL A:287 , TYR A:312 , ARG A:314 , GLU A:317 , HOH A:621 , HOH A:623 , HOH A:632 , HOH A:636 , HOH A:641 , HOH A:673 , HOH A:738 , HOH A:803BINDING SITE FOR RESIDUE GDP A 602
3AC3SOFTWAREARG A:61 , SER A:62 , SER A:63 , HOH A:635 , HOH A:651 , GLY B:35 , THR B:37 , GLY B:38 , GLN B:39 , ASP B:40 , ARG B:60 , ASP B:91 , LEU B:92 , LEU B:113 , ALA B:114 , ALA B:115 , SER B:117 , TYR B:128 , VAL B:132 , ALA B:160 , GLY B:161 , SER B:162 , TYR B:185 , LYS B:189 , LEU B:212 , ASN B:214 , HIS B:215 , ARG B:220 , HOH B:706 , HOH B:708 , HOH B:710 , HOH B:714 , HOH B:721 , HOH B:722 , HOH B:724 , HOH B:726 , HOH B:740 , HOH B:783 , HOH B:811BINDING SITE FOR RESIDUE NDP B 701
4AC4SOFTWAREVAL B:119 , GLU B:164 , ASN B:214 , ASN B:223 , PHE B:224 , VAL B:225 , LYS B:228 , LEU B:246 , GLY B:247 , ASN B:248 , ALA B:251 , ARG B:253 , VAL B:287 , TYR B:312 , ARG B:314 , GLU B:317 , HOH B:720 , HOH B:723 , HOH B:730 , HOH B:753 , HOH B:770 , HOH B:780 , HOH B:812BINDING SITE FOR RESIDUE GDP B 702

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N7H)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:171 -Pro A:172
2Pro B:171 -Pro B:172

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N7H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1N7H)

(-) Exons   (0, 0)

(no "Exon" information available for 1N7H)

(-) 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:331
 aligned with GMD2_ARATH | P93031 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:339
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357         
           GMD2_ARATH    28 RKIALITGITGQDGSYLTEFLLGKGYEVHGLIRRSSNFNTQRINHIYIDPHNVNKALMKLHYADLTDASSLRRWIDVIKPDEVYNLAAQSHVAVSFEIPDYTADVVATGALRLLEAVRSHTIDSGRTVKYYQAGSSEMFGSTPPPQSETTPFHPRSPYAASKCAAHWYTVNYREAYGLFACNGILFNHESPRRGENFVTRKITRALGRIKVGLQTKLFLGNLQASRDWGFAGDYVEAMWLMLQQEKPDDYVVATEEGHTVEEFLDVSFGYLGLNWKDYVEIDQRYFRPAEVDNLQGDASKAKEVLGWKPQVGFEKLVKMMVDEDLELAKREKVLVDAGY 366
               SCOP domains d1n7ha_ A: GDP-mannose 4,6-dehydratase                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1n7hA02 A:28-220,A:255-283,A:321-337 NAD(P)-bin        ding Rossmann-like Domain                                                                                                                 1n7hA01                           1n7hA02                      1n7hA01 A:221-254,A:284-320,A:338-3661n7hA02          1n7hA01                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeeee...............--------..eeeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh...............hhhhhhhhhhhhhhhhhhhhhh.eeeeeee..ee.......hhhhhhhhhhhhhhh.....eee.....eee.eehhhhhhhhhhhhh.....eeee....eeehhhhhhhhhhhh..hhhh.eee.hhhh...........hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n7h A  28 RKIALITGITGQDGSYLTEFLLGKGYEVHGLIRRSSNFNTQRINHIY--------ALMKLHYADLTDASSLRRWIDVIKPDEVYNLAAQSHVAVSFEIPDYTADVVATGALRLLEAVRSHTIDSGRTVKYYQAGSSEMFGSTPPPQSETTPFHPRSPYAASKCAAHWYTVNYREAYGLFACNGILFNHESPRRGENFVTRKITRALGRIKVGLQTKLFLGNLQASRDWGFAGDYVEAMWLMLQQEKPDDYVVATEEGHTVEEFLDVSFGYLGLNWKDYVEIDQRYFRPAEVDNLQGDASKAKEVLGWKPQVGFEKLVKMMVDEDLELAKREKVLVDAGY 366
                                    37        47        57        67      |  -     |  87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357         
                                                                         74       83                                                                                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:334
 aligned with GMD2_ARATH | P93031 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:340
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367
           GMD2_ARATH    28 RKIALITGITGQDGSYLTEFLLGKGYEVHGLIRRSSNFNTQRINHIYIDPHNVNKALMKLHYADLTDASSLRRWIDVIKPDEVYNLAAQSHVAVSFEIPDYTADVVATGALRLLEAVRSHTIDSGRTVKYYQAGSSEMFGSTPPPQSETTPFHPRSPYAASKCAAHWYTVNYREAYGLFACNGILFNHESPRRGENFVTRKITRALGRIKVGLQTKLFLGNLQASRDWGFAGDYVEAMWLMLQQEKPDDYVVATEEGHTVEEFLDVSFGYLGLNWKDYVEIDQRYFRPAEVDNLQGDASKAKEVLGWKPQVGFEKLVKMMVDEDLELAKREKVLVDAGYM 367
               SCOP domains d1n7hb_ B: GDP-mannose 4,6-dehydratase                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1n7hB02 B:28-220,B:255-283,B:321-337 NAD(P)-bind      ing Rossmann-like Domain                                                                                                                   1n7hB01                           1n7hB02                      1n7hB01 B:221-254,B:284-320,B:338-3671n7hB02          1n7hB01                        CATH domains
           Pfam domains (1) ---Epimerase-1n7hB01 B:31-280                                                                                                                                                                                                                                --------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---Epimerase-1n7hB02 B:31-280                                                                                                                                                                                                                                --------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeeee..........hhhhhh------...eeeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh...............hhhhhhhhhhhhhhhhhhhhhh.eeeeeee..ee.......hhhhhhhhhhhhhhh.....eee.....eee.eehhhhhhhhhhhhh.....eeee....eeehhhhhhhhhhhh..hhhh.eee.hhhh...........hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n7h B  28 RKIALITGITGQDGSYLTEFLLGKGYEVHGLIRRSSNFNTQRINHIYI------KALMKLHYADLTDASSLRRWIDVIKPDEVYNLAAQSHVAVSFEIPDYTADVVATGALRLLEAVRSHTIDSGRTVKYYQAGSSEMFGSTPPPQSETTPFHPRSPYAASKCAAHWYTVNYREAYGLFACNGILFNHESPRRGENFVTRKITRALGRIKVGLQTKLFLGNLQASRDWGFAGDYVEAMWLMLQQEKPDDYVVATEEGHTVEEFLDVSFGYLGLNWKDYVEIDQRYFRPAEVDNLQGDASKAKEVLGWKPQVGFEKLVKMMVDEDLELAKREKVLVDAGYM 367
                                    37        47        57        67       | -    |   87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367
                                                                          75     82
   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  (1, 2)

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

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GMD2_ARATH | P93031)
molecular function
    GO:0008446    GDP-mannose 4,6-dehydratase activity    Catalysis of the reaction: GDP-alpha-D-mannose = GDP-4-dehydro-6-deoxy-alpha-D-mannose + H(2)O.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    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.
biological process
    GO:0042351    'de novo' GDP-L-fucose biosynthetic process    The chemical reactions and pathways resulting in the formation of GDP-L-fucose from GDP-D-mannose via GDP-4-dehydro-6-deoxy-D-mannose, requiring the functions of GDP-mannose 4,6-dehydratase (EC:4.2.1.47) and GDP-L-fucose synthase (EC:1.1.1.271).
    GO:0019673    GDP-mannose metabolic process    The chemical reactions and pathways involving GDP-mannose, a substance composed of mannose in glycosidic linkage with guanosine diphosphate.
    GO:0009826    unidimensional cell growth    The process in which a cell irreversibly increases in size in one [spatial] dimension or along one axis, resulting in the morphogenesis of the cell.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  1n7h
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GMD2_ARATH | P93031: 1n7g

(-) Related Entries Specified in the PDB File

1n7g