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(-) Description

Title :  CRYSTAL STRUCTURE OF NDP-N-ACETYL-D-GALACTOSAMINURONIC ACID DEHYDROGENASE FROM METHANOSARCINA MAZEI GO1
 
Authors :  V. N. Malashkevich, R. Toro, J. M. Sauder, S. K. Burley, S. C. Almo, New Y Research Center For Structural Genomics (Nysgxrc)
Date :  09 Feb 09  (Deposition) - 17 Feb 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Protein Structure Initiative, New York Structural Genomix Research Consortium, Nysgxrc, Ndp-N-Acetyl-D- Galactosaminuronic Acid Dehydrogenase, Oxidoreductase, Psi-2, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. N. Malashkevich, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Ndp-N-Acetyl-D-Galactosaminuronic Acid Dehydrogenase From Methanosarcina Mazei Go1
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NDP-N-ACETYL-D-GALACTOSAMINURONIC ACID DEHYDROGENASE
    Atcc: BAA-159
    Chains: A, B
    EC Number: 1.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)CODON+RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 3-469
    Gene: MM_1154
    Organism Scientific: METHANOSARCINA MAZEI GO1
    Organism Taxid: 192952
    Strain: GO1 / DSM 3647 / GOE1 / JCM 11883 / OCM 88

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3G79)

(-) Sites  (0, 0)

(no "Site" information available for 3G79)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3G79)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Phe A:113 -Ala A:114
2Ala A:114 -Asn A:115
3Asp A:118 -Leu A:119
4Gly A:275 -Glu A:276
5Glu A:471 -Gly A:472
6Lys B:71 -Gly B:72
7Glu B:471 -Gly B:472

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3G79)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3G79)

(-) Exons   (0, 0)

(no "Exon" information available for 3G79)

(-) Sequences/Alignments

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:475
 aligned with Q8PXR2_METMA | Q8PXR2 from UniProtKB/TrEMBL  Length:478

    Alignment length:475
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472     
         Q8PXR2_METMA     3 SMSKLEKLLKERGPIKKIGVLGMGYVGIPAAVLFADAPCFEKVLGFQRNSKSSGYKIEMLNRGESPLKGEEPGLEELIGKVVKAGKFECTPDFSRISELDAVTLAIQTPFANPKDLEPDFSALIDGIRNVGKYLKPGMLVVLESTITPGTTEGMAKQILEEESGLKAGEDFALAHAPERVMVGRLLKNIREHDRIVGGIDEASTKRAVELYSPVLTVGQVIPMSATAAEVTKTAENTFRDLQIAAINQLALYCEAMGINVYDVRTGVDSLKGEGITRAVLWPGAGVGGHCLTKDTYHLERGVKIGRGELDYPEGADSIYVLARKVNDFMPAHMYNLTVAALERLGKKMDGSKVAMLGWAFIKDSDDARNTPSEPYRDLCLKAGASVMVHDPYVVNYPGVEISDNLEEVVRNADAIVVLAGHSAYSSLKADWAKKVSAKANPVIIDGRNVIEPDEFIGKGFVYKGIGRGDKNSHKI 477
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh...eeeee....hhhhhhhhhhhh....eeeee........hhhhhhh........hhhhhhhhhhhhhhh..eeee.hhhhhhhh.eeee...............hhhhhhhhhhhhhhh....eeee..........hhhhhhhhhhhh.......eeee........hhhhhhhhh.eeeee.hhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...................hhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeee..............hhhhhhhhhhhhh.eeeee...........ee.hhhhhhh...eeee...hhhhhh.hhhhhhhhhh....eeee.....hhhhhhh...eeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g79 A   4 SMSKLEKLLKERGPIKKIGVLGMGYVGIPAAVLFADAPCFEKVLGFQRNSKSSGYKIEMLNRGESPLKGEEPGLEELIGKVVKAGKFECTPDFSRISELDAVTLAIQTPFANPKDLEPDFSALIDGIRNVGKYLKPGMLVVLESTITPGTTEGMAKQILEEESGLKAGEDFALAHAPERVMVGRLLKNIREHDRIVGGIDEASTKRAVELYSPVLTVGQVIPMSATAAEVTKTAENTFRDLQIAAINQLALYCEAMGINVYDVRTGVDSLKGEGITRAVLWPGAGVGGHCLTKDTYHLERGVKIGRGELDYPEGADSIYVLARKVNDFMPAHMYNLTVAALERLGKKMDGSKVAMLGWAFIKDSDDARNTPSEPYRDLCLKAGASVMVHDPYVVNYPGVEISDNLEEVVRNADAIVVLAGHSAYSSLKADWAKKVSAKANPVIIDGRNVIEPDEFIGKGFVYKGIGREGHHHHHH 478
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473     


Chain B from PDB  Type:PROTEIN  Length:475
 aligned with Q8PXR2_METMA | Q8PXR2 from UniProtKB/TrEMBL  Length:478

    Alignment length:475
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472     
         Q8PXR2_METMA     3 SMSKLEKLLKERGPIKKIGVLGMGYVGIPAAVLFADAPCFEKVLGFQRNSKSSGYKIEMLNRGESPLKGEEPGLEELIGKVVKAGKFECTPDFSRISELDAVTLAIQTPFANPKDLEPDFSALIDGIRNVGKYLKPGMLVVLESTITPGTTEGMAKQILEEESGLKAGEDFALAHAPERVMVGRLLKNIREHDRIVGGIDEASTKRAVELYSPVLTVGQVIPMSATAAEVTKTAENTFRDLQIAAINQLALYCEAMGINVYDVRTGVDSLKGEGITRAVLWPGAGVGGHCLTKDTYHLERGVKIGRGELDYPEGADSIYVLARKVNDFMPAHMYNLTVAALERLGKKMDGSKVAMLGWAFIKDSDDARNTPSEPYRDLCLKAGASVMVHDPYVVNYPGVEISDNLEEVVRNADAIVVLAGHSAYSSLKADWAKKVSAKANPVIIDGRNVIEPDEFIGKGFVYKGIGRGDKNSHKI 477
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh...eeeee....hhhhhhhhhhh.....eeeee.......hhhhhhhh...........hhhhhhhhhhhh..eeee..........eeee...............hhhhhhhhhhhhhhh....eeee..........hhhhhhhhhhhh.......eeee........hhhhhhhhh.eeeee.hhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...................hhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeee..............hhhhhhhhhhhhh.eeeee...........ee...........eeee...hhhhh..hhhhhhhhhh....eeee.....hhhhhhh...eeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g79 B   4 SMSKLEKLLKERGPIKKIGVLGMGYVGIPAAVLFADAPCFEKVLGFQRNSKSSGYKIEMLNRGESPLKGEEPGLEELIGKVVKAGKFECTPDFSRISELDAVTLAIQTPFANPKDLEPDFSALIDGIRNVGKYLKPGMLVVLESTITPGTTEGMAKQILEEESGLKAGEDFALAHAPERVMVGRLLKNIREHDRIVGGIDEASTKRAVELYSPVLTVGQVIPMSATAAEVTKTAENTFRDLQIAAINQLALYCEAMGINVYDVRTGVDSLKGEGITRAVLWPGAGVGGHCLTKDTYHLERGVKIGRGELDYPEGADSIYVLARKVNDFMPAHMYNLTVAALERLGKKMDGSKVAMLGWAFIKDSDDARNTPSEPYRDLCLKAGASVMVHDPYVVNYPGVEISDNLEEVVRNADAIVVLAGHSAYSSLKADWAKKVSAKANPVIIDGRNVIEPDEFIGKGFVYKGIGREGHHHHHH 478
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3G79)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3G79)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G79)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8PXR2_METMA | Q8PXR2)
molecular function
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    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:0016628    oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces NAD or NADP.
    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: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.
    GO:0000271    polysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  Cis Peptide Bonds
    Ala A:114 - Asn A:115   [ RasMol ]  
    Asp A:118 - Leu A:119   [ RasMol ]  
    Glu A:471 - Gly A:472   [ RasMol ]  
    Glu B:471 - Gly B:472   [ RasMol ]  
    Gly A:275 - Glu A:276   [ RasMol ]  
    Lys B:71 - Gly B:72   [ RasMol ]  
    Phe A:113 - Ala A:114   [ RasMol ]  
 

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  3g79
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 Related Entries

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