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(-) Description

Title :  STRUCTURE AND MUTATIONAL ANALYSIS OF A PLANT MITOCHONDRIAL NUCLEOSIDE DIPHOSPHATE KINASE: IDENTIFICATION OF RESIDUES INVOLVED IN SERINE PHOSPHORYLATION AND OLIGOMERIZATION.
 
Authors :  M. Johansson, A. Mackenzie-Hose, I. Andersson, C. Knorpp
Date :  13 Sep 04  (Deposition) - 22 Oct 04  (Release) - 19 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Mitochondrial Nucleoside Diphosphate Kinase, Ndpk3, Pisum Sativum, Transferase, Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Johansson, A. Mackenzie-Hose, I. Andersson, C. Knorpp
Structure And Mutational Analysis Of A Plant Mitochondrial Nucleoside Diphosphate Kinase: Identification Of Residues Involved In Serine Phosphorylation And Oligomerisation
Plant Physiol. V. 136 3034 2004
PubMed-ID: 15466238  |  Reference-DOI: 10.1104/PP.104.044040

(-) Compounds

Molecule 1 - NUCLEOSIDE DIPHOSPHATE KINASE
    Chains: A, B, C, D, E, F
    EC Number: 2.7.4.6
    Engineered: YES
    Expression System: ESHERICHIA COLI
    Expression System Plasmid: PPROEX
    Expression System Strain: DH5A
    Organism Common: PEA
    Organism Scientific: PISUM SATIVUM
    Organism Taxid: 3888
    Strain: OREGON SUGAR POD

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1W7W)

(-) Sites  (0, 0)

(no "Site" information available for 1W7W)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W7W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1W7W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W7W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1W7W)

(-) Exons   (0, 0)

(no "Exon" information available for 1W7W)

(-) 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:151
 aligned with Q9SP13_PEA | Q9SP13 from UniProtKB/TrEMBL  Length:233

    Alignment length:151
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 
           Q9SP13_PEA    81 AELERTFIAIKPDGVQRGLISEIISRFERKGFKLVGIKVLIPTKQFAQQHYHDLKERPFFNGLCDFLSSGPVIAMVWEGEGVITYGRKLIGATDPQKSAPGTIRGDLAVVVGRNIIHGSDGPETAKDEIKLWFKPEELVSFTSNSEKWIYG 231
               SCOP domains d1w7wa_ A: Nucleoside diphosphate kinase, NDK                                                                                                           SCOP domains
               CATH domains 1w7wA00 A:1-151  [code=3.30.70.141, no name defined]                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.hhhhhh..hhhhhhhhhhh..eeeeeeee...hhhhhhh........hhhhhhhhhh...eeeeeee..hhhhhhhhhhh........................eee...hhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w7w A   1 AELERTFIAIKPDGVQRGLISEIISRFERKGFKLVGIKVLIPTKQFAQQHYHDLKERPFFNGLCDFLSSGPVIAMVWEGEGVITYGRKLIGATDPQKSAPGTIRGDLAVVVGRNIIHGSDGPETAKDEIKLWFKPEELVSFTSNSEKWIYG 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 


Chain B from PDB  Type:PROTEIN  Length:150
 aligned with Q9SP13_PEA | Q9SP13 from UniProtKB/TrEMBL  Length:233

    Alignment length:150
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
           Q9SP13_PEA    81 AELERTFIAIKPDGVQRGLISEIISRFERKGFKLVGIKVLIPTKQFAQQHYHDLKERPFFNGLCDFLSSGPVIAMVWEGEGVITYGRKLIGATDPQKSAPGTIRGDLAVVVGRNIIHGSDGPETAKDEIKLWFKPEELVSFTSNSEKWIY 230
               SCOP domains d1w7wb_ B: Nucleoside diphosphate kinase, NDK                                                                                                          SCOP domains
               CATH domains 1w7wB00 B:1-150  [code=3.30.70.141, no name defined]                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee.hhhhhh..hhhhhhhhhhh..eeeeeeee...hhhhhhh........hhhhhhhhhh...eeeeeee..hhhhhhhhhhh........................eee...hhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1w7w B   1 AELERTFIAIKPDGVQRGLISEIISRFERKGFKLVGIKVLIPTKQFAQQHYHDLKERPFFNGLCDFLSSGPVIAMVWEGEGVITYGRKLIGATDPQKSAPGTIRGDLAVVVGRNIIHGSDGPETAKDEIKLWFKPEELVSFTSNSEKWIY 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150


Chain C from PDB  Type:PROTEIN  Length:151
 aligned with Q9SP13_PEA | Q9SP13 from UniProtKB/TrEMBL  Length:233

    Alignment length:151
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 
           Q9SP13_PEA    81 AELERTFIAIKPDGVQRGLISEIISRFERKGFKLVGIKVLIPTKQFAQQHYHDLKERPFFNGLCDFLSSGPVIAMVWEGEGVITYGRKLIGATDPQKSAPGTIRGDLAVVVGRNIIHGSDGPETAKDEIKLWFKPEELVSFTSNSEKWIYG 231
               SCOP domains d1w7wc_ C: Nucleoside diphosphate kinase, NDK                                                                                                           SCOP domains
               CATH domains 1w7wC00 C:1-151  [code=3.30.70.141, no name defined]                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.hhhhhh..hhhhhhhhhhh..eeeeeeee...hhhhhhh........hhhhhhhhhh...eeeeeee..hhhhhhhhhhh........................eee...hhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w7w C   1 AELERTFIAIKPDGVQRGLISEIISRFERKGFKLVGIKVLIPTKQFAQQHYHDLKERPFFNGLCDFLSSGPVIAMVWEGEGVITYGRKLIGATDPQKSAPGTIRGDLAVVVGRNIIHGSDGPETAKDEIKLWFKPEELVSFTSNSEKWIYG 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 


Chain D from PDB  Type:PROTEIN  Length:150
 aligned with Q9SP13_PEA | Q9SP13 from UniProtKB/TrEMBL  Length:233

    Alignment length:150
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
           Q9SP13_PEA    81 AELERTFIAIKPDGVQRGLISEIISRFERKGFKLVGIKVLIPTKQFAQQHYHDLKERPFFNGLCDFLSSGPVIAMVWEGEGVITYGRKLIGATDPQKSAPGTIRGDLAVVVGRNIIHGSDGPETAKDEIKLWFKPEELVSFTSNSEKWIY 230
               SCOP domains d1w7wd_ D: Nucleoside diphosphate kinase, NDK                                                                                                          SCOP domains
               CATH domains 1w7wD00 D:1-150  [code=3.30.70.141, no name defined]                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee.hhhhhh..hhhhhhhhhhh..eeeeeeee...hhhhhhh........hhhhhhhhhh...eeeeeee..hhhhhhhhhhh........................eee...hhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1w7w D   1 AELERTFIAIKPDGVQRGLISEIISRFERKGFKLVGIKVLIPTKQFAQQHYHDLKERPFFNGLCDFLSSGPVIAMVWEGEGVITYGRKLIGATDPQKSAPGTIRGDLAVVVGRNIIHGSDGPETAKDEIKLWFKPEELVSFTSNSEKWIY 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150


Chain E from PDB  Type:PROTEIN  Length:151
 aligned with Q9SP13_PEA | Q9SP13 from UniProtKB/TrEMBL  Length:233

    Alignment length:151
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 
           Q9SP13_PEA    81 AELERTFIAIKPDGVQRGLISEIISRFERKGFKLVGIKVLIPTKQFAQQHYHDLKERPFFNGLCDFLSSGPVIAMVWEGEGVITYGRKLIGATDPQKSAPGTIRGDLAVVVGRNIIHGSDGPETAKDEIKLWFKPEELVSFTSNSEKWIYG 231
               SCOP domains d1w7we_ E: Nucleoside diphosphate kinase, NDK                                                                                                           SCOP domains
               CATH domains 1w7wE00 E:1-151  [code=3.30.70.141, no name defined]                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.hhhhhh..hhhhhhhhhhh..eeeeeeee...hhhhhhh........hhhhhhhhhh...eeeeeee..hhhhhhhhhhh........................eee...hhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w7w E   1 AELERTFIAIKPDGVQRGLISEIISRFERKGFKLVGIKVLIPTKQFAQQHYHDLKERPFFNGLCDFLSSGPVIAMVWEGEGVITYGRKLIGATDPQKSAPGTIRGDLAVVVGRNIIHGSDGPETAKDEIKLWFKPEELVSFTSNSEKWIYG 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 


Chain F from PDB  Type:PROTEIN  Length:150
 aligned with Q9SP13_PEA | Q9SP13 from UniProtKB/TrEMBL  Length:233

    Alignment length:150
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
           Q9SP13_PEA    81 AELERTFIAIKPDGVQRGLISEIISRFERKGFKLVGIKVLIPTKQFAQQHYHDLKERPFFNGLCDFLSSGPVIAMVWEGEGVITYGRKLIGATDPQKSAPGTIRGDLAVVVGRNIIHGSDGPETAKDEIKLWFKPEELVSFTSNSEKWIY 230
               SCOP domains d1w7wf_ F: Nucleoside diphosphate kinase, NDK                                                                                                          SCOP domains
               CATH domains 1w7wF00 F:1-150  [code=3.30.70.141, no name defined]                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee.hhhhhh..hhhhhhhhhhh..eeeeeeee...hhhhhhh........hhhhhhhhhh...eeeeeee..hhhhhhhhhhh........................eee...hhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1w7w F   1 AELERTFIAIKPDGVQRGLISEIISRFERKGFKLVGIKVLIPTKQFAQQHYHDLKERPFFNGLCDFLSSGPVIAMVWEGEGVITYGRKLIGATDPQKSAPGTIRGDLAVVVGRNIIHGSDGPETAKDEIKLWFKPEELVSFTSNSEKWIY 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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  (1, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1W7W)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (Q9SP13_PEA | Q9SP13)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0004550    nucleoside diphosphate kinase activity    Catalysis of the reaction: ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
    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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006241    CTP biosynthetic process    The chemical reactions and pathways resulting in the formation of CTP, cytidine 5'-triphosphate.
    GO:0006183    GTP biosynthetic process    The chemical reactions and pathways resulting in the formation of GTP, guanosine triphosphate.
    GO:0006228    UTP biosynthetic process    The chemical reactions and pathways resulting in the formation of UTP, uridine (5'-)triphosphate.
    GO:0006165    nucleoside diphosphate phosphorylation    The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

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  1w7w
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 Related Entries

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