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(-) Description

Title :  STRUCTURAL ANALYSIS OF ESCHERICHIA COLI THIF
 
Authors :  D. M. Duda, H. Walden, J. Sfondouris, B. A. Schulman
Date :  20 Apr 05  (Deposition) - 14 Jun 05  (Release) - 19 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A,B,C,D  (3x)
Biol. Unit 4:  A,B,C,D  (2x)
Keywords :  Rossmann Fold, P-Loop, Atp-Binding, Adenylation, This, Thif, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. M. Duda, H. Walden, J. Sfondouris, B. A. Schulman
Structural Analysis Of Escherichia Coli Thif.
J. Mol. Biol. V. 349 774 2005
PubMed-ID: 15896804  |  Reference-DOI: 10.1016/J.JMB.2005.04.011

(-) Compounds

Molecule 1 - ADENYLYLTRANSFERASE THIF
    Chains: A, B, C, D
    EC Number: 2.7.7.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX4T1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: THIF
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (3x): ABCD
Biological Unit 4 (2x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1ATP4Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 12)
No.NameCountTypeFull Name
1ATP12Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 8)
No.NameCountTypeFull Name
1ATP8Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:169 , CYS A:172 , CYS A:240 , CYS A:243BINDING SITE FOR RESIDUE ZN A 252
2AC2SOFTWARECYS B:169 , CYS B:172 , CYS B:240 , VAL B:242 , CYS B:243BINDING SITE FOR RESIDUE ZN B 252
3AC3SOFTWARECYS C:169 , CYS C:172 , CYS C:240 , CYS C:243BINDING SITE FOR RESIDUE ZN C 345
4AC4SOFTWARECYS D:169 , CYS D:172 , CYS D:240 , CYS D:243BINDING SITE FOR RESIDUE ZN D 445
5AC5SOFTWAREILE C:34 , GLY C:35 , GLY C:37 , GLY C:38 , ASP C:59 , ASP C:61 , SER C:66 , ASN C:67 , ARG C:70 , GLN C:71 , LYS C:83 , ARG C:106 , LEU C:107 , CYS C:125 , THR C:126 , ASP C:127 , THR C:131 , ARG D:11BINDING SITE FOR RESIDUE ATP C 346
6AC6SOFTWAREARG C:11 , ILE D:34 , GLY D:35 , GLY D:37 , GLY D:38 , ALA D:58 , ASP D:59 , ASP D:61 , SER D:66 , ASN D:67 , ARG D:70 , GLN D:71 , LYS D:83 , ARG D:106 , LEU D:107 , CYS D:125 , THR D:126 , ASP D:127 , THR D:131BINDING SITE FOR RESIDUE ATP D 446
7AC7SOFTWAREILE A:34 , GLY A:35 , GLY A:37 , GLY A:38 , ASP A:59 , ASP A:61 , ARG A:70 , GLN A:71 , LYS A:83 , GLN A:105 , ARG A:106 , LEU A:107 , CYS A:125 , THR A:126 , ASP A:127 , THR A:131 , ARG B:11BINDING SITE FOR RESIDUE ATP A 253
8AC8SOFTWAREARG A:11 , GLY B:35 , GLY B:37 , GLY B:38 , ASP B:59 , ASP B:61 , SER B:66 , ASN B:67 , ARG B:70 , GLN B:71 , LYS B:83 , GLN B:105 , ARG B:106 , LEU B:107 , CYS B:125 , THR B:126 , ASP B:127 , THR B:131BINDING SITE FOR RESIDUE ATP B 253

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ZFN)

(-) 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:244
 aligned with THIF_ECOLI | P30138 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:244
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    
           THIF_ECOLI     1 MNDRDFMRYSRQILLDDIALDGQQKLLDSQVLIIGLGGLGTPAALYLAGAGVGTLVLADDDDVHLSNLQRQILFTTEDIDRPKSQVSQQRLTQLNPDIQLTALQQRLTGEALKDAVARADVVLDCTDNMATRQEINAACVALNTPLITASAVGFGGQLMVLTPPWEQGCYRCLWPDNQEPERNCRTAGVVGPVVGVMGTLQALEAIKLLSGIETPAGELRLFDGKSSQWRSLALRRASGCPVCG 244
               SCOP domains d1zfna_ A: automated matches                                                                                                                                                                                                                         SCOP domains
               CATH domains 1zfnA00 A:1-244 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh...hhhhhhhhhhhheeeee....hhhhhhhhhhhh...eeeee.....hhhhhhh....hhhhh..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh...eeeeeee..eeeeeee............................hhhhhhhhhhhhhhhhhhhhh.......eeeeee....eeeeee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zfn A   1 MNDRDFMRYSRQILLDDIALDGQQKLLDSQVLIIGLGGLGTPAALYLAGAGVGTLVLADDDDVHLSNLQRQILFTTEDIDRPKSQVSQQRLTQLNPDIQLTALQQRLTGEALKDAVARADVVLDCTDNMATRQEINAACVALNTPLITASAVGFGGQLMVLTPPWEQGCYRCLWPDNQEPERNCRTAGVVGPVVGVMGTLQALEAIKLLSGIETPAGELRLFDGKSSQWRSLALRRASGCPVCG 244
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    


Chain B from PDB  Type:PROTEIN  Length:232
 aligned with THIF_ECOLI | P30138 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:244
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    
           THIF_ECOLI     1 MNDRDFMRYSRQILLDDIALDGQQKLLDSQVLIIGLGGLGTPAALYLAGAGVGTLVLADDDDVHLSNLQRQILFTTEDIDRPKSQVSQQRLTQLNPDIQLTALQQRLTGEALKDAVARADVVLDCTDNMATRQEINAACVALNTPLITASAVGFGGQLMVLTPPWEQGCYRCLWPDNQEPERNCRTAGVVGPVVGVMGTLQALEAIKLLSGIETPAGELRLFDGKSSQWRSLALRRASGCPVCG 244
               SCOP domains d1zfnb_ B: automated matches                                                                                                                                                                                                                         SCOP domains
               CATH domains 1zfnB00 B:1-244 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...hhhhhhhhhh..eeeee....hhhhhhhhhhhhh..eeeee.....hhhhhhh....hhhhh..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh...eeeeeee..eeeeeee.......hhhhhh------------...hhhhhhhhhhhhhhhhhhhhh.......eeeeee....eeeeee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zfn B   1 MNDRDFMRYSRQILLDDIALDGQQKLLDSQVLIIGLGGLGTPAALYLAGAGVGTLVLADDDDVHLSNLQRQILFTTEDIDRPKSQVSQQRLTQLNPDIQLTALQQRLTGEALKDAVARADVVLDCTDNMATRQEINAACVALNTPLITASAVGFGGQLMVLTPPWEQGCYRCLW------------AGVVGPVVGVMGTLQALEAIKLLSGIETPAGELRLFDGKSSQWRSLALRRASGCPVCG 244
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   |     -      |190       200       210       220       230       240    
                                                                                                                                                                                                       174          187                                                         


Chain C from PDB  Type:PROTEIN  Length:244
 aligned with THIF_ECOLI | P30138 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:244
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    
           THIF_ECOLI     1 MNDRDFMRYSRQILLDDIALDGQQKLLDSQVLIIGLGGLGTPAALYLAGAGVGTLVLADDDDVHLSNLQRQILFTTEDIDRPKSQVSQQRLTQLNPDIQLTALQQRLTGEALKDAVARADVVLDCTDNMATRQEINAACVALNTPLITASAVGFGGQLMVLTPPWEQGCYRCLWPDNQEPERNCRTAGVVGPVVGVMGTLQALEAIKLLSGIETPAGELRLFDGKSSQWRSLALRRASGCPVCG 244
               SCOP domains d1zfnc_ C: automated matches                                                                                                                                                                                                                         SCOP domains
               CATH domains 1zfnC00 C:1-244 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...hhhhhhhhhhhheeeee....hhhhhhhhhhhhh..eeeee.....hhhhhhh....hhhhh..hhhhhhhhhhhh.....eeeee....hhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh...eeeeeee..eeeeeee.......hhhhhh...............hhhhhhhhhhhhhhhhhhhhh.......eeeeee....eeeeee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zfn C   1 MNDRDFMRYSRQILLDDIALDGQQKLLDSQVLIIGLGGLGTPAALYLAGAGVGTLVLADDDDVHLSNLQRQILFTTEDIDRPKSQVSQQRLTQLNPDIQLTALQQRLTGEALKDAVARADVVLDCTDNMATRQEINAACVALNTPLITASAVGFGGQLMVLTPPWEQGCYRCLWPDNQEPERNCRTAGVVGPVVGVMGTLQALEAIKLLSGIETPAGELRLFDGKSSQWRSLALRRASGCPVCG 244
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    


Chain D from PDB  Type:PROTEIN  Length:235
 aligned with THIF_ECOLI | P30138 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:244
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    
           THIF_ECOLI     1 MNDRDFMRYSRQILLDDIALDGQQKLLDSQVLIIGLGGLGTPAALYLAGAGVGTLVLADDDDVHLSNLQRQILFTTEDIDRPKSQVSQQRLTQLNPDIQLTALQQRLTGEALKDAVARADVVLDCTDNMATRQEINAACVALNTPLITASAVGFGGQLMVLTPPWEQGCYRCLWPDNQEPERNCRTAGVVGPVVGVMGTLQALEAIKLLSGIETPAGELRLFDGKSSQWRSLALRRASGCPVCG 244
               SCOP domains d1zfnd_ D: automated matches                                                                                                                                                                                                                         SCOP domains
               CATH domains 1zfnD00 D:1-244 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                  CATH domains
           Pfam domains (1) --------------------------ThiF-1zfnD01 D:27-161                                                                                                                  ----MoeZ_MoeB-1z         fnD05 D:166-244                                            Pfam domains (1)
           Pfam domains (2) --------------------------ThiF-1zfnD02 D:27-161                                                                                                                  ----MoeZ_MoeB-1z         fnD06 D:166-244                                            Pfam domains (2)
           Pfam domains (3) --------------------------ThiF-1zfnD03 D:27-161                                                                                                                  ----MoeZ_MoeB-1z         fnD07 D:166-244                                            Pfam domains (3)
           Pfam domains (4) --------------------------ThiF-1zfnD04 D:27-161                                                                                                                  ----MoeZ_MoeB-1z         fnD08 D:166-244                                            Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhh...hhhhhhhhhhh.eeeee....hhhhhhhhhhhh...eeeee.....hhhhh......hhhhh..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhh...eeeeeee..eeeeeee.......hhhhhh...---------...hhhhhhhhhhhhhhhhhhhhh.......eeeeee....eeeeee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zfn D   1 MNDRDFMRYSRQILLDDIALDGQQKLLDSQVLIIGLGGLGTPAALYLAGAGVGTLVLADDDDVHLSNLQRQILFTTEDIDRPKSQVSQQRLTQLNPDIQLTALQQRLTGEALKDAVARADVVLDCTDNMATRQEINAACVALNTPLITASAVGFGGQLMVLTPPWEQGCYRCLWPDN---------AGVVGPVVGVMGTLQALEAIKLLSGIETPAGELRLFDGKSSQWRSLALRRASGCPVCG 244
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170      |  -      |190       200       210       220       230       240    
                                                                                                                                                                                                          177       187
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (2, 8)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Family: ThiF (14)
(-)
Clan: no clan defined [family: MoeZ_MoeB] (6)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (THIF_ECOLI | P30138)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0008641    small protein activating enzyme activity    Catalysis of the activation of small proteins, such as ubiquitin or ubiquitin-like proteins, through the formation of an ATP-dependent high-energy thiolester bond.
    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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0009228    thiamine biosynthetic process    The chemical reactions and pathways resulting in the formation of thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
    GO:0009229    thiamine diphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of thiamine diphosphate, a derivative of thiamine (vitamin B1) which acts as a coenzyme in a range of processes including the Krebs cycle.
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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  1zfn
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  THIF_ECOLI | P30138
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  2.7.7.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        THIF_ECOLI | P30138: 1zkm 1zud

(-) Related Entries Specified in the PDB File

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