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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF TM0651 FROM THERMOTOGA MARITIMA
 
Authors :  D. H. Shin, Berkeley Structural Genomics Center (Bsgc)
Date :  12 Dec 02  (Deposition) - 16 Sep 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  A (2x),B (2x),C (2x)
Keywords :  Thermotoga Maritima, Structural Proteomics, Phosphatase, Had Family, New Fold, Structural Genomics, Bsgc Structure Funded By Nih, Protein Structure Initiative, Psi, Berkeley Structural Genomics Center, Structural Genomics-Unknown Function Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. H. Shin, A. Roberts, J. Jancarik, H. Yokota, R. Kim, D. E. Wemmer, S. H. Kim
Crystal Structure Of A Phosphatase With A Unique Substrate Binding Domain From Thermotoga Maritima
Protein Sci. V. 12 1464 2003
PubMed-ID: 12824492  |  Reference-DOI: 10.1110/PS.0302703

(-) Compounds

Molecule 1 - PHOSPHATASE
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C
Biological Unit 4 (2x): A (2x)B (2x)C (2x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION
2SO46Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SO42Ligand/IonSULFATE ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SO42Ligand/IonSULFATE ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SO4-1Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:8 , GLY A:42 , LYS A:191 , ASN A:215 , ASN A:217 , MG A:282 , HOH A:1002BINDING SITE FOR RESIDUE SO4 A 280
2AC2SOFTWAREARG A:25 , ARG A:26 , HOH A:1093 , HOH A:1175 , HOH A:1259 , SER B:321 , GLU B:322 , LYS B:323BINDING SITE FOR RESIDUE SO4 A 281
3AC3SOFTWAREASP A:8 , ASP A:10 , ASP A:214 , ASN A:215 , SO4 A:280 , HOH A:1126BINDING SITE FOR RESIDUE MG A 282
4AC4SOFTWAREASP B:308 , SER B:341 , GLY B:342 , LYS B:491 , ASN B:515 , ASN B:517 , MG B:582 , HOH B:1015 , HOH B:1240BINDING SITE FOR RESIDUE SO4 B 580
5AC5SOFTWAREARG A:26 , LYS B:323 , HOH B:1040 , ARG C:626 , HOH C:1023BINDING SITE FOR RESIDUE SO4 B 581
6AC6SOFTWAREASP B:308 , ASP B:310 , ASP B:514 , ASN B:515 , SO4 B:580 , HOH B:1206BINDING SITE FOR RESIDUE MG B 582
7AC7SOFTWAREASP C:608 , SER C:641 , GLY C:642 , LYS C:791 , ASN C:815 , ASN C:817 , MG C:882 , HOH C:1007BINDING SITE FOR RESIDUE SO4 C 880
8AC8SOFTWARESER A:21 , GLU A:22 , LYS C:623 , ARG C:626 , LYS C:630 , GLU C:859 , HOH C:1012 , HOH C:1275 , HOH C:1408BINDING SITE FOR RESIDUE SO4 C 881
9AC9SOFTWAREASP C:608 , ASP C:610 , ASP C:814 , ASN C:815 , SO4 C:880 , HOH C:1124BINDING SITE FOR RESIDUE MG C 882

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:35 -A:265
2B:335 -B:565
3C:635 -C:865

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NF2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NF2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1NF2)

(-) Exons   (0, 0)

(no "Exon" information available for 1NF2)

(-) 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:267
 aligned with Q9WZB9_THEMA | Q9WZB9 from UniProtKB/TrEMBL  Length:268

    Alignment length:267
                                    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       
         Q9WZB9_THEMA     1 MYRVFVFDLDGTLLNDNLEISEKDRRNIEKLSRKCYVVFASGRMLVSTLNVEKKYFKRTFPTIAYNGAIVYLPEEGVILNEKIPPEVAKDIIEYIKPLNVHWQAYIDDVLYSEKDNEEIKSYARHSNVDYRVEPNLSELVSKMGTTKLLLIDTPERLDELKEILSERFKDVVKVFKSFPTYLEIVPKNVDKGKALRFLRERMNWKKEEIVVFGDNENDLFMFEEAGLRVAMENAIEKVKEASDIVTLTNNDSGVSYVLERISTDCLD 267
               SCOP domains d1nf2a_ A: Hypothetical protein TM0651                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1nf2A01 A:1-81,A:188-267  [code=3.40.50.1000, no name defined]                   1nf2A02 A:82-187  [code=3.30.1240.10, no name defined]                                                    1nf2A01 A:1-81,A:188-267  [code=3.40.50.1000, no name defined]                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee............hhhhhhhhhhhh...eeeee...hhhhhhhhhhhhh.....eeehhh.eeee...eeeee...hhhhhhhhhhhhhhhh..eeee....eee...hhhhhhhhhhh...eee..hhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhh..eeeeeee..eeeeee...hhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhh...eeee....hhhhhhhh.ee......hhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nf2 A   1 MYRVFVFDLDGTLLNDNLEISEKDRRNIEKLSRKCYVVFASGRMLVSTLNVEKKYFKRTFPTIAYNGAIVYLPEEGVILNEKIPPEVAKDIIEYIKPLNVHWQAYIDDVLYSEKDNEEIKSYARHSNVDYRVEPNLSELVSKMGTTKLLLIDTPERLDELKEILSERFKDVVKVFKSFPTYLEIVPKNVDKGKALRFLRERMNWKKEEIVVFGDNENDLFMFEEAGLRVAMENAIEKVKEASDIVTLTNNDSGVSYVLERISTDCLD 267
                                    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       


Chain B from PDB  Type:PROTEIN  Length:267
 aligned with Q9WZB9_THEMA | Q9WZB9 from UniProtKB/TrEMBL  Length:268

    Alignment length:267
                                    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       
         Q9WZB9_THEMA     1 MYRVFVFDLDGTLLNDNLEISEKDRRNIEKLSRKCYVVFASGRMLVSTLNVEKKYFKRTFPTIAYNGAIVYLPEEGVILNEKIPPEVAKDIIEYIKPLNVHWQAYIDDVLYSEKDNEEIKSYARHSNVDYRVEPNLSELVSKMGTTKLLLIDTPERLDELKEILSERFKDVVKVFKSFPTYLEIVPKNVDKGKALRFLRERMNWKKEEIVVFGDNENDLFMFEEAGLRVAMENAIEKVKEASDIVTLTNNDSGVSYVLERISTDCLD 267
               SCOP domains d1nf2b_ B: Hypothetical protein TM0651                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1nf2B01 B:301-381,B:488-567  [code=3.40.50.1000, no name defined]                1nf2B02 B:382-487  [code=3.30.1240.10, no name defined]                                                   1nf2B01 B:301-381,B:488-567  [code=3.40.50.1000, no name defined]                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee............hhhhhhhhhhhh...eeeee...hhhhhhhhhhhhh.....eeehhh.eeee...eeeee...hhhhhhhhhhhhhhhh.eeeee....eee...hhhhhhhhhhh....ee..hhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhh..eeeeeee..eeeeee...hhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhh...eeee....hhhhhhhh.ee......hhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nf2 B 301 MYRVFVFDLDGTLLNDNLEISEKDRRNIEKLSRKCYVVFASGRMLVSTLNVEKKYFKRTFPTIAYNGAIVYLPEEGVILNEKIPPEVAKDIIEYIKPLNVHWQAYIDDVLYSEKDNEEIKSYARHSNVDYRVEPNLSELVSKMGTTKLLLIDTPERLDELKEILSERFKDVVKVFKSFPTYLEIVPKNVDKGKALRFLRERMNWKKEEIVVFGDNENDLFMFEEAGLRVAMENAIEKVKEASDIVTLTNNDSGVSYVLERISTDCLD 567
                                   310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       


Chain C from PDB  Type:PROTEIN  Length:267
 aligned with Q9WZB9_THEMA | Q9WZB9 from UniProtKB/TrEMBL  Length:268

    Alignment length:267
                                    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       
         Q9WZB9_THEMA     1 MYRVFVFDLDGTLLNDNLEISEKDRRNIEKLSRKCYVVFASGRMLVSTLNVEKKYFKRTFPTIAYNGAIVYLPEEGVILNEKIPPEVAKDIIEYIKPLNVHWQAYIDDVLYSEKDNEEIKSYARHSNVDYRVEPNLSELVSKMGTTKLLLIDTPERLDELKEILSERFKDVVKVFKSFPTYLEIVPKNVDKGKALRFLRERMNWKKEEIVVFGDNENDLFMFEEAGLRVAMENAIEKVKEASDIVTLTNNDSGVSYVLERISTDCLD 267
               SCOP domains d1nf2c_ C: Hypothetical protein TM0651                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1nf2C01 C:601-681,C:788-867  [code=3.40.50.1000, no name defined]                1nf2C02 C:682-787  [code=3.30.1240.10, no name defined]                                                   1nf2C01 C:601-681,C:788-867  [code=3.40.50.1000, no name defined]                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee............hhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhh.....eeehhh.eeee...eeeee...hhhhhhhhhhhhhhhh.eeeeee..eeee...hhhhhhhhhhh....ee..hhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh..eeeeeee..eeeeee...hhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhh...eeeee...hhhhhhhh.eee.....hhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nf2 C 601 MYRVFVFDLDGTLLNDNLEISEKDRRNIEKLSRKCYVVFASGRMLVSTLNVEKKYFKRTFPTIAYNGAIVYLPEEGVILNEKIPPEVAKDIIEYIKPLNVHWQAYIDDVLYSEKDNEEIKSYARHSNVDYRVEPNLSELVSKMGTTKLLLIDTPERLDELKEILSERFKDVVKVFKSFPTYLEIVPKNVDKGKALRFLRERMNWKKEEIVVFGDNENDLFMFEEAGLRVAMENAIEKVKEASDIVTLTNNDSGVSYVLERISTDCLD 867
                                   610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860
   Legend:   → Mismatch (orange background)
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  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, 3)

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

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1NF2)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q9WZB9_THEMA | Q9WZB9)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0044283    small molecule biosynthetic process    The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  1nf2
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 Related Entries

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