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(-) Description

Title :  CRYSTAL STRUCTURE OF MTNX PHOSPHATASE FROM BACILLUS SUBTILIS AT 2.00 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  15 Dec 05  (Deposition) - 27 Dec 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  2633731, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Xu, K. S. Saikatendu, S. S. Krishna, D. Mcmullan, P. Abdubek, S. Agarwalla, E. Ambing, T. Astakhova, H. L. Axelrod, D. Carlton, H. J. Chiu, T. Clayton, M. Didonato, L. Duan, M. A. Elsliger, J. Feuerhelm, S. K. Grzechnik, J. Hale, E. Hampton, G. W. Han, J. Haugen L. Jaroszewski, K. K. Jin, H. E. Klock, M. W. Knuth, E. Koesema, M. D. Miller, A. T. Morse, E. Nigoghossian, L. Okach, S. Oommachen, J. Paulsen, R. Reyes, C. L. Rife, R. Schwarzenbacher, H. Van Den Bedem, A. White, G. Wolf, K. O. Hodgson, J. Wooley, A. M. Deacon, A. Godzik, S. A. Lesley, I. A. Wilson
Crystal Structure Of Mtnx Phosphatase From Bacillus Subtili At 2. 0 A Resolution Provides A Structural Basis For Bipartite Phosphomonoester Hydrolysis Of 2-Hydroxy-3-Keto-5-Methylthiopentenyl-1-Phosphate.
Proteins V. 69 433 2007
PubMed-ID: 17654724  |  Reference-DOI: 10.1002/PROT.21602

(-) Compounds

Molecule 1 - 2-HYDROXY-3-KETO-5-METHYLTHIOPENTENYL-1-PHOSPHATE PHOSPHATASE
    Chains: A, B
    EC Number: 3.1.3.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MTNX
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: HK-MTPENYL-1-P PHOSPHATASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 26)

Asymmetric Unit (4, 26)
No.NameCountTypeFull Name
1EDO10Ligand/Ion1,2-ETHANEDIOL
2MG2Ligand/IonMAGNESIUM ION
3MSE12Mod. Amino AcidSELENOMETHIONINE
4ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2MG-1Ligand/IonMAGNESIUM ION
3MSE6Mod. Amino AcidSELENOMETHIONINE
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 12)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2MG-1Ligand/IonMAGNESIUM ION
3MSE6Mod. Amino AcidSELENOMETHIONINE
4ZN-1Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:11 , ASP A:13 , ASP A:170 , SER A:171 , HOH A:1453BINDING SITE FOR RESIDUE MG A 1301
02AC2SOFTWARECYS A:139 , CYS A:143 , CYS A:147 , CYS A:150BINDING SITE FOR RESIDUE ZN A 1302
03AC3SOFTWAREASP B:11 , ASP B:13 , ASP B:170 , HOH B:2322 , HOH B:2354BINDING SITE FOR RESIDUE MG B 2301
04AC4SOFTWARECYS B:139 , CYS B:143 , CYS B:147 , CYS B:150BINDING SITE FOR RESIDUE ZN B 2302
05AC5SOFTWAREHIS A:137 , SER A:138 , LYS A:140 , SER A:153 , HOH A:1340BINDING SITE FOR RESIDUE EDO A 1303
06AC6SOFTWARELYS A:116 , ASP A:117 , ILE A:119 , TYR A:120 , HIS A:137 , HOH A:1407 , HOH A:1452BINDING SITE FOR RESIDUE EDO A 1304
07AC7SOFTWARETHR A:17 , MSE A:18 , ASN A:19 , ASN A:21 , ASN A:24 , ASP A:74 , ALA A:75 , LYS A:76BINDING SITE FOR RESIDUE EDO A 1305
08AC8SOFTWAREASP A:20BINDING SITE FOR RESIDUE EDO A 1306
09AC9SOFTWAREPRO B:60 , SER B:62 , HOH B:2415BINDING SITE FOR RESIDUE EDO B 2303
10BC1SOFTWAREASP B:117 , ILE B:119 , HIS B:137BINDING SITE FOR RESIDUE EDO B 2304
11BC2SOFTWAREASP B:20 , LYS B:38BINDING SITE FOR RESIDUE EDO B 2305
12BC3SOFTWAREGLU B:115 , ASP B:117 , ARG B:118BINDING SITE FOR RESIDUE EDO B 2306
13BC4SOFTWAREARG A:54 , HOH A:1331 , PRO B:32 , GLU B:33 , ALA B:36 , HOH B:2398BINDING SITE FOR RESIDUE EDO B 2307
14BC5SOFTWAREHIS B:137 , SER B:138 , LYS B:140 , SER B:153 , GLU B:157 , HOH B:2450 , HOH B:2454BINDING SITE FOR RESIDUE EDO B 2308

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FEA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2FEA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FEA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2FEA)

(-) Exons   (0, 0)

(no "Exon" information available for 2FEA)

(-) 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:226
 aligned with MTNX_BACSU | O31667 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:226
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221      
           MTNX_BACSU     2 TTRKPFIICDFDGTITMNDNIINIMKTFAPPEWMALKDGVLSKTLSIKEGVGRMFGLLPSSLKEEITSFVLEDAKIREGFREFVAFINEHEIPFYVISGGMDFFVYPLLEGIVEKDRIYCNHASFDNDYIHIDWPHSCKGTCSNQCGCCKPSVIHELSEPNQYIIMIGDSVTDVEAAKLSDLCFARDYLLNECREQNLNHLPYQDFYEIRKEIENVKEVQEWLQNK 227
               SCOP domains d2feaa1 A:2-227 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase MtnX                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.........hhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..eeeeeeeehhhhhhhhh...hhh.eeeeeee......eee...............hhhhhhhhhh....eeeeee.hhhhhhhhhh..eeeehhhhhhhhhhh...ee...hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fea A   2 TTRKPFIICDFDGTITmNDNIINImKTFAPPEWmALKDGVLSKTLSIKEGVGRmFGLLPSSLKEEITSFVLEDAKIREGFREFVAFINEHEIPFYVISGGmDFFVYPLLEGIVEKDRIYCNHASFDNDYIHIDWPHSCKGTCSNQCGCCKPSVIHELSEPNQYIImIGDSVTDVEAAKLSDLCFARDYLLNECREQNLNHLPYQDFYEIRKEIENVKEVQEWLQNK 227
                                    11      | 21    |   31   |    41        51   |    61        71        81        91       101|      111       121       131       141       151       161     | 171       181       191       201       211       221      
                                           18-MSE  26-MSE   35-MSE              55-MSE                                        102-MSE                                                          167-MSE                                                        


Chain B from PDB  Type:PROTEIN  Length:224
 aligned with MTNX_BACSU | O31667 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:224
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222    
           MTNX_BACSU     3 TRKPFIICDFDGTITMNDNIINIMKTFAPPEWMALKDGVLSKTLSIKEGVGRMFGLLPSSLKEEITSFVLEDAKIREGFREFVAFINEHEIPFYVISGGMDFFVYPLLEGIVEKDRIYCNHASFDNDYIHIDWPHSCKGTCSNQCGCCKPSVIHELSEPNQYIIMIGDSVTDVEAAKLSDLCFARDYLLNECREQNLNHLPYQDFYEIRKEIENVKEVQEWLQN 226
               SCOP domains d2feab_ B: 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase MtnX                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.........hhhhhhhhhhh..hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh...eeeeeeeehhhhhhhhh...hhh.eeeeeee......eee...............hhhhhhhhhh...eeeeeee.hhhhhhhhhh..eeeehhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fea B   3 TRKPFIICDFDGTITmNDNIINImKTFAPPEWmALKDGVLSKTLSIKEGVGRmFGLLPSSLKEEITSFVLEDAKIREGFREFVAFINEHEIPFYVISGGmDFFVYPLLEGIVEKDRIYCNHASFDNDYIHIDWPHSCKGTCSNQCGCCKPSVIHELSEPNQYIImIGDSVTDVEAAKLSDLCFARDYLLNECREQNLNHLPYQDFYEIRKEIENVKEVQEWLQN 226
                                    12     |  22   |    32  |     42        52  |     62        72        82        92       102       112       122       132       142       152       162    |  172       182       192       202       212       222    
                                          18-MSE  26-MSE   35-MSE              55-MSE                                        102-MSE                                                          167-MSE
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2FEA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FEA)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MTNX_BACSU | O31667)
molecular function
    GO:0043716    2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase activity    Catalysis of the reaction: 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate + H2O = 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + phosphate. 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate is also known as HK-MTPenyl-P, and 1,2-dihydroxy-3-keto-5-methylthiopentene as DHK-MTPene.
    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:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
biological process
    GO:0071267    L-methionine salvage    Any process that generates L-methionine from derivatives of it, without de novo synthesis.
    GO:0019284    L-methionine salvage from S-adenosylmethionine    The chemical reactions and pathways resulting in the formation of L-methionine from S-adenosylmethionine.
    GO:0019509    L-methionine salvage from methylthioadenosine    The generation of L-methionine (2-amino-4-(methylthio)butanoic acid) from methylthioadenosine.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0009086    methionine biosynthetic process    The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.

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  2fea
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  MTNX_BACSU | O31667
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