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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE 2-PHOSPHOSULFOLACTATE PHOSPHATASE (15026306) FROM CLOSTRIDIUM ACETOBUTYLICUM AT 2.6 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  26 Jan 05  (Deposition) - 15 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Keywords :  15026306, Putative 2-Phosphosulfolactate Phosphatase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Didonato, S. S. Krishna, R. Schwarzenbacher, D. Mcmullan, S. Agarwalla, S. M. Brittain, M. D. Miller, P. Abdubek, E. Ambing, H. L. Axelrod, J. M. Canaves, H. J. Chiu, A. M. Deacon, L. Duan, M. A. Elsliger, A. Godzik, S. K. Grzechnik, J. Hale, E. Hampton, J. Haugen, L. Jaroszewski, K. K. Jin, H. E. Klock, M. W. Knuth, E. Koesema, A. Kreusch, P. Kuhn, S. A. Lesley, I. Levin, A. T. Morse, E. Nigoghossian, L. Okach, S. Oommachen, J. Paulsen, K. Quijano, R. Reyes, C. L. Rife, G. Spraggon, R. C. Stevens, H. Van Den Bedem, A. White, G. Wolf, Q. Xu, K. O. Hodgson, J. Wooley, I. A. Wilson
Crystal Structure Of 2-Phosphosulfolactate Phosphatase (Comb) From Clostridium Acetobutylicum At 2. 6 A Resolution Reveals A New Fold With A Novel Active Site.
Proteins V. 65 771 2006
PubMed-ID: 16927339  |  Reference-DOI: 10.1002/PROT.20978

(-) Compounds

Molecule 1 - PROBABLE 2-PHOSPHOSULFOLACTATE PHOSPHATASE
    Chains: A, B, C
    EC Number: 3.1.3.71
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: COMB
    Organism Scientific: CLOSTRIDIUM ACETOBUTYLICUM
    Organism Taxid: 1488

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): A  
Biological Unit 2 (1x):  BC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 26)

Asymmetric Unit (3, 26)
No.NameCountTypeFull Name
13SL3Ligand/Ion(2R)-3-SULFOLACTIC ACID
2MG2Ligand/IonMAGNESIUM ION
3MSE21Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 16)
No.NameCountTypeFull Name
13SL2Ligand/Ion(2R)-3-SULFOLACTIC ACID
2MG-1Ligand/IonMAGNESIUM ION
3MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 16)
No.NameCountTypeFull Name
13SL2Ligand/Ion(2R)-3-SULFOLACTIC ACID
2MG-1Ligand/IonMAGNESIUM ION
3MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:26 , GLY A:146 , ASP A:155 , HOH A:406 , HOH A:411 , HOH A:452BINDING SITE FOR RESIDUE MG A 400
2AC2SOFTWAREASP B:26 , GLY B:146 , ASP B:155 , HOH B:404 , HOH B:412 , HOH B:423BINDING SITE FOR RESIDUE MG B 400
3AC3SOFTWARELEU A:28 , ARG A:29 , GLU A:70 , GLY A:73 , ASN A:83 , ASN A:104 , TYR A:148 , HIS A:201 , ARG A:204 , HOH A:406 , HOH A:453BINDING SITE FOR RESIDUE 3SL A 300
4AC4SOFTWAREASP B:26 , LEU B:28 , ARG B:29 , ALA B:30 , GLU B:70 , LYS B:72 , GLY B:73 , ASN B:83 , THR B:103 , ASN B:104 , HIS B:201 , ARG B:204 , HOH B:412BINDING SITE FOR RESIDUE 3SL B 300
5AC5SOFTWARELEU C:28 , ARG C:29 , GLU C:70 , GLY C:73 , ASN C:83 , THR C:103 , ASN C:104 , TYR C:148 , HIS C:201 , ARG C:204 , HOH C:305BINDING SITE FOR RESIDUE 3SL C 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VR0)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Leu A:28 -Arg A:29
2Leu B:28 -Arg B:29
3Leu C:28 -Arg C:29

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VR0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VR0)

(-) Exons   (0, 0)

(no "Exon" information available for 1VR0)

(-) 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:236
 aligned with COMB_CLOAB | Q97E82 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:236
                             1                                                                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229      
           COMB_CLOAB     - -MKIDLIISADDIKEEKVKNKTAVVIDMLRATSVITTALNNGCKRVVPVLTVEEALKKVKEYGKDAILGGERKGLKIEGFDFSNSPMEYTEDVVKGKTLIMTTTNGTRAIKGSETARDILIGSVLNGEAVAEKIVELNNDVVIVNAGTYGEFSIDDFICSGYIINCVMDRMKKLELTDAATTAQYVYKTNEDIKGFVKYAKHYKRIMELGLKKDFEYCCKKDIVKLVPQYTNGEIL 235
               SCOP domains -d1vr0a1 A:1-235 2-phosphosulfolactate phosphatase ComB                                                                                                                                                                                      SCOP domains
               CATH domains 1vr0A00 A:0-235 putative 2-phosphosulfolactate phosphatase                                                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhh...eeeee...hhhhhhhhhhhh...eeee..hhhhhhhhhhhhh..eeeee..............hhhhhhhhhhh..eeeee..hhhhhhhhh....eeeee...hhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhh..eeehhhhhhhhhhhhh...hhhhhh.hhhhhhhhhh.hhhhhhhhh.........eee..eee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vr0 A   0 HmKIDLIISADDIKEEKVKNKTAVVIDmLRATSVITTALNNGCKRVVPVLTVEEALKKVKEYGKDAILGGERKGLKIEGFDFSNSPmEYTEDVVKGKTLImTTTNGTRAIKGSETARDILIGSVLNGEAVAEKIVELNNDVVIVNAGTYGEFSIDDFICSGYIINCVmDRmKKLELTDAATTAQYVYKTNEDIKGFVKYAKHYKRImELGLKKDFEYCCKKDIVKLVPQYTNGEIL 235
                             |       9        19       |29        39        49        59        69        79      | 89        99|      109       119       129       139       149       159       169|      179       189       199      |209       219       229      
                             |                        27-MSE                                                     86-MSE       100-MSE                                                            167-MSE                                206-MSE                         
                             1-MSE                                                                                                                                                                  170-MSE                                                             


Chain B from PDB  Type:PROTEIN  Length:235
 aligned with COMB_CLOAB | Q97E82 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:235
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230     
           COMB_CLOAB     1 MKIDLIISADDIKEEKVKNKTAVVIDMLRATSVITTALNNGCKRVVPVLTVEEALKKVKEYGKDAILGGERKGLKIEGFDFSNSPMEYTEDVVKGKTLIMTTTNGTRAIKGSETARDILIGSVLNGEAVAEKIVELNNDVVIVNAGTYGEFSIDDFICSGYIINCVMDRMKKLELTDAATTAQYVYKTNEDIKGFVKYAKHYKRIMELGLKKDFEYCCKKDIVKLVPQYTNGEIL 235
               SCOP domains d1vr0b_ B: 2-phosphosulfolactate phosphatase ComB                                                                                                                                                                                           SCOP domains
               CATH domains -1vr0B00 B:2-235 putative 2-phosphosulfolactate phosphatase                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhh...eeeee...hhhhhhhhhhhh...eeee..hhhhhhhhhhhhh..eeeee..............hhhhhhhhhhh..eeeee..hhhhhhhhh....eeeee...hhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh...hhhhhh.hhhhhhhhhh.hhhhhhhhh.........eee..eee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vr0 B   1 mKIDLIISADDIKEEKVKNKTAVVIDmLRATSVITTALNNGCKRVVPVLTVEEALKKVKEYGKDAILGGERKGLKIEGFDFSNSPmEYTEDVVKGKTLImTTTNGTRAIKGSETARDILIGSVLNGEAVAEKIVELNNDVVIVNAGTYGEFSIDDFICSGYIINCVmDRmKKLELTDAATTAQYVYKTNEDIKGFVKYAKHYKRImELGLKKDFEYCCKKDIVKLVPQYTNGEIL 235
                            |       10        20      | 30        40        50        60        70        80     |  90       100       110       120       130       140       150       160      |170       180       190       200     | 210       220       230     
                            1-MSE                    27-MSE                                                     86-MSE       100-MSE                                                            167-MSE                                206-MSE                         
                                                                                                                                                                                                   170-MSE                                                             


Chain C from PDB  Type:PROTEIN  Length:237
 aligned with COMB_CLOAB | Q97E82 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:237
                              1                                                                                                                                                                                                                                          
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       
           COMB_CLOAB     - --MKIDLIISADDIKEEKVKNKTAVVIDMLRATSVITTALNNGCKRVVPVLTVEEALKKVKEYGKDAILGGERKGLKIEGFDFSNSPMEYTEDVVKGKTLIMTTTNGTRAIKGSETARDILIGSVLNGEAVAEKIVELNNDVVIVNAGTYGEFSIDDFICSGYIINCVMDRMKKLELTDAATTAQYVYKTNEDIKGFVKYAKHYKRIMELGLKKDFEYCCKKDIVKLVPQYTNGEIL 235
               SCOP domains d1vr0c_ C: 2-phosphosulfolactate phosphatase ComB                                                                                                                                                                                             SCOP domains
               CATH domains 1vr0C00 C:-1-235 putative 2-phosphosulfolactate phosphatase                                                                                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhh..eeeee...hhhhhhhhhhhh...eeee..hhhhhhhhhhhhh..eeeee..............hhhhhhhhhhh..eeeee..hhhhhhhhh....eeeee...hhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhh..eeehhhhhhhhhhhhh...hhhhhh.hhhhhhhhhh.hhhhhhhhh.........eee..eee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vr0 C  -1 HHmKIDLIISADDIKEEKVKNKTAVVIDmLRATSVITTALNNGCKRVVPVLTVEEALKKVKEYGKDAILGGERKGLKIEGFDFSNSPmEYTEDVVKGKTLImTTTNGTRAIKGSETARDILIGSVLNGEAVAEKIVELNNDVVIVNAGTYGEFSIDDFICSGYIINCVmDRmKKLELTDAATTAQYVYKTNEDIKGFVKYAKHYKRImELGLKKDFEYCCKKDIVKLVPQYTNGEIL 235
                              |      8        18        28        38        48        58        68        78       |88        98 |     108       118       128       138       148       158       168 |     178       188       198       208       218       228       
                              1-MSE                    27-MSE                                                     86-MSE       100-MSE                                                            167-MSE                                206-MSE                         
                                                                                                                                                                                                     170-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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1VR0)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (COMB_CLOAB | Q97E82)
molecular function
    GO:0050532    2-phosphosulfolactate phosphatase activity    Catalysis of the reaction: (2R)-O-phospho-3-sulfolactate + H(2)O = (R)-3-sulfolactate + phosphate.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
biological process
    GO:0019295    coenzyme M biosynthetic process    The chemical reactions and pathways resulting in the formation of coenzyme M (2-thioethansulfonate), a coenzyme involved in the utilization of methane by methanogenic prokaryotes.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.

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