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(-) Description

Title :  CRYSTAL STRUCTURE OF PROTEIN FROM MOUSE MM.236127
 
Authors :  J. G. Mccoy, G. E. Wesenberg, E. Bitto, G. N. Phillips Jr. , C. A. Bingman, Center For Eukaryotic Structural Genomics (Cesg
Date :  13 Jul 06  (Deposition) - 15 Aug 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Haloacid Dehalogenase-Like Hydrolase Domain Containing 2, Hdhd2, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. G. Mccoy, G. E. Wesenberg, E. Bitto, G. N. Phillips Jr. , C. A. Bingman
Crystal Structure Of Protein From Mouse Mm. 236127
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HALOACID DEHALOGENASE-LIKE HYDROLASE DOMAIN CONTAINING 2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PVP 16
    Expression System Strain: BL834 P(RARE2)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HDHD2
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 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  (3, 18)

Asymmetric Unit (3, 18)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2MSE10Mod. Amino AcidSELENOMETHIONINE
3PO46Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE5Mod. Amino AcidSELENOMETHIONINE
3PO43Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE5Mod. Amino AcidSELENOMETHIONINE
3PO43Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:13 , ASN A:15 , ASP A:204 , HOH A:446BINDING SITE FOR RESIDUE MG A 260
2AC2SOFTWAREASP B:13 , ASN B:15 , ASP B:204 , PO4 B:401 , HOH B:459 , HOH B:461BINDING SITE FOR RESIDUE MG B 301
3AC3SOFTWAREASP B:13 , ASN B:15 , THR B:46 , ASN B:47 , LYS B:179 , MG B:301BINDING SITE FOR RESIDUE PO4 B 401
4AC4SOFTWAREARG A:207 , LYS A:235 , HOH A:460BINDING SITE FOR RESIDUE PO4 A 402
5AC5SOFTWAREARG B:207 , LYS B:235BINDING SITE FOR RESIDUE PO4 B 403
6AC6SOFTWAREASN A:47 , THR A:48 , THR A:49 , LYS A:50 , GLU A:51BINDING SITE FOR RESIDUE PO4 A 404
7AC7SOFTWARELYS B:50 , ARG B:97BINDING SITE FOR RESIDUE PO4 B 405
8AC8SOFTWARELYS A:182BINDING SITE FOR RESIDUE PO4 A 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HO4)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys A:179 -Pro A:180
2Asn A:237 -Pro A:238
3Lys B:179 -Pro B:180
4Asn B:237 -Pro B:238

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2HO4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2HO4)

(-) Exons   (0, 0)

(no "Exon" information available for 2HO4)

(-) 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:251
 aligned with HDHD2_MOUSE | Q3UGR5 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:254
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255    
          HDHD2_MOUSE     6 ALKAVLVDLNGTLHIEDAAVPGAQEALKRLRATSVMVRFVTNTTKESKKDLLERLKKLEFEISEDEIFTSLTAARNLIEQKQVRPMLLVDDRALPEFTGVQTQDPNAVVIGLAPEHFHYQLLNQAFRLLLDGAPLIAIHKARYYKRKDGLALGPGPFVTALEYATDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCRDDVDGAQNIGMLGILVKTGKYKAADEEKINPPPYLTCESFPHAVDHILQHLL 259
               SCOP domains d2ho4a_ A: auto   mated matches                                                                                                                                                                                                                                SCOP domains
               CATH domains 2ho4A01 A:6-88,   A:178-259  [code=3.40.50.1000, no name defined]                  2ho4A02 A:89-177 4-nitrophenylphosphatase; domain 2                                      2ho4A01 A:6-88,A:178-259  [code=3.40.50.1000, no name defined]                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.......---...hhhhhhhhhhh...eeeeee.....hhhhhhhhhhhh....hhh.eeehhhhhhhhhhhhh..eeee.hhhhhhhhh........eeee..hhhhhhhhhhhhhhhhhhh...eee.....eeee..eeee.hhhhhhhhhhhhh...ee....hhhhhhhhhhhhh.hhh.eeeee.....hhhhhhhh..eeeee.......hhhhhh.....eee.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ho4 A   6 ALKAVLVDLNGTLHI---AVPGAQEALKRLRATSVmVRFVTNTTKETKKDLLERLKKLEFEISEDEIFTSLTAARNLIEQKQVRPmLLLDDRALPEFTGVQTQDPNAVVIGLAPEHFHYQLLNQAFRLLLDGAPLIAIHKARYYKRKDGLALGPGPFVTALEYATDTKAmVVGKPEKTFFLEALRDADCAPEEAVmIGDDCRDDVDGAQNIGmLGILVKTGKYKAADEEKINPPPYLTCESFPHAVDHILQHLL 259
                                    15    |   25        35     |  45        55        65        75        85     |  95       105       115       125       135       145       155       165       175       185       195     | 205       215  |    225       235       245       255    
                                         20  24               41-MSE                                            91-MSE                                                                             175-MSE                   201-MSE          218-MSE                                     


Chain B from PDB  Type:PROTEIN  Length:252
 aligned with HDHD2_MOUSE | Q3UGR5 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:253
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256   
          HDHD2_MOUSE     7 LKAVLVDLNGTLHIEDAAVPGAQEALKRLRATSVMVRFVTNTTKESKKDLLERLKKLEFEISEDEIFTSLTAARNLIEQKQVRPMLLVDDRALPEFTGVQTQDPNAVVIGLAPEHFHYQLLNQAFRLLLDGAPLIAIHKARYYKRKDGLALGPGPFVTALEYATDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCRDDVDGAQNIGMLGILVKTGKYKAADEEKINPPPYLTCESFPHAVDHILQHLL 259
               SCOP domains d2ho4b_ B: automated matches                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2ho4B01 B:7-88,B:178-259  [code=3.40.50.1000, no name defined]                    2ho4B02 B:89-177 4-nitrophenylphosphatase; domain 2                                      2ho4B01 B:7-88,B:17 8-259  [code=3.40.50.1000, no name defined]                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....ee..ee..hhhhhhhhhh....eeeeee.....hhhhhhhhhhhh....hhh.eeehhhhhhhhhhhhh..eeee.hhhhhhhhh........eeee..hhhhhhhhhhhhhhhhhhh...eee.....eeee..eeee.hhhhhhhhhhhhh...ee....hhhhhhhhhhhhh...-.eeeee.....hhhhhhh...eeeee..................eee.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ho4 B   7 LKAVLVDLNGTLHIEDAAVPGAQEALKRLRATSVmVRFVTNTTKETKKDLLERLKKLEFEISEDEIFTSLTAARNLIEQKQVRPmLLLDDRALPEFTGVQTQDPNAVVIGLAPEHFHYQLLNQAFRLLLDGAPLIAIHKARYYKRKDGLALGPGPFVTALEYATDTKAmVVGKPEKTFFLEALRDADCAP-EAVmIGDDCRDDVDGAQNIGmLGILVKTGKYKAADEEKINPPPYLTCESFPHAVDHILQHLL 259
                                    16        26        36    |   46        56        66        76        86    |   96       106       116       126       136       146       156       166       176       186       196 |  |  206       216 |     226       236       246       256   
                                                             41-MSE                                            91-MSE                                                                             175-MSE              196 |  |              218-MSE                                     
                                                                                                                                                                                                                         198  |                                                          
                                                                                                                                                                                                                            201-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  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HO4)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HDHD2_MOUSE | Q3UGR5)
molecular function
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    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.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

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