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(-) Description

Title :  CRYSTAL STRUCTURE OF N-CARBAMOYLSARCOSINE AMIDASE FROM THERMOPLASMA ACIDOPHILUM
 
Authors :  H. -B. Luo, H. Zheng, M. Chruszcz, M. D. Zimmerman, T. Skarina, O. Egorov A. Savchenko, A. Joachimiak, W. Minor, Midwest Center For Structu Genomics (Mcsg)
Date :  04 Sep 08  (Deposition) - 16 Sep 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  N-Carbamoylsarcosine Amidase, Protein, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. B. Luo, H. Zheng, M. D. Zimmerman, M. Chruszcz, T. Skarina, O. Egorova, A. Savchenko, A. M. Edwards, W. Minor
Crystal Structure And Molecular Modeling Study Of N-Carbamoylsarcosine Amidase Ta0454 From Thermoplasma Acidophilum.
J. Struct. Biol. V. 169 304 2010
PubMed-ID: 19932181  |  Reference-DOI: 10.1016/J.JSB.2009.11.008

(-) Compounds

Molecule 1 - N-CARBAMOYLSARCOSINE AMIDASE RELATED PROTEIN
    Chains: A, B
    EC Number: 3.5.1.59
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15TV LIC
    Expression System Strain: BL21-CODONPLUS(DE3)-RIPL
    Expression System Vector Type: PLASMID
    Gene: TA0454
    Organism Scientific: THERMOPLASMA ACIDOPHILUM
    Organism Taxid: 2303

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 20)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
2ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:50 , HIS A:52 , GLU A:58 , HIS A:65BINDING SITE FOR RESIDUE ZN A 183
2AC2SOFTWAREHOH A:190 , ASP B:50 , HIS B:52 , GLU B:58 , HIS B:65BINDING SITE FOR RESIDUE ZN B 183

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EEF)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Leu A:118 -Asp A:119
2Ala B:83 -Gly B:84
3Leu B:118 -Asp B:119

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EEF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EEF)

(-) Exons   (0, 0)

(no "Exon" information available for 3EEF)

(-) 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:173
 aligned with Q9HKY9_THEAC | Q9HKY9 from UniProtKB/TrEMBL  Length:182

    Alignment length:173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   
         Q9HKY9_THEAC     1 MKPALVVVDMVNEFIHGRLATPEAMKTVGPARKVIETFRRSGLPVVYVNDSHYPDDPEIRIWGRHSMKGDDGSEVIDEIRPSAGDYVLEKHAYSGFYGTNLDMILRANGIDTVVLIGLDADICVRHTAADALYRNYRIIVVEDAVAARIDPNWKDYFTRVYGATVKRSDEIEG 173
               SCOP domains d3eefa_ A: automated matches                                                                                                                                                  SCOP domains
               CATH domains -3eefA00 A:2-173  [code=3.40.50.850, no name defined]                                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhh....hhhhhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhh......hhhhh.hhhhh.....eeeee.........hhhhhhhhh...eeeeeee...hhhhhhhhhhhhh..eeeeeeeeee.....hhhhhhhhhhh.eee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eef A   1 mKPALVVVDmVNEFIHGRLATPEAmKTVGPARKVIETFRRSGLPVVYVNDSHYPDDPEIRIWGRHSmKGDDGSEVIDEIRPSAGDYVLEKHAYSGFYGTNLDmILRANGIDTVVLIGLDADICVRHTAADALYRNYRIIVVEDAVAARIDPNWKDYFTRVYGATVKRSDEIEG 173
                            |       10        20    |   30        40        50        60      | 70        80        90       100  |    110       120       130       140       150       160       170   
                            |       10-MSE         25-MSE                                    67-MSE                             103-MSE                                                                  
                            1-MSE                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:173
 aligned with Q9HKY9_THEAC | Q9HKY9 from UniProtKB/TrEMBL  Length:182

    Alignment length:173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   
         Q9HKY9_THEAC     1 MKPALVVVDMVNEFIHGRLATPEAMKTVGPARKVIETFRRSGLPVVYVNDSHYPDDPEIRIWGRHSMKGDDGSEVIDEIRPSAGDYVLEKHAYSGFYGTNLDMILRANGIDTVVLIGLDADICVRHTAADALYRNYRIIVVEDAVAARIDPNWKDYFTRVYGATVKRSDEIEG 173
               SCOP domains d3eefb_ B: automated matches                                                                                                                                                  SCOP domains
               CATH domains -3eefB00 B:2-173  [code=3.40.50.850, no name defined]                                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhh....hhhhhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhh......hhhhh.hhhhh.....eeeee.........hhhhhhhhh...eeeeeee...hhhhhhhhhhhhh..eeeeeeeeee.....hhhhhhhhhhh.eee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eef B   1 mKPALVVVDmVNEFIHGRLATPEAmKTVGPARKVIETFRRSGLPVVYVNDSHYPDDPEIRIWGRHSmKGDDGSEVIDEIRPSAGDYVLEKHAYSGFYGTNLDmILRANGIDTVVLIGLDADICVRHTAADALYRNYRIIVVEDAVAARIDPNWKDYFTRVYGATVKRSDEIEG 173
                            |       10        20    |   30        40        50        60      | 70        80        90       100  |    110       120       130       140       150       160       170   
                            1-MSE   10-MSE         25-MSE                                    67-MSE                             103-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EEF)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9HKY9_THEAC | Q9HKY9)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    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.

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