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(-) Description

Title :  CRYSTAL STRUCTURE OF A ZN-BOUND HISTIDINE TRIAD FAMILY PROTEIN FROM MYCOBACTERIUM SMEGMATIS
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  19 Jul 10  (Deposition) - 04 Aug 10  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Ssgcid, Nih, Niaid, Sbri, Uw, Emerald Biostructures, Hydrolase, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Baugh, I. Phan, D. W. Begley, M. C. Clifton, B. Armour, D. M. Dranow, B. M. Taylor, M. M. Muruthi, J. Abendroth, J. W. Fairman, D. Fox, S. H. Dieterich, B. L. Staker, A. S. Gardberg, R. Choi, S. N. Hewitt, A. J. Napuli, J. Myers, L. K. Barrett, Y. Zhang, M. Ferrell, E. Mundt, K. Thompkins, N. Tran, S. Lyons-Abbott, A. Abramov, A. Sekar, D. Serbzhinskiy, D. Lorimer, G. W. Buchko, R. Stacy, L. J. Stewart, T. E. Edwards, W. C. Van Voorhis, P. J. Myler
Increasing The Structural Coverage Of Tuberculosis Drug Targets.
Tuberculosis (Edinb) V. 95 142 2015
PubMed-ID: 25613812  |  Reference-DOI: 10.1016/J.TUBE.2014.12.003

(-) Compounds

Molecule 1 - HIT FAMILY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 4533102, MSMEG_5028
    Organism Scientific: MYCOBACTERIUM SMEGMATIS STR. MC2 155
    Organism Taxid: 246196
    Strain: ATCC 700084 / MC(2)155

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2AMP2Ligand/IonADENOSINE MONOPHOSPHATE
3MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4ZN2Ligand/IonZINC ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2AMP2Ligand/IonADENOSINE MONOPHOSPHATE
3MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2AMP2Ligand/IonADENOSINE MONOPHOSPHATE
3MPD-1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:3 , CYS A:6 , HIS A:45 , HIS A:97BINDING SITE FOR RESIDUE ZN A 151
2AC2SOFTWARECYS B:3 , CYS B:6 , HIS B:45 , HIS B:97BINDING SITE FOR RESIDUE ZN B 151
3AC3SOFTWAREASP A:124 , ARG A:130 , PHE B:96 , HOH B:188BINDING SITE FOR RESIDUE ACT A 146
4AC4SOFTWAREVAL A:4 , PHE A:5 , LEU A:28 , ASP A:29 , ILE A:30 , ARG A:31 , LEU A:39 , ASN A:86 , PHE A:92 , GLN A:93 , THR A:94 , VAL A:95 , HIS A:99 , HIS A:101 , HOH A:186 , HOH A:189 , HOH A:192 , HOH A:232BINDING SITE FOR RESIDUE AMP A 155
5AC5SOFTWAREVAL B:4 , PHE B:5 , ILE B:8 , ILE B:27 , ASP B:29 , ILE B:30 , ARG B:31 , LEU B:39 , ASN B:86 , PHE B:92 , GLN B:93 , THR B:94 , VAL B:95 , HIS B:99 , HIS B:101 , HOH B:165 , HOH B:180 , HOH B:190 , HOH B:203 , HOH B:227 , HOH B:245BINDING SITE FOR RESIDUE AMP B 155
6AC6SOFTWAREARG A:72 , HOH A:239 , HOH A:240 , HOH A:242 , GLU B:73 , ALA B:135 , HOH B:159BINDING SITE FOR RESIDUE MPD A 147

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O0M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3O0M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O0M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3O0M)

(-) Exons   (0, 0)

(no "Exon" information available for 3O0M)

(-) 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:139
 aligned with A0R291_MYCS2 | A0R291 from UniProtKB/TrEMBL  Length:145

    Alignment length:145
                              1                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138     
         A0R291_MYCS2     - --MSCVFCAIVSGDAPAIRIYEDENFLGILDIRPFTRGHTLVIPKTHTVDLTDTPPETVAGMAAVGQRIARAARESGLHADGNNIAINDGKAAFQTVFHIHLHVVPRRNGDKLSFAKGMVMRRDPDREESGRLLRAALAQLDSAE 143
               SCOP domains d3o0ma_ A: automated matches                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh......eeee...eeeee.........eeeee..........hhhhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhh.......eeeeee........------....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o0m A  -1 GSMSCVFCAIVSGDAPAIRIYEDENFLGILDIRPFTRGHTLVIPKTHTVDLTDTPPETVAGMAAVGQRIARAARESGLHADGNNIAINDGKAAFQTVFHIHLHVVPRRNGDKLSF------RRDPDREESGRLLRAALAQLDSAE 143
                                     8        18        28        38        48        58        68        78        88        98       108    |    - |     128       138     
                                                                                                                                            113    120                       


Chain B from PDB  Type:PROTEIN  Length:135
 aligned with A0R291_MYCS2 | A0R291 from UniProtKB/TrEMBL  Length:145

    Alignment length:141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 
         A0R291_MYCS2     2 SCVFCAIVSGDAPAIRIYEDENFLGILDIRPFTRGHTLVIPKTHTVDLTDTPPETVAGMAAVGQRIARAARESGLHADGNNIAINDGKAAFQTVFHIHLHVVPRRNGDKLSFAKGMVMRRDPDREESGRLLRAALAQLDSA 142
               SCOP domains d3o0mb_ B: automated matches                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------HIT-3o0mB01 B:10-108                                                                               ---------------------------------- Pfam domains (1)
           Pfam domains (2) --------HIT-3o0mB02 B:10-108                                                                               ---------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhh......eeee...eeeee.........eeeee..........hhhhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhh.......eeeeee........------....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o0m B   2 SCVFCAIVSGDAPAIRIYEDENFLGILDIRPFTRGHTLVIPKTHTVDLTDTPPETVAGMAAVGQRIARAARESGLHADGNNIAINDGKAAFQTVFHIHLHVVPRRNGDKLSF------RRDPDREESGRLLRAALAQLDSA 142
                                    11        21        31        41        51        61        71        81        91       101       111 |     121       131       141 
                                                                                                                                         113    120
   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) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O0M)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: HIT (23)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A0R291_MYCS2 | A0R291)
molecular function
    GO:0004081    bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity    Catalysis of the reaction: P(1),P(4)-bis(5'-nucleosyl)tetraphosphate + H2O = NTP + NMP. Acts on bis(5'-guanosyl)-, bis(5'-xanthosyl)-, bis(5'-adenosyl)- and bis(5'-uridyl)-tetraphosphate.
    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: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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

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