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(-) Description

Title :  CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE MHF COMPLEX
 
Authors :  H. Yang, T. Zhang, C. Zhong, H. Li, J. Zhou, J. Ding
Date :  28 Dec 11  (Deposition) - 29 Feb 12  (Release) - 29 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Mhf1, Mhf2, Histone Fold, Fanconi Anemia, Dna Repair, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Yang, T. Zhang, Y. Tao, L. Wu, H. T. Li, J. Q. Zhou, C. Zhong, J. Ding
Saccharomyces Cerevisiae Mhf Complex Structurally Resembles The Histones (H3-H4)(2) Heterotetramer And Functions As A Heterotetramer
Structure V. 20 364 2012
PubMed-ID: 22325783  |  Reference-DOI: 10.1016/J.STR.2011.12.012

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN YOL086W-A
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETDUET
    Expression System Strain: BL21(DE3) CODON PLUS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YOL086W-A
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: MHF1
 
Molecule 2 - UNCHARACTERIZED PROTEIN YDL160C-A
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3) CODON PLUS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YDL160C-A
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: MHF2

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric/Biological Unit (2, 15)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:34 , ARG A:36 , SER B:65 , HIS B:66BINDING SITE FOR RESIDUE SO4 A 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3V9R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3V9R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3V9R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3V9R)

(-) Exons   (0, 0)

(no "Exon" information available for 3V9R)

(-) Sequences/Alignments

Asymmetric/Biological 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:88
 aligned with MHF1_YEAST | Q3E835 from UniProtKB/Swiss-Prot  Length:90

    Alignment length:88
                                    11        21        31        41        51        61        71        81        
            MHF1_YEAST    2 NDDEDRAQLKARLWIRVEERLQQVLSSEDIKYTPRFINSLLELAYLQLGEMGSDLQAFARHAGRGVVNKSDLMLYLRKQPDLQERVTQ 89
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhh..hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                  3v9r A  2 NDDEDRAQLKARLWIRVEERLQQVLSSEDIKYTPRFINSLLELAYLQLGEmGSDLQAFARHAGRGVVNKSDLmLYLRKQPDLQERVTQ 89
                                    11        21        31        41        51|       61        71  |     81        
                                                                             52-MSE                74-MSE           


Chain B from PDB  Type:PROTEIN  Length:73
 aligned with MHF2_YEAST | Q3E829 from UniProtKB/Swiss-Prot  Length:80

    Alignment length:84
                                                                                                          80    
                                    10        20        30        40        50        60        70        80    
            MHF2_YEAST    1 MLSKEALIKILSQNEGGNDMKIADEVVPMIQKYLDIFIDEAVLRSLQSHKDINGERGDKSPLELSHQDLERIVGLLLMDM----  -
               SCOP domains ------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhh........ee...hhhhhhhhhhhhhhhhhhhhhhhhhh.-----------.hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  3v9r B  1 mLSKEALIKILSQNEGGNDmKIADEVVPmIQKYLDIFIDEAVLRSLQSHKDI-----------LSHQDLERIVGLLLmDmLEHH 84
                            |       10        20        30        40        50 |       -   |    70       |80    
                            1-MSE             20-MSE   29-MSE                 52          64            78-MSE  
                                                                                                          80-MSE


Chain C from PDB  Type:PROTEIN  Length:87
 aligned with MHF1_YEAST | Q3E835 from UniProtKB/Swiss-Prot  Length:90

    Alignment length:87
                                    12        22        32        42        52        62        72        82       
            MHF1_YEAST    3 DDEDRAQLKARLWIRVEERLQQVLSSEDIKYTPRFINSLLELAYLQLGEMGSDLQAFARHAGRGVVNKSDLMLYLRKQPDLQERVTQ 89
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhh..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                  3v9r C  3 DDEDRAQLKARLWIRVEERLQQVLSSEDIKYTPRFINSLLELAYLQLGEmGSDLQAFARHAGRGVVNKSDLmLYLRKQPDLQERVTQ 89
                                    12        22        32        42        52        62        72 |      82       
                                                                            52-MSE                74-MSE           


Chain D from PDB  Type:PROTEIN  Length:72
 aligned with MHF2_YEAST | Q3E829 from UniProtKB/Swiss-Prot  Length:80

    Alignment length:80
                                    10        20        30        40        50        60        70        80
            MHF2_YEAST    1 MLSKEALIKILSQNEGGNDMKIADEVVPMIQKYLDIFIDEAVLRSLQSHKDINGERGDKSPLELSHQDLERIVGLLLMDM 80
               SCOP domains -------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh........ee...hhhhhhhhhhhhhhhhhhhhhhhhhhh.--------.eehhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                  3v9r D  1 mLSKEALIKILSQNEGGNDmKIADEVVPmIQKYLDIFIDEAVLRSLQSHKDIN--------LELSHQDLERIVGLLLmDm 80
                            |       10        20        30        40        50  |      - |      70       |80
                            |                 20-MSE   29-MSE                  53       62              78-MSE
                            1-MSE                                                                         80-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  (0, 0)

(no "SCOP Domain" information available for 3V9R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V9R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V9R)

(-) Gene Ontology  (7, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (MHF1_YEAST | Q3E835)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
cellular component
    GO:0071821    FANCM-MHF complex    A protein complex contains the proteins FANCM and MHF, or their orthologs, plays an essential role in DNA remodeling, protects replication forks, and is conserved in eukaryotes.

Chain B,D   (MHF2_YEAST | Q3E829)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0051382    kinetochore assembly    The aggregation, arrangement and bonding together of a set of components to form the kinetochore, a multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
cellular component
    GO:0071821    FANCM-MHF complex    A protein complex contains the proteins FANCM and MHF, or their orthologs, plays an essential role in DNA remodeling, protects replication forks, and is conserved in eukaryotes.

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