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(-) Description

Title :  CRYSTAL STRUCTURE OF TYPE-I RESTRICTION-MODIFICATION SYSTEM METHYLATION SUBUNIT (MM_0429) FROM METHANOSARCHINA MAZEI.
 
Authors :  U. A. Ramagopal, R. Toro, S. K. Burley, S. C. Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  30 Oct 09  (Deposition) - 19 Jan 10  (Release) - 19 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Type I Restriction-Modification System Methylation Subunit. , Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. A. Ramagopal, R. Toro, S. K. Burley, S. C. Almo
Crystal Structure Of Type-I Restriction-Modification System Methylation Subunit (Mm_0429) From Methanosarchina Mazei.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TYPE I RESTRICTION-MODIFICATION SYSTEM METHYLATION SUBUNIT
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: BC-PSGX4(BC)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MM_0429
    Organism Common: METHANOSARCINA FRISIA
    Organism Scientific: METHANOSARCINA MAZEI
    Organism Taxid: 2209

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:325 , ASP A:326 , ARG A:328 , TYR A:382 , LYS B:22BINDING SITE FOR RESIDUE SO4 A 600
2AC2SOFTWAREPRO B:325 , LEU B:327 , ARG B:328 , TYR B:382BINDING SITE FOR RESIDUE SO4 B 600

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KHK)

(-) 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:488
 aligned with Q8PZR3_METMA | Q8PZR3 from UniProtKB/TrEMBL  Length:576

    Alignment length:524
                                    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       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525    
         Q8PZR3_METMA     6 QQFLNDLDNQLWRAADKLRSNLDAANYKHVVLGLIFLKYVSDAFEERQQELTELFQKDDDDNIYYLPREDYDSDEAYQQAIAEELEIGDYYTEKNVFWVPKTARWNKLRDVITLPTGSVIWQDEQGEDVKLRSVSWLIDNAFDDIEKANPKLKGILNRISQYQLDADKLIGLINEFSLTSFNNPEYNGEKLNLKSKDILGHVYEYFLGQFALAEGKQGGQYYTPKSIVTLIVEMLEPYKGRVYDPAMGSGGFFVSSDKFIEKHANVKHYNASEQKKQISVYGQESNPTTWKLAAMNMVIRGIDFNFGKKNADSFLDDQHPDLRADFVMTNPPFNMKDWWHEKLADDPRWTINTNGEKRILTPPTGNANFAWMLHMLYHLAPTGSMALLLANGSMSSNTNNEGEIRKTLVEQDLVECMVALPGQLFTNTQIPACIWFLTKDKNAKNGKRDRRGQVLFIDARKLGYMKDRVLRDFKDEDIQKLADTFHNWQQEWSEENNQAGFCFSADLALIRKNDFVLTPGRYVG 529
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh.hhhhhhhhhhhhhh.hhhhhh..........hhhhhhhh.....----------------hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh------------------..hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhh.hhhhhh..eeeee...hhhhhhhhhhhhhhh.......................eeeeee..........hhhhh.hhh.ee...--.ee.......hhhhhhhhhhhheeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhh..eeeeee............eeeeeee..............eeeeee.....ee.....ee.hhhhhhhhhhhhhhhhhh..........eeeeehhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3khk A   6 QQFLNDLDNQLWRAADKLRSNLDAANYKHVVLGLIFLKYVSDAFEERQQELTELFQKDDDDNIYYLPREDYDSDEAYQQAIAEELEIGDYYTEKNVFWVPKTARWNKLRDVITLPT----------------SVSWLIDNAFDDIEKANPKLKGILNRISQYQLDADKLIGLINEFS------------------KDILGHVYEYFLGQFALAEGKQGGQYYTPKSIVTLIVEMLEPYKGRVYDPAMGSGGFFVSSDKFIEKHANVKHYNASEQKKQISVYGQESNPTTWKLAAMNMVIRGIDFNFGKKNADSFLDDQHPDLRADFVMTNPPFNMKDWWHEKLADDPRWTINTN--KRILTPPTGNANFAWMLHMLYHLAPTGSMALLLANGSMSSNTNNEGEIRKTLVEQDLVECMVALPGQLFTNTQIPACIWFLTKDKNAKNGKRDRRGQVLFIDARKLGYMKDRVLRDFKDEDIQKLADTFHNWQQEWSEENNQAGFCFSADLALIRKNDFVLTPGRYVG 529
                                    15        25        35        45        55        65        75        85        95       105       115     |   -         -  |    145       155       165       175      |  -         -     | 205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355   |  |365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525    
                                                                                                                                             121              138                                         182                201                                                                                                                                                           359  |                                                                                                                                                                       
                                                                                                                                                                                                                                                                                                                                                                                              362                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:487
 aligned with Q8PZR3_METMA | Q8PZR3 from UniProtKB/TrEMBL  Length:576

    Alignment length:524
                                    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       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525    
         Q8PZR3_METMA     6 QQFLNDLDNQLWRAADKLRSNLDAANYKHVVLGLIFLKYVSDAFEERQQELTELFQKDDDDNIYYLPREDYDSDEAYQQAIAEELEIGDYYTEKNVFWVPKTARWNKLRDVITLPTGSVIWQDEQGEDVKLRSVSWLIDNAFDDIEKANPKLKGILNRISQYQLDADKLIGLINEFSLTSFNNPEYNGEKLNLKSKDILGHVYEYFLGQFALAEGKQGGQYYTPKSIVTLIVEMLEPYKGRVYDPAMGSGGFFVSSDKFIEKHANVKHYNASEQKKQISVYGQESNPTTWKLAAMNMVIRGIDFNFGKKNADSFLDDQHPDLRADFVMTNPPFNMKDWWHEKLADDPRWTINTNGEKRILTPPTGNANFAWMLHMLYHLAPTGSMALLLANGSMSSNTNNEGEIRKTLVEQDLVECMVALPGQLFTNTQIPACIWFLTKDKNAKNGKRDRRGQVLFIDARKLGYMKDRVLRDFKDEDIQKLADTFHNWQQEWSEENNQAGFCFSADLALIRKNDFVLTPGRYVG 529
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------HsdM_N-3khkB03 B:12-181                                                                                                                                                   ----              N6_Mtase-3khkB01 B:200-529                                                                                                                                                                                                                                                                                                                 Pfam domains (1)
           Pfam domains (2) ------HsdM_N-3khkB04 B:12-181                                                                                                                                                   ----              N6_Mtase-3khkB02 B:200-529                                                                                                                                                                                                                                                                                                                 Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhh.hhhhhhhhhhhhh..hhhhhh..........hhhhhhhhh--------------------hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh...--------------hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhh.hhhhhhh.eeeee...hhhhhhhhhhhhhhh.......................eeeeee..........hhhhh.hhh.ee..---.ee.......hhhhhhhhhhhheeeeeeeeeeee.hhhh....hhhhhhhhhhhh..eeeeee............eeeeeee..............eeeeee.....ee.....ee.hhhhhhhhhhhhhhhh............eeeeehhhhhhh.....hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3khk B   6 QQFLNDLDNQLWRAADKLRSNLDAANYKHVVLGLIFLKYVSDAFEERQQELTELFQKDDDDNIYYLPREDYDSDEAYQQAIAEELEIGDYYTEKNVFWVPKTARWNKLRDVI--------------------SVSWLIDNAFDDIEKANPKLKGILNRISQYQLDADKLIGLINEFSLTS--------------SKDILGHVYEYFLGQFALAEGKQGGQYYTPKSIVTLIVEMLEPYKGRVYDPAMGSGGFFVSSDKFIEKHANVKHYNASEQKKQISVYGQESNPTTWKLAAMNMVIRGIDFNFGKKNADSFLDDQHPDLRADFVMTNPPFNMKDWWHEKLADDPRWTINT---KRILTPPTGNANFAWMLHMLYHLAPTGSMALLLANGSMSSNTNNEGEIRKTLVEQDLVECMVALPGQLFTNTQIPACIWFLTKDKNAKNGKRDRRGQVLFIDARKLGYMKDRVLRDFKDEDIQKLADTFHNWQQEWSEENNQAGFCFSADLALIRKNDFVLTPGRYVG 529
                                    15        25        35        45        55        65        75        85        95       105       115 |       -         -  |    145       155       165       175       185         -    |  205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355  |   |365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525    
                                                                                                                                         117                  138                                            185            200                                                                                                                                                           358 362
   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 3KHK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: no clan defined [family: HsdM_N] (3)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8PZR3_METMA | Q8PZR3)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008170    N-methyltransferase activity    Catalysis of the transfer of a methyl group to the nitrogen atom of an acceptor molecule.
biological process
    GO:0006306    DNA methylation    The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.

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