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(-) Description

Title :  METHIONINE AMINOPEPTIDASE FROM HYPERTHERMOPHILE PYROCOCCUS FURIOSUS
 
Authors :  T. H. Tahirov, T. Tsukihara
Date :  17 Nov 97  (Deposition) - 25 Feb 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminopeptidase, Hyperthermophile (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. H. Tahirov, H. Oki, T. Tsukihara, K. Ogasahara, K. Yutani, K. Ogata, Y. Izu, S. Tsunasawa, I. Kato
Crystal Structure Of Methionine Aminopeptidase From Hyperthermophile, Pyrococcus Furiosus.
J. Mol. Biol. V. 284 101 1998
PubMed-ID: 9811545  |  Reference-DOI: 10.1006/JMBI.1998.2146
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METHIONINE AMINOPEPTIDASE
    Chains: A, B
    EC Number: 3.4.11.18
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Other Details: TWO COBALT IONS IN ACTIVE SITE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1CO4Ligand/IonCOBALT (II) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:93 , HIS A:153 , GLU A:187 , GLU A:280 , CO A:297BINDING SITE FOR RESIDUE CO A 296
2AC2SOFTWAREASP A:82 , ASP A:93 , GLU A:280 , CO A:296BINDING SITE FOR RESIDUE CO A 297
3AC3SOFTWAREASP B:93 , HIS B:153 , GLU B:187 , GLU B:280 , CO B:297BINDING SITE FOR RESIDUE CO B 296
4AC4SOFTWAREASP B:82 , ASP B:93 , GLU B:280 , CO B:296BINDING SITE FOR RESIDUE CO B 297
5ACAUNKNOWNASP A:82 , ASP A:93 , HIS A:153 , GLU A:187 , GLU A:280 , CO A:296 , CO A:297SIDE CHAINS OF FIVE AMINO ACID RESIDUES ASP 82, ASP 93, HIS 153, GLU 187, GLU 280, AND TWO COBALT IONS FORM AN ACTIVE SITE OF MOLECULE IN CHAIN A.
6ACBUNKNOWNASP B:82 , ASP B:93 , HIS B:153 , GLU B:187 , GLU B:280 , CO B:296 , CO B:297SIDE CHAINS OF FIVE AMINO ACID RESIDUES ASP 82, ASP 93, HIS 153, GLU 187, GLU 280, AND TWO COBALT IONS FORM AN ACTIVE SITE OF MOLECULE IN CHAIN B.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XGM)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:201 -Pro A:202
2Pro B:201 -Pro B:202

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XGM)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MAP_2PS01202 Methionine aminopeptidase subfamily 2 signature.MAP2_PYRFU77-93
 		  2A:77-93
B:77-93

(-) Exons   (0, 0)

(no "Exon" information available for 1XGM)

(-) 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:295
 aligned with MAP2_PYRFU | P56218 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:295
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290     
           MAP2_PYRFU     1 MDTEKLMKAGEIAKKVREKAIKLARPGMLLLELAESIEKMIMELGGKPAFPVNLSINEIAAHYTPYKGDTTVLKEGDYLKIDVGVHIDGFIADTAVTVRVGMEEDELMEAAKEALNAAISVARAGVEIKELGKAIENEIRKRGFKPIVNLSGHKIERYKLHAGISIPNIYRPHDNYVLKEGDVFAIEPFATIGAGQVIEVPPTLIYMYVRDVPVRVAQARFLLAKIKREYGTLPFAYRWLQNDMPEGQLKLALKTLEKAGAIYGYPVLKEIRNGIVAQFEHTIIVEKDSVIVTTE 295
               SCOP domains d1xgma2 A:1-194,A:272-295 Methionine aminopeptidase                                                                                                                                               d1xgma1 A:195-271 Methionine aminopeptidase, insert domain                   d1xgma2                  SCOP domains
               CATH domains 1xgmA01 A:1-194,A:272-295 Creatinase/methionine aminopeptidase superfamily                                                                                                                        1xgmA02 A:195-271 'winged helix' repressor DNA binding domain                1xgmA01                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.........eeee.....................eeeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.......................................eeeeeeeeee.....eeee....eeee........hhhhhhhhhhhhh....eee.........hhhhhhhhhhhhhh..eee..eeee.....eeeeeeeeee....eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------MAP_2            ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xgm A   1 MDTEKLMKAGEIAKKVREKAIKLARPGMLLLELAESIEKMIMELGGKPAFPVNLSINEIAAHYTPYKGDTTVLKEGDYLKIDVGVHIDGFIADTAVTVRVGMEEDELMEAAKEALNAAISVARAGVEIKELGKAIENEIRKRGFKPIVNLSGHKIERYKLHAGISIPNIYRPHDNYVLKEGDVFAIEPFATIGAGQVIEVPPTLIYMYVRDVPVRVAQARFLLAKIKREYGTLPFAYRWLQNDMPEGQLKLALKTLEKAGAIYGYPVLKEIRNGIVAQFEHTIIVEKDSVIVTTE 295
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290     


Chain B from PDB  Type:PROTEIN  Length:295
 aligned with MAP2_PYRFU | P56218 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:295
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290     
           MAP2_PYRFU     1 MDTEKLMKAGEIAKKVREKAIKLARPGMLLLELAESIEKMIMELGGKPAFPVNLSINEIAAHYTPYKGDTTVLKEGDYLKIDVGVHIDGFIADTAVTVRVGMEEDELMEAAKEALNAAISVARAGVEIKELGKAIENEIRKRGFKPIVNLSGHKIERYKLHAGISIPNIYRPHDNYVLKEGDVFAIEPFATIGAGQVIEVPPTLIYMYVRDVPVRVAQARFLLAKIKREYGTLPFAYRWLQNDMPEGQLKLALKTLEKAGAIYGYPVLKEIRNGIVAQFEHTIIVEKDSVIVTTE 295
               SCOP domains d1xgmb2 B:1-194,B:272-295 Methionine aminopeptidase                                                                                                                                               d1xgmb1 B:195-271 Methionine aminopeptidase, insert domain                   d1xgmb2                  SCOP domains
               CATH domains 1xgmB01 B:1-194,B:272-295 Creatinase/methionine aminopeptidase superfamily                                                                                                                        1xgmB02 B:195-271 'winged helix' repressor DNA binding domain                1xgmB01                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh..eeee..eeee.....................eeeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.......................................eeeeeeeeee.....eeee....eeee........hhhhhhhhhhhhhh...eeehhh......hhhhhhhhhhhhhh..eee..eeee.....eeeeeeeeee....eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------MAP_2            ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xgm B   1 MDTEKLMKAGEIAKKVREKAIKLARPGMLLLELAESIEKMIMELGGKPAFPVNLSINEIAAHYTPYKGDTTVLKEGDYLKIDVGVHIDGFIADTAVTVRVGMEEDELMEAAKEALNAAISVARAGVEIKELGKAIENEIRKRGFKPIVNLSGHKIERYKLHAGISIPNIYRPHDNYVLKEGDVFAIEPFATIGAGQVIEVPPTLIYMYVRDVPVRVAQARFLLAKIKREYGTLPFAYRWLQNDMPEGQLKLALKTLEKAGAIYGYPVLKEIRNGIVAQFEHTIIVEKDSVIVTTE 295
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1XGM)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MAP2_PYRFU | P56218)
molecular function
    GO:0004177    aminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
    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:0070006    metalloaminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008235    metalloexopeptidase activity    Catalysis of the hydrolysis of a peptide bond not more than three residues from the N- or C-terminus of a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0070084    protein initiator methionine removal    The protein modification process in which the translation-initiating methionine or formylmethionine residue is removed from a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MAP2_PYRFU | P56218: 1wkm 1xgn 1xgo 1xgs 2dfi

(-) Related Entries Specified in the PDB File

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