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(-) Description

Title :  CRYSTAL STRUCTURE OF X-PRO AMINOPEPTIDASE FROM THERMOTOGA MARITIMA MSB8
 
Authors :  H. Mizutani, N. Kunishima
Date :  10 Sep 08  (Deposition) - 14 Oct 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminopeptidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Mizutani, N. Kunishima
Crystal Structure Of X-Pro Aminopeptidase From Thermotoga Maritima Msb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - AMINOPEPTIDASE P, PUTATIVE
    Chains: A, B
    EC Number: 3.4.11.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21D
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM_0042
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Strain: MSB8
    Synonym: X-PRO AMINOPEPTIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3NA3Ligand/IonSODIUM ION
4ZN1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:218 , ASP A:229 , GLU A:322 , GLU A:336BINDING SITE FOR RESIDUE ZN A1001
2AC2SOFTWARELYS A:259 , THR A:351 , CL A:1006 , HOH A:1020 , HOH A:1022 , HOH A:1065BINDING SITE FOR RESIDUE NA A1002
3AC3SOFTWAREGLU A:155 , LYS A:179 , GLU A:180 , HOH A:1223 , VAL B:359BINDING SITE FOR RESIDUE NA A1003
4AC4SOFTWAREPHE A:120 , ARG A:275 , ARG A:279 , HOH A:1173BINDING SITE FOR RESIDUE CL A1005
5AC5SOFTWARELYS A:143 , LYS A:259 , LYS A:262 , NA A:1002BINDING SITE FOR RESIDUE CL A1006
6AC6SOFTWARELYS A:342BINDING SITE FOR RESIDUE CL A1007
7AC7SOFTWAREARG A:109 , HOH A:1361 , HOH B:1041 , HOH B:1054BINDING SITE FOR RESIDUE CL A1008
8AC8SOFTWAREGLY A:194 , GLY A:212 , VAL A:214 , VAL A:243 , HOH A:1076 , HOH A:1184BINDING SITE FOR RESIDUE GOL A1011
9AC9SOFTWARELYS B:65 , THR B:68 , HOH B:1162 , HOH B:1265 , HOH B:1355BINDING SITE FOR RESIDUE NA B1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZSG)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:302 -Pro A:303
2Gly B:302 -Pro B:303

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZSG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZSG)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZSG)

(-) 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:356
 aligned with Q9WXP9_THEMA | Q9WXP9 from UniProtKB/TrEMBL  Length:359

    Alignment length:359
                                    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       300       310       320       330       340       350         
         Q9WXP9_THEMA     1 MDRSERLIQLISEEGIDAFLIMNIENSARASSVYFSGFTGSFSIILISENTRLLITDSRYTVQAKQETDFEVREVKGGDFIDVLKKTVNDLKIKTIALEEERVSLSLFRRISSAFGDRKFIGIDDEVKQMRMVKDEGEIEKIKQAIEISERAFLETVQQIRAGMTEKEIAALLEYTMRKEGAEGVAFDTIVASGCRSALPHGKASDKVVERGDVIVIDFGATYENYCADITRVVSIGEPSDEVKEVHSIVLEAQERALKIAKAGVTGKLLDSVAREFIREKGYGEFFGHSLGHGIGLEVHEGPAISFRNDSPLPENVVFTVEPGIYLEGKFGIRIEEDVVLKEQGCEILTTLPRSIFVV 359
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------------------------2zsgA02 A:132-359 Creatinase/methionine aminopeptidase superfamily                                                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh....eeeeee....hhhhhhhhhh.....eeeeee..eeeeee...hhhhhhhhh..eeee.---.hhhhhhhhhhhh...eeee.....hhhhhhhhhhhh...eeeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh...ee....eeee.hhhhh..............eeeeee.eee..ee..eeeeee....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhh....eee......eeeee............eeee..eeee...eeee..eeeeee..eeee........ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zsg A   1 MDRSERLIQLISEEGIDAFLIMNIENSARASSVYFSGFTGSFSIILISENTRLLITDSRYTVQAKQETDFEVREV---DFIDVLKKTVNDLKIKTIALEEERVSLSLFRRISSAFGDRKFIGIDDEVKQMRMVKDEGEIEKIKQAIEISERAFLETVQQIRAGMTEKEIAALLEYTMRKEGAEGVAFDTIVASGCRSALPHGKASDKVVERGDVIVIDFGATYENYCADITRVVSIGEPSDEVKEVHSIVLEAQERALKIAKAGVTGKLLDSVAREFIREKGYGEFFGHSLGHGIGLEVHEGPAISFRNDSPLPENVVFTVEPGIYLEGKFGIRIEEDVVLKEQGCEILTTLPRSIFVV 359
                                    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       300       310       320       330       340       350         
                                                                                                     75  79                                                                                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:352
 aligned with Q9WXP9_THEMA | Q9WXP9 from UniProtKB/TrEMBL  Length:359

    Alignment length:358
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351        
         Q9WXP9_THEMA     2 DRSERLIQLISEEGIDAFLIMNIENSARASSVYFSGFTGSFSIILISENTRLLITDSRYTVQAKQETDFEVREVKGGDFIDVLKKTVNDLKIKTIALEEERVSLSLFRRISSAFGDRKFIGIDDEVKQMRMVKDEGEIEKIKQAIEISERAFLETVQQIRAGMTEKEIAALLEYTMRKEGAEGVAFDTIVASGCRSALPHGKASDKVVERGDVIVIDFGATYENYCADITRVVSIGEPSDEVKEVHSIVLEAQERALKIAKAGVTGKLLDSVAREFIREKGYGEFFGHSLGHGIGLEVHEGPAISFRNDSPLPENVVFTVEPGIYLEGKFGIRIEEDVVLKEQGCEILTTLPRSIFVV 359
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------2zsgB02 B:132-359 Creatinase/methionine aminopeptidase superfamily                                                                                                                                                                   CATH domains
           Pfam domains (1) -Creati      nase_N-2zsgB01 B:3-133                                                                                                 ------Peptidase_M24-2zsgB03 B:140-343                                                                                                                                                                             ---------------- Pfam domains (1)
           Pfam domains (2) -Creati      nase_N-2zsgB02 B:3-133                                                                                                 ------Peptidase_M24-2zsgB04 B:140-343                                                                                                                                                                             ---------------- Pfam domains (2)
         Sec.struct. author hhhhhhh------...eeeeee....hhhhhhhhhh.....eeeee....eeeee...hhhhhhhhh..eeee....hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhh..eeeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh...ee....eeee.hhhhh..............eeeeee.eee..ee..eeeeeee...hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhh....eee......eeeee............eeee..eeee...eeee..eeeee....eee........eee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zsg B   2 DRSERLI------GIDAFLIMNIENSARASSVYFSGFTGSFSIILISENTRLLITDSRYTVQAKQETDFEVREVKGGDFIDVLKKTVNDLKIKTIALEEERVSLSLFRRISSAFGDRKFIGIDDEVKQMRMVKDEGEIEKIKQAIEISERAFLETVQQIRAGMTEKEIAALLEYTMRKEGAEGVAFDTIVASGCRSALPHGKASDKVVERGDVIVIDFGATYENYCADITRVVSIGEPSDEVKEVHSIVLEAQERALKIAKAGVTGKLLDSVAREFIREKGYGEFFGHSLGHGIGLEVHEGPAISFRNDSPLPENVVFTVEPGIYLEGKFGIRIEEDVVLKEQGCEILTTLPRSIFVV 359
                                  |  -   |    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351        
                                  8     15
   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 2ZSG)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: AMP_N-like (22)
(-)
Clan: no clan defined [family: Peptidase_M24] (23)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9WXP9_THEMA | Q9WXP9)
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.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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