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(-) Description

Title :  THREE-DIMENSIONAL STRUCTURE OF BETA-ACROSIN FROM RAM SPERMATOZOA
 
Authors :  R. Tranter, J. A. Read, R. Jones, R. L. Brady
Date :  07 Aug 00  (Deposition) - 08 Nov 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,L
Keywords :  Anti-Parallel Beta-Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Tranter, J. A. Read, R. Jones, R. L. Brady
Effector Sites In The Three-Dimensional Structure Of Mammalian Sperm Beta-Acrosin.
Structure Fold. Des. V. 8 1179 2000
PubMed-ID: 11080640  |  Reference-DOI: 10.1016/S0969-2126(00)00523-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-ACROSIN HEAVY CHAIN
    Cell: SPERMATOZOA
    Chains: A
    Organ: TESTIS
    Organism Common: SHEEP
    Organism Scientific: OVIS ARIES
    Organism Taxid: 9940
 
Molecule 2 - BETA-ACROSIN LIGHT CHAIN
    Cell: SPERMATOZOA
    Chains: L
    Organ: TESTIS
    Organism Common: SHEEP
    Organism Scientific: OVIS ARIES
    Organism Taxid: 9940

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric/Biological Unit (5, 7)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2FUL1Ligand/IonBETA-L-FUCOSE
3MAN1Ligand/IonALPHA-D-MANNOSE
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
5PBZ2Ligand/IonP-AMINO BENZAMIDINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:61D , THR A:61E , ASN A:169 , GLY A:174 , ILE A:176 , ARG A:177 , SER A:178 , FUL A:300 , NAG A:302 , HOH A:320BINDING SITE FOR RESIDUE NAG A 301
2AC2SOFTWAREARG A:60 , ASN A:169 , ASN A:173 , GLY A:174 , NAG A:301 , NAG A:302BINDING SITE FOR RESIDUE FUL A 300
3AC3SOFTWARESER A:97 , FUL A:300 , NAG A:301 , BMA A:303BINDING SITE FOR RESIDUE NAG A 302
4AC4SOFTWARENAG A:302 , MAN A:304BINDING SITE FOR RESIDUE BMA A 303
5AC5SOFTWARELYS A:87 , ILE A:88 , BMA A:303 , HOH A:358 , HOH A:432BINDING SITE FOR RESIDUE MAN A 304
6AC6SOFTWAREASP A:189 , THR A:190 , GLN A:192 , SER A:195 , TRP A:215 , GLY A:216 , GLY A:219 , CYS A:220 , GLY A:226BINDING SITE FOR RESIDUE PBZ A 305
7AC7SOFTWAREVAL A:85 , GLU A:86 , THR A:109 , PRO A:128 , LEU A:165 , SER A:178 , HOH A:308BINDING SITE FOR RESIDUE PBZ A 306

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:42 -A:58
2A:114 -L:5
3A:122 -L:9
4A:136 -A:201
5A:168 -A:182
6A:191 -A:220

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Pro A:78 -Pro A:79
2Thr A:109 -Pro A:110
3Val A:132 -Pro A:133
4Ser A:202 -Ala A:202A

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.ACRO_SHEEP40-288  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.ACRO_SHEEP82-87  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.ACRO_SHEEP232-243  1A:189-200

(-) Exons   (0, 0)

(no "Exon" information available for 1FIW)

(-) 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:260
 aligned with ACRO_SHEEP | Q9GL10 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:260
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299
          ACRO_SHEEP     40 IIGGQDAAHGAWPWMVSLQIFTYHNNRRYHVCGGSLLNSQWLLTAAHCFRIKKKVTDWRLIFGAKEVEWGTNKPVKPPLQERYVEKIIIHEKYSASSEANDIALMKITPPVTCGHFIGPGCLPQFRAGPPRVPQTCWVAGWGFLQENARRTSPMLQEARVDLIDLGLCNSTRWYNGRIRSTNVCAGYPEGKIDTCQGDSGGPLMCKDSAENSYVVVGITSWGVGCARAKRPGVYTSTWSYLNWIASKIGSTAVHMIQLPT  299
               SCOP domains d1fiw.1 L:,A: Beta-acrosin                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1fiwA01     1fiwA02 A:28-120,A:233-245 Trypsin-like serine proteases                                                   1fiwA01 A:16-27,A:121-232 Trypsin-like serine proteases                                                                1fiwA02      --------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeeeee....eeeeeeeeeeee..eeeehhhhhh.......eeeee.................eeeeeeeeee.............eeeeee..........................eeeeee...............eeeeeeeehhhhhh............eeeee...............eeeee......eeeeeeeee..........eeeee...hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 40-288                                                                                                                                                                                                               ----------- PROSITE (1)
                PROSITE (2) ------------------------------------------TRYPSI------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1fiw A   16 IIGGQDAAHGAWPWMVSLQIFTYHNNRRYHVCGGSLLNSQWLLTAAHCFRIKKKVTDWRLIFGAKEVEWGTNKPVKPPLQERYVEKIIIHEKYSASSEANDIALMKITPPVTCGHFIGPGCLPQFRAGPPRVPQTCWVAGWGFLQENARRTSPMLQEARVDLIDLGLCNSTRWYNGRIRSTNVCAGYPEGKIDTCQGDSGGPLMCKDSAENSYVVVGITSWGVGCARAKRPGVYTSTWSYLNWIASKIGSTAVHMIQLPT  254
                                    25        37||||||| 40        50        60 |||||  65|||    75A||||    81        91       101       111       121     ||129||     140       150       160       170||     178      |187 |     196     |202B|| ||  214  ||  |224       234       244       254
                                             34||||||||                      61A||||  65A||    75A||||                                                126A| 130|                                   170A|           184A 188A          201A| |||| ||     217|  |                                 
                                              37|||||||                       61B|||    66|     75B|||                                                 126B  132                                    170B                               201B |||| ||      219  |                                 
                                              37A||||||                        61C||     69      75C||                                                                                                                                   202A||| ||        221A                                 
                                               37B|||||                         61D|              75D|                                                                                                                                    202B|| ||                                             
                                                37C||||                          61E               75E                                                                                                                                     202C| ||                                             
                                                 37D|||                                                                                                                                                                                     202D ||                                             
                                                  37E||                                                                                                                                                                                        204|                                             
                                                   37F|                                                                                                                                                                                         209                                             
                                                    37G                                                                                                                                                                                                                                         


Chain L from PDB  Type:PROTEIN  Length:14
 aligned with ACRO_SHEEP | Q9GL10 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:14
                                    29    
          ACRO_SHEEP     20 TTCDGPCGVRFRQN   33
               SCOP domains d1fiw.1 L:,A:  SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .............. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                PROSITE (1) -------------- PROSITE (1)
                PROSITE (2) -------------- PROSITE (2)
                 Transcript -------------- Transcript
                1fiw L    3 TTCDGPCGVRFRQN   16
                                    12
   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, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,L   (ACRO_SHEEP | Q9GL10)
molecular function
    GO:0004040    amidase activity    Catalysis of the reaction: a monocarboxylic acid amide + H2O = a monocarboxylate + NH3.
    GO:0008144    drug binding    Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
    GO:0042806    fucose binding    Interacting selectively and non-covalently with fucose, the pentose 6-deoxygalactose.
    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:0005537    mannose binding    Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans.
    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.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0007340    acrosome reaction    The discharge, by sperm, of a single, anterior secretory granule following the sperm's attachment to the zona pellucida surrounding the oocyte. The process begins with the fusion of the outer acrosomal membrane with the sperm plasma membrane and ends with the exocytosis of the acrosomal contents into the egg.
    GO:0007190    activation of adenylate cyclase activity    Any process that initiates the activity of the inactive enzyme adenylate cyclase.
    GO:0007341    penetration of zona pellucida    The infiltration by sperm of the zona pellucida to reach the oocyte. The process involves digestive enzymes from a modified lysosome called the acrosome, situated at the head of the sperm.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0007338    single fertilization    The union of male and female gametes to form a zygote.
cellular component
    GO:0001669    acrosomal vesicle    A structure in the head of a spermatozoon that contains acid hydrolases, and is concerned with the breakdown of the outer membrane of the ovum during fertilization. It lies just beneath the plasma membrane and is derived from the lysosome.

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1fiz THREE DIMENSIONAL STRUCTURE OF BETA-ACROSIN FROM BOAR SPERMATOZOA.